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1.  The Chromatin Remodeler SPLAYED Regulates Specific Stress Signaling Pathways 
PLoS Pathogens  2008;4(12):e1000237.
Organisms are continuously exposed to a myriad of environmental stresses. Central to an organism's survival is the ability to mount a robust transcriptional response to the imposed stress. An emerging mechanism of transcriptional control involves dynamic changes in chromatin structure. Alterations in chromatin structure are brought about by a number of different mechanisms, including chromatin modifications, which covalently modify histone proteins; incorporation of histone variants; and chromatin remodeling, which utilizes ATP hydrolysis to alter histone-DNA contacts. While considerable insight into the mechanisms of chromatin remodeling has been gained, the biological role of chromatin remodeling complexes beyond their function as regulators of cellular differentiation and development has remained poorly understood. Here, we provide genetic, biochemical, and biological evidence for the critical role of chromatin remodeling in mediating plant defense against specific biotic stresses. We found that the Arabidopsis SWI/SNF class chromatin remodeling ATPase SPLAYED (SYD) is required for the expression of selected genes downstream of the jasmonate (JA) and ethylene (ET) signaling pathways. SYD is also directly recruited to the promoters of several of these genes. Furthermore, we show that SYD is required for resistance against the necrotrophic pathogen Botrytis cinerea but not the biotrophic pathogen Pseudomonas syringae. These findings demonstrate not only that chromatin remodeling is required for selective pathogen resistance, but also that chromatin remodelers such as SYD can regulate specific pathways within biotic stress signaling networks.
Author Summary
In eukaryotes, genomic DNA is organized into a complex DNA-protein structure termed chromatin. The organization of chromatin serves to compact DNA within the nucleus and plays a central role in regulating transcription by controlling the access of DNA to transcriptional machinery. Chromatin structure can be altered through several mechanisms, one of which is chromatin remodeling, a process that disrupts DNA–protein interactions resulting in altered accessibility of specific DNA regions to regulatory proteins in the transcriptional machinery. In this study, we investigated the biological role of chromatin remodeling in defense responses to biotic stresses using the model plant Arabidopsis. We found that a chromatin remodeling protein, SPLAYED, is required for gene expression within specific biotic stress signaling networks. Consistent with this observation, loss of SPLAYED chromatin-remodeling activity resulted in increased susceptibility to a fungal pathogen, Botrytis cinerea, but not to a bacterial pathogen, Pseudomonas syringae. These results demonstrate that reduced stress tolerance in a chromatin-remodeling mutant plant can be stress specific, and is not simply due to a decrease in overall fitness as a result of non-specific global mis-regulation of gene expression.
doi:10.1371/journal.ppat.1000237
PMCID: PMC2588541  PMID: 19079584
2.  A Mechanism for the Inhibition of Neural Progenitor Cell Proliferation by Cocaine 
PLoS Medicine  2008;5(6):e117.
Background
Prenatal exposure of the developing brain to cocaine causes morphological and behavioral abnormalities. Recent studies indicate that cocaine-induced proliferation inhibition and/or apoptosis in neural progenitor cells may play a pivotal role in causing these abnormalities. To understand the molecular mechanism through which cocaine inhibits cell proliferation in neural progenitors, we sought to identify the molecules that are responsible for mediating the effect of cocaine on cell cycle regulation.
Methods and Findings
Microarray analysis followed by quantitative real-time reverse transcription PCR was used to screen cocaine-responsive and cell cycle-related genes in a neural progenitor cell line where cocaine exposure caused a robust anti-proliferative effect by interfering with the G1-to-S transition. Cyclin A2, among genes related to the G1-to-S cell cycle transition, was most strongly down-regulated by cocaine. Down-regulation of cyclin A was also found in cocaine-treated human primary neural and A2B5+ progenitor cells, as well as in rat fetal brains exposed to cocaine in utero. Reversing cyclin A down-regulation by gene transfer counteracted the proliferation inhibition caused by cocaine. Further, we found that cocaine-induced accumulation of reactive oxygen species, which involves N-oxidation of cocaine via cytochrome P450, promotes cyclin A down-regulation by causing an endoplasmic reticulum (ER) stress response, as indicated by increased phosphorylation of eIF2α and expression of ATF4. In the developing rat brain, the P450 inhibitor cimetidine counteracted cocaine-induced inhibition of neural progenitor cell proliferation as well as down-regulation of cyclin A.
Conclusions
Our results demonstrate that down-regulation of cyclin A underlies cocaine-induced proliferation inhibition in neural progenitors. The down-regulation of cyclin A is initiated by N-oxidative metabolism of cocaine and consequent ER stress. Inhibition of cocaine N-oxidative metabolism by P450 inhibitors may provide a preventive strategy for counteracting the adverse effects of cocaine on fetal brain development.
Investigating the mechanism of cocaine's effect on fetal brain development, Chun-Ting Lee and colleagues find that down-regulation of cyclin A by a cocaine metabolite inhibits neural proliferation.
Editors' Summary
Background.
Every year, cocaine abuse by mothers during pregnancy exposes thousands of unborn infants (fetuses) to this powerful and addictive stimulant. Maternal cocaine abuse during early pregnancy increases the risk of miscarriage; its use during late pregnancy slows the baby's growth and can trigger premature labor. Babies exposed to cocaine shortly before birth are often irritable and have disturbed sleep patterns. They can also be very sensitive to sound and touch and consequently hard to comfort. These problems usually resolve spontaneously within the first few weeks of life but some permanent birth defects are also associated with frequent cocaine abuse during pregnancy. In particular, babies exposed to cocaine before birth sometimes have small heads—an abnormality that generally indicates a small brain—and, although they usually have normal intelligence, the development of their thinking skills and language is often delayed, and they can have behavioral problems.
Why Was This Study Done?
Exposure to cocaine before birth clearly interferes with some aspects of brain development. More specifically, it reduces the number and position of neurons (the cells that transmit information in the form of electrical impulses around the body) within the brain. All neurons develop from neural progenitor cells, and previous research suggests that cocaine exposure before birth inhibits the proliferation of these cells in the developing brain. It would be useful to understand exactly how cocaine affects neural progenitor cells, because it might then be possible to prevent the drug's adverse effects on brain development. In this study, therefore, the researchers investigate the molecular mechanism that underlies cocaine's effect on neural progenitor cells.
What Did the Researchers Do and Find?
When the researchers investigated the effects of cocaine on AF5 cells (rat neural progenitor cells that grow indefinitely in the laboratory), they found that concentrations of cocaine similar to those measured in fetal brains after maternal drug exposure inhibited the proliferation of AF5 cells by blocking the “G1-to-S transition.” This is a stage that cells have to pass through between each round of cell division (the production of two daughter cells from one parent cell). Next, the researchers showed that cocaine-treated AF5 cells made much less cyclin A2, a protein that controls the G1-to-S transition, than untreated cells. Cocaine also decreased cyclin A2 levels in neural progenitor cells freshly isolated from human fetal brains and in fetal rat brains exposed to the drug while in their mother's womb. Treatment of AF5 cells with a cyclin A2 expression vector (a piece of DNA that directs the production of cyclin A2) counteracted the down-regulation of cyclin A2 and restored AF5 proliferation in the presence of cocaine. Other experiments indicate that the reduction of cyclin A2 by cocaine in AF5 cells involves the accumulation of “reactive oxygen species,” by-products of the breakdown of cocaine by a protein that is a member of a family of proteins called cytochrome P450. Finally, treatment of pregnant rats with cimetidine (which inhibits the action of cytochrome P450) counteracted both the inhibition of neural progenitor cell proliferation and the cyclin A2 down-regulation that cocaine exposure induced in the brains of their unborn pups.
What Do These Findings Mean?
These findings show that the cocaine-induced inhibition of neural progenitor cell proliferation involves, at least in part, interfering with the production (that is, causing down-regulation) of cyclin A2. They also show that this down-regulation is induced by the breakdown of cocaine by cytochrome P450, and that in both a rat cell line and in fetal rats, the cytochrome P450 inhibitor cimetidine (a drug that is already used clinically for stomach problems) can block the adverse effects of cocaine on the proliferation of neural progenitor cells. These findings need to be confirmed in animals more closely related to people than rats, and the long-term effects of cimetidine need to be investigated, in particular its effects on cocaine toxicity. Nevertheless these results raise the possibility that giving cimetidine or other drugs with similar effects to pregnant women who are addicted to cocaine might prevent some of the harm that their drug habit does to their unborn children, although it is not clear whether there is a dosage of cimetidine that might be both safe and adequate for this purpose.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050117.
A PLoS Medicine Perspective article by Steven Hyman further discusses this study
The US National Institute on Drug Abuse provides a fact sheet on cocaine (in English and Spanish)
The UK charity Release provides information and advice to the public and professionals about the law and drugs, including information about cocaine
MedlinePlus also provides a list of links to information about cocaine (in English and Spanish)
The March of Dimes Foundation, a US nonprofit organization for the improvement of child health, provides information about illicit drug use during pregnancy (in English and Spanish)
The Organization of Teratology Information Specialists also provides a fact sheet on cocaine and pregnancy (in English, Spanish, and French)
doi:10.1371/journal.pmed.0050117
PMCID: PMC2504032  PMID: 18593214
3.  SIRT1-FOXO3a Regulate Cocaine Actions in the Nucleus Accumbens 
The Journal of Neuroscience  2015;35(7):3100-3111.
Previous studies have shown that chronic cocaine administration induces SIRT1, a Class III histone deacetylase, in the nucleus accumbens (NAc), a key brain reward region, and that such induction influences the gene regulation and place conditioning effects of cocaine. To determine the mechanisms by which SIRT1 mediates cocaine-induced plasticity in NAc, we used chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq), 1 d after 7 daily cocaine (20 mg/kg) or saline injections, to map SIRT1 binding genome-wide in mouse NAc. Our unbiased results revealed two modes of SIRT1 action. First, despite its induction in NAc, chronic cocaine causes depletion of SIRT1 from most affected gene promoters in concert with enrichment of H4K16ac (itself a deacetylation target of SIRT1), which is associated with increased expression of these genes. Second, we deduced the forkhead transcription factor (FOXO) family to be a downstream mechanism through which SIRT1 regulates cocaine action. We proceeded to demonstrate that SIRT1 induction causes the deacetylation and activation of FOXO3a in NAc, which leads to the induction of several known FOXO3a gene targets in other systems. Finally, we directly establish a role for FOXO3a in promoting cocaine-elicited behavioral responses by use of viral-mediated gene transfer: we show that overexpressing FOXO3a in NAc enhances cocaine place conditioning. The discovery of these two actions of SIRT1 in NAc in the context of behavioral adaptations to cocaine represents an important step forward in advancing our understanding of the molecular adaptations underlying cocaine action.
doi:10.1523/JNEUROSCI.4012-14.2015
PMCID: PMC4331629  PMID: 25698746
addiction; behavior; ChIP-Seq; cocaine; genomics; SIRT1
4.  ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling 
eLife  2013;2:e00863.
Chromatin assembly involves the combined action of ATP-dependent motor proteins and histone chaperones. Because motor proteins in chromatin assembly also function as chromatin remodeling factors, we investigated the relationship between ATP-driven chromatin assembly and chromatin remodeling in the generation of periodic nucleosome arrays. We found that chromatin remodeling-defective Chd1 motor proteins are able to catalyze ATP-dependent chromatin assembly. The resulting nucleosomes are not, however, spaced in periodic arrays. Wild-type Chd1, but not chromatin remodeling-defective Chd1, can catalyze the conversion of randomly-distributed nucleosomes into periodic arrays. These results reveal a functional distinction between ATP-dependent nucleosome assembly and chromatin remodeling, and suggest a model for chromatin assembly in which randomly-distributed nucleosomes are formed by the nucleosome assembly function of Chd1, and then regularly-spaced nucleosome arrays are generated by the chromatin remodeling activity of Chd1. These findings uncover an unforeseen level of specificity in the role of motor proteins in chromatin assembly.
DOI: http://dx.doi.org/10.7554/eLife.00863.001
eLife digest
In many cells, genomic DNA is wrapped around proteins known as histones to produce particles called nucleosomes. These particles then join together—like beads on a string—to form a highly periodic structure called chromatin. In the nucleus, chromatin is further folded and condensed into chromosomes. However, many important processes, including the replication of DNA and the transcription of genes, require access to the DNA. The cell must therefore be able to disassemble chromatin and remove the histones, and then, once these processes are complete, to reassemble the chromatin. Enzymes known as chromatin assembly factors are responsible for the disassembly and reassembly of chromatin.
There are two main types of chromatin assembly factors in eukaryotic cells (i.e., cells with nuclei)—histone chaperones and motor proteins. The histone chaperones escort histones from the cytoplasm, where they are made, to the nucleus. The motor proteins—using energy supplied by ATP molecules—then catalyze the formation of nucleosomes. This involves two activities: the motor proteins assemble nucleosomes by helping the DNA to wrap around the histones, and they also remodel chromatin by altering the positions of nucleosomes along the DNA to ensure that they are periodic—that is, regularly spaced.
A conserved motor protein called Chd1 performs chromatin assembly and remodeling in eukaryotic cells. Chd1 works in conjunction with histone chaperones—both are needed for chromatin assembly, and so are DNA, histones and ATP. However, whether or not chromatin assembly and chromatin remodeling by Chd1 are identical or distinct processes is not well understood.
Torigoe et al. have now discovered a mutant Chd1 protein that has nucleosome assembly activity (i.e., it can make nucleosomes) but cannot remodel chromatin (i.e., it is unable to move nucleosomes), and thus have demonstrated that these two processes are functionally distinct. Torigoe et al. additionally have found that the mutant Chd1 proteins produce randomly distributed nucleosomes rather than the periodic arrays normally found in chromatin. Further analysis then revealed that the wild-type Chd1 protein, which can remodel chromatin, is able to convert randomly distributed nucleosomes into periodic arrays.
These findings have led to a new model for chromatin assembly in which Chd1 initially generates randomly distributed nucleosomes (via its assembly function), and then converts them into periodic arrays of nucleosomes (via its remodeling function). Together, these studies shed light on the mechanisms by which chromatin is created and manipulated in cells.
DOI: http://dx.doi.org/10.7554/eLife.00863.002
doi:10.7554/eLife.00863
PMCID: PMC3748710  PMID: 23986862
chromatin assembly; chromatin remodeling; Chd1; D. melanogaster; S. cerevisiae
5.  Akirin Links Twist-Regulated Transcription with the Brahma Chromatin Remodeling Complex during Embryogenesis 
PLoS Genetics  2012;8(3):e1002547.
The activities of developmentally critical transcription factors are regulated via interactions with cofactors. Such interactions influence transcription factor activity either directly through protein–protein interactions or indirectly by altering the local chromatin environment. Using a yeast double-interaction screen, we identified a highly conserved nuclear protein, Akirin, as a novel cofactor of the key Drosophila melanogaster mesoderm and muscle transcription factor Twist. We find that Akirin interacts genetically and physically with Twist to facilitate expression of some, but not all, Twist-regulated genes during embryonic myogenesis. akirin mutant embryos have muscle defects consistent with altered regulation of a subset of Twist-regulated genes. To regulate transcription, Akirin colocalizes and genetically interacts with subunits of the Brahma SWI/SNF-class chromatin remodeling complex. Our results suggest that, mechanistically, Akirin mediates a novel connection between Twist and a chromatin remodeling complex to facilitate changes in the chromatin environment, leading to the optimal expression of some Twist-regulated genes during Drosophila myogenesis. We propose that this Akirin-mediated link between transcription factors and the Brahma complex represents a novel paradigm for providing tissue and target specificity for transcription factor interactions with the chromatin remodeling machinery.
Author Summary
The proper development of the diverse array of cell types in an organism depends upon the induction and repression of specific genes at particular times and places. This gene regulation requires both the activity of tissue-specific transcriptional regulators and the modulation of the chromatin environment. To date, a complete picture of the interplay between these two processes remains unclear. To address this, we examined the activity of the evolutionarily conserved transcription factor Twist during embryogenesis of Drosophila melanogaster. While Twist has multiple activities and roles during development, a direct link between Twist and chromatin remodeling is unknown. We identified a highly conserved protein, Akirin, as a link between Twist and chromatin remodeling factors. Akirin is required for optimal expression of a Twist-dependent target during muscle development via interactions with the Drosophila SWI/SNF chromatin remodeling complex. Interestingly, Akirin is not required for activation of all Twist-dependent enhancers, suggesting that Akirin refines Twist activity outputs and that different Twist-dependent targets have different requirements for chromatin remodeling during development. Our data further suggests that Akirin similarly links the SWI/SNF chromatin remodeling complex with other transcription factors during development. This work has important ramifications for understanding both normal development and diseases such as cancer.
doi:10.1371/journal.pgen.1002547
PMCID: PMC3291577  PMID: 22396663
6.  Cocaine-induced chromatin remodeling increases BDNF transcription in the rat medial prefrontal cortex, which alters the reinforcing efficacy of cocaine 
Cocaine self-administration alters patterns of gene expression in the brain that may underlie cocaine-induced neuronal plasticity. In the present study, male Sprague-Dawley rats were allowed to self-administer cocaine (0.25 µg/infusion) two hours per day for fourteen days followed by seven days of forced abstinence. Compared to yoked saline control rats, cocaine self-administration resulted in increased brain-derived neurotrophic factor (BDNF) protein levels in the rat medial prefrontal cortex (mPFC). In order to examine the functional relevance of this finding, cocaine self-administration maintained under a progressive ratio (PR) schedule of reinforcement was assessed following shRNA-induced suppression of BDNF expression in the mPFC. Decreased mPFC BDNF expression in the mPFC increased the cocaine self-administration break point. Next, the effect of cocaine self-administration on specific BDNF exons was assessed; results revealed selectively increased BDNF exon IV-containing transcripts in the mPFC. Moreover, there were significant cocaine-induced increases in acetylated histone H3 (AcH3) and phospho-cAMP response element binding protein (pCREB) association with BDNF promoter IV. In contrast, there was decreased methyl-CpG-binding protein 2 (MeCP2) association with BDNF promoter IV in the mPFC of rats that previously self-administered cocaine. Taken together, these results indicate that cocaine-induced increases in BDNF promoter IV transcript in the mPFC are driven by increased binding of AcH3 and pCREB as well as decreased MeCP2 binding at this BDNF promoter. Collectively, these results indicate that cocaine self-administration remodels chromatin in the mPFC resulting in increased expression of BDNF, which appears to represent a compensatory neuroadaptation that reduces the reinforcing efficacy of cocaine.
doi:10.1523/JNEUROSCI.2328-10.2010
PMCID: PMC2943400  PMID: 20810894
BDNF; cocaine; chromatin remodeling; medial prefrontal cortex; addiction; histones; transcription; self-administration
7.  MicroRNAs and Drug Addiction 
Drug addiction is considered a disorder of neuroplasticity in brain reward and cognition systems resulting from aberrant activation of gene expression programs in response to prolonged drug consumption. Non-coding RNAs (ncRNAs) are key regulators of almost all aspects of cellular physiology. MicroRNAs (miRNAs) are small (∼21–23 nucleotides) ncRNAs transcripts that regulate gene expression at the post-transcriptional level. Recently, miRNAs were shown to play key roles in the drug-induced remodeling of brain reward systems that likely drives the emergence of addiction. Here, we review evidence suggesting that one particular miRNA, miR-212, plays a particularly prominent role in vulnerability to cocaine addiction. We review evidence showing that miR-212 expression is increased in the dorsal striatum of rats that show compulsive-like cocaine-taking behaviors. Increases in miR-212 expression appear to protect against cocaine addiction, as virus-mediated striatal miR-212 overexpression decreases cocaine consumption in rats. Conversely, disruption of striatal miR-212 signaling using an antisense oligonucleotide increases cocaine intake. We also review data that identify two mechanisms by which miR-212 may regulate cocaine intake. First, miR-212 has been shown to amplify striatal cAMP response element binding protein (CREB) signaling through a mechanism involving activation of Raf1 kinase. Second, miR-212 was also shown to regulate cocaine intake by repressing striatal expression of methyl CpG binding protein 2 (MeCP2), consequently decreasing protein levels of brain-derived neurotrophic factor (BDNF). The concerted actions of miR-212 on striatal CREB and MeCP2/BDNF activity greatly attenuate the motivational effects of cocaine. These findings highlight the unique role for miRNAs in simultaneously controlling multiple signaling cascades implicated in addiction.
doi:10.3389/fgene.2013.00043
PMCID: PMC3650656  PMID: 23717324
miRNA; miR-212; MeCP2; cocaine
8.  BAZ1B in Nucleus Accumbens Regulates Reward-Related Behaviors in Response to Distinct Emotional Stimuli 
The Journal of Neuroscience  2016;36(14):3954-3961.
ATP-dependent chromatin remodeling proteins are being implicated increasingly in the regulation of complex behaviors, including models of several psychiatric disorders. Here, we demonstrate that Baz1b, an accessory subunit of the ISWI family of chromatin remodeling complexes, is upregulated in the nucleus accumbens (NAc), a key brain reward region, in both chronic cocaine-treated mice and mice that are resilient to chronic social defeat stress. In contrast, no regulation is seen in mice that are susceptible to this chronic stress. Viral-mediated overexpression of Baz1b, along with its associated subunit Smarca5, in mouse NAc is sufficient to potentiate both rewarding responses to cocaine, including cocaine self-administration, and resilience to chronic social defeat stress. However, despite these similar, proreward behavioral effects, genome-wide mapping of BAZ1B in NAc revealed mostly distinct subsets of genes regulated by these chromatin remodeling proteins after chronic exposure to either cocaine or social stress. Together, these findings suggest important roles for BAZ1B and its associated chromatin remodeling complexes in NAc in the regulation of reward behaviors to distinct emotional stimuli and highlight the stimulus-specific nature of the actions of these regulatory proteins.
SIGNIFICANCE STATEMENT We show that BAZ1B, a component of chromatin remodeling complexes, in the nucleus accumbens regulates reward-related behaviors in response to chronic exposure to both rewarding and aversive stimuli by regulating largely distinct subsets of genes.
doi:10.1523/JNEUROSCI.3254-15.2016
PMCID: PMC4821908  PMID: 27053203
Addiction; Baz1b; chromatin; depression; epigenetics; remodeler
9.  Gene Expression in Human Hippocampus from Cocaine Abusers Identifies Genes which Regulate Extracellular Matrix Remodeling 
PLoS ONE  2007;2(11):e1187.
The chronic effects of cocaine abuse on brain structure and function are blamed for the inability of most addicts to remain abstinent. Part of the difficulty in preventing relapse is the persisting memory of the intense euphoria or cocaine “rush”. Most abused drugs and alcohol induce neuroplastic changes in brain pathways subserving emotion and cognition. Such changes may account for the consolidation and structural reconfiguration of synaptic connections with exposure to cocaine. Adaptive hippocampal plasticity could be related to specific patterns of gene expression with chronic cocaine abuse. Here, we compare gene expression profiles in the human hippocampus from cocaine addicts and age-matched drug-free control subjects. Cocaine abusers had 151 gene transcripts upregulated, while 91 gene transcripts were downregulated. Topping the list of cocaine-regulated transcripts was RECK in the human hippocampus (FC = 2.0; p<0.05). RECK is a membrane-anchored MMP inhibitor that is implicated in the coordinated regulation of extracellular matrix integrity and angiogenesis. In keeping with elevated RECK expression, active MMP9 protein levels were decreased in the hippocampus from cocaine abusers. Pathway analysis identified other genes regulated by cocaine that code for proteins involved in the remodeling of the cytomatrix and synaptic connections and the inhibition of blood vessel proliferation (PCDH8, LAMB1, ITGB6, CTGF and EphB4). The observed microarray phenotype in the human hippocampus identified RECK and other region-specific genes that may promote long-lasting structural changes with repeated cocaine abuse. Extracellular matrix remodeling in the hippocampus may be a persisting effect of chronic abuse that contributes to the compulsive and relapsing nature of cocaine addiction.
doi:10.1371/journal.pone.0001187
PMCID: PMC2063513  PMID: 18000554
10.  Molecular Mechanism for a Gateway Drug: Epigenetic Changes Initiated by Nicotine Prime Gene Expression by Cocaine 
Science translational medicine  2011;3(107):107ra109.
In human populations, cigarettes and alcohol generally serve as gateway drugs, which people use first before progressing to marijuana, cocaine or other illicit substances. To understand the biological basis of the gateway sequence of drug use, we developed an animal model in mice and focused on the effects of nicotine on subsequent responses to cocaine. We found that pretreatment of mice with nicotine increased the response to cocaine as assessed by both addiction-related behaviors and synaptic plasticity in the striatum, a brain region critical for addiction-related reward. Locomotor sensitization was increased by 98%, conditioned place preference was increased by 78%, and cocaine-induced reduction in long-term potentiation (LTP) was enhanced by 24%. The responses to cocaine were altered only when nicotine was administered first, and nicotine and cocaine were then administered concurrently. Reversing the order of drug administration was ineffective. Cocaine had no effect on nicotine induced behaviors and synaptic plasticity. Nicotine primed the response to cocaine by enhancing its ability to induce transcriptional activation of the FosB gene through inhibiting histone deacetylase, causing global histone acetylation in the striatum. We tested this conclusion further with a histone deacetylase inhibitor and found that it similarly simulated the actions of nicotine on cocaine by priming the response to cocaine, and enhancing FosB gene expression and LTP depression in the nucleus accumbens. Conversely, in a genetic mouse model of Rubinstein Taybi’s syndrome, characterized by reduced histone acetylation, the effects of cocaine on LTP were diminished. We achieved a similar effect pharmacologically by infusing a low-dose of theophylline, an activator of histone deacetylase, into the nucleus accumbens. These data from mice prompted an analysis of epidemiological data, which indicated that most cocaine users initiate cocaine use after the onset of smoking while actively smoking and that initiating cocaine use after smoking increases the risk of becoming dependent on cocaine, consistent with our data in mice. If our findings in mice apply to humans, a decrease in smoking rates in young people could also lead to a decrease in cocaine addiction.
doi:10.1126/scitranslmed.3003062
PMCID: PMC4042673  PMID: 22049069
11.  Inhibition of chromatin remodeling by Polycomb Group protein Posterior Sex Combs is mechanistically distinct from nucleosome binding1 
Biochemistry  2010;49(44):9438-9448.
Polycomb Group (PcG) proteins are essential regulators of development that maintain gene silencing in Drosophila and mammals through alterations of chromatin structure. One key PcG protein, Posterior Sex Combs (PSC), is part of at least two complexes: Polycomb Repressive Complex 1 (PRC1) and dRING Associated Factors (dRAF). PRC1-class complexes compact chromatin and inhibit chromatin remodeling, while dRAF has E3 ligase activity for ubiquitylation of histone H2A; activities of both complexes can inhibit transcription. The noncovalent effects of PRC1-class complexes on chromatin can be recapitulated by PSC alone, and the region of PSC required for these activities is essential for PSC function in vivo. To understand how PSC interacts with chromatin to exert its repressive effects, we compared the ability of PSC to bind to and inhibit remodeling of various nucleosomal templates, and determined which regions of PSC are required for mononucleosome binding and inhibition of chromatin remodeling. We find that PSC binds mononucleosome templates but inhibits their remodeling poorly. Addition of linker DNA to mononucleosomes allows their remodeling to be inhibited, although higher concentrations of PSC are required than for inhibition of multi-nucleosome templates. The C-terminal region of PSC (aa 456-1603) is important for inhibition of chromatin remodeling, and we identified aa 456-909 as sufficient for stable nucleosome binding but not for inhibition of chromatin remodeling. Our data suggest distinct mechanistic steps between nucleosome binding and inhibition of chromatin remodeling.
doi:10.1021/bi100532a
PMCID: PMC3037448  PMID: 20873869
chromatin; Polycomb Group; nucleosome; chromatin remodeling
12.  The ISWI Chromatin Remodeler Organizes the hsrω ncRNA–Containing Omega Speckle Nuclear Compartments 
PLoS Genetics  2011;7(5):e1002096.
The complexity in composition and function of the eukaryotic nucleus is achieved through its organization in specialized nuclear compartments. The Drosophila chromatin remodeling ATPase ISWI plays evolutionarily conserved roles in chromatin organization. Interestingly, ISWI genetically interacts with the hsrω gene, encoding multiple non-coding RNAs (ncRNA) essential, among other functions, for the assembly and organization of the omega speckles. The nucleoplasmic omega speckles play important functions in RNA metabolism, in normal and stressed cells, by regulating availability of hnRNPs and some other RNA processing proteins. Chromatin remodelers, as well as nuclear speckles and their associated ncRNAs, are emerging as important components of gene regulatory networks, although their functional connections have remained poorly defined. Here we provide multiple lines of evidence showing that the hsrω ncRNA interacts in vivo and in vitro with ISWI, regulating its ATPase activity. Remarkably, we found that the organization of nucleoplasmic omega speckles depends on ISWI function. Our findings highlight a novel role for chromatin remodelers in organization of nucleoplasmic compartments, providing the first example of interaction between an ATP-dependent chromatin remodeler and a large ncRNA.
Author Summary
Chromatin structure and function are regulated by the concerted activity of covalent modifiers of chromatin, nucleosome remodeling factors, and several emerging classes of non-coding RNAs. ISWI is an evolutionarily conserved ATP-dependent chromatin remodeler playing essential roles in chromosome condensation, gene expression, and DNA replication. ISWI activity has been involved in a variety of nuclear functions including telomere silencing, stem cell renewal, neural morphogenesis, and epigenetic reprogramming. Using an in vivo assay to identify factors regulating ISWI activity in the model system Drosophila melanogaster, we recovered a genetic interaction between ISWI and hsrω. The hsrω gene encodes multiple non-coding RNAs (ncRNAs), of which the >10 kb nuclear hsrω-n RNA, with functional homolog in mammals, is essential for the assembly and organization of hnRNP-containing nucleoplasmic omega speckles. These special nuclear compartments play essential roles in the storage/sequestration of hnRNP family and other proteins, thus playing important roles in mRNA maturation and other regulatory processes. Here we show that the hsrω-n ncRNA interacts in vivo and in vitro with ISWI to directly regulate its ATPase activity. We also provide in vivo data showing that omega speckle nuclear organization depends on ISWI function, highlighting a novel role for chromatin remodelers in nuclear speckles organization.
doi:10.1371/journal.pgen.1002096
PMCID: PMC3102753  PMID: 21637796
13.  Persistent alterations in mesolimbic gene expression with abstinence from cocaine self-administration 
Cocaine-responsive gene expression changes have been described after either no drug abstinence or short periods of abstinence. Little data exist on the persistence of these changes after long-term abstinence. Previously, we reported that after discrete-trial, cocaine self-administration and 10 days of forced abstinence, incubation of cocaine reinforcement was observable by a progressive ratio schedule. The present study used rat discrete-trial cocaine self-administration and long-term forced abstinence to examine: extinction responding, mRNA abundance of known cocaine-responsive genes, and chromatin remodeling. At 30 and 100 days of abstinence, extinction responding increased compared to 3-day abstinent rats. Decreases in both medial prefrontal cortex (mPFC) and nucleus accumbens (NAc) c-fos, Nr4a1, Arc, and EGR1 mRNA were observed, and in most cases persisted, for 100 days of abstinence. The signaling peptides CART and NPY transiently increased in the mPFC, but returned to baseline levels following 10 days of abstinence. To investigate a potential regulatory mechanism for these persistent mRNA changes, levels of histone H3 acetylation at promoters for genes with altered mRNA expression were examined. In the mPFC, histone H3 acetylation decreased after 1 and 10 days of abstinence at the promoter for EGR1. H3 acetylation increased for NPY after 1 day of abstinence and returned to control levels by 10 days of abstinence. Behaviorally, these results demonstrate incubation after discrete-trial cocaine self-administration and prolonged forced abstinence. This incubation is accompanied by changes in gene expression that persist long after cessation of drug administration and may be regulated by chromatin remodeling.
doi:10.1038/sj.npp.1301577
PMCID: PMC2810407  PMID: 17851536
cocaine; abstinence; behavior; medial prefrontal cortex; nucleus accumbens; functional genomics; extinction; incubation; addiction
14.  Altered Attention and Prefrontal Cortex Gene Expression in Rats after Binge-Like Exposure to Cocaine during Adolescence 
Illicit use of drugs frequently begins and escalates during adolescence, with long-term adverse consequences. Because it is increasingly accepted that neural development continues through adolescence, addiction research has become more invested in understanding the behavioral and molecular consequences of early exposure to drugs of abuse. In a novel binge administration paradigm designed to model the pattern of human adolescent drug use, we administered ascending doses of cocaine or saline during a 12-d developmental period [postnatal day 35 (P35) to P46] corresponding to human adolescence. During adulthood (P70), rats treated with this regimen displayed increased responsiveness to the stimulant effects of cocaine. Adult rats also displayed abnormally rapid shifts in attention when performing an attentional set-shifting task, which measures the ability to shift attention between stimuli and whose performance requires an intact prefrontal cortex (PFC). Treatment with cocaine during adolescence also caused acute alterations in the expression of genes encoding cell adhesion molecules and transcription factors within the PFC. Furthermore, we observed decreases in histone methylation, which may indicate a role for chromatin remodeling in the observed changes in gene expression patterns. These findings suggest that exposure to cocaine during adolescence has far-reaching molecular and behavioral consequences in the rat PFC that develop over time and endure long after drug administration has ceased.
doi:10.1523/JNEUROSCI.2391-06.2006
PMCID: PMC4203339  PMID: 16988036
medial prefrontal cortex; attentional set-shifting task; cell adhesion; adolescence; cocaine; gene expression
15.  Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens 
Genome Biology  2014;15(4):R65.
Background
Increasing evidence supports a role for altered gene expression in mediating the lasting effects of cocaine on the brain, and recent work has demonstrated the involvement of chromatin modifications in these alterations. However, all such studies to date have been restricted by their reliance on microarray technologies that have intrinsic limitations.
Results
We use next generation sequencing methods, RNA-seq and ChIP-seq for RNA polymerase II and several histone methylation marks, to obtain a more complete view of cocaine-induced changes in gene expression and associated adaptations in numerous modes of chromatin regulation in the mouse nucleus accumbens, a key brain reward region. We demonstrate an unexpectedly large number of pre-mRNA splicing alterations in response to repeated cocaine treatment. In addition, we identify combinations of chromatin changes, or signatures, that correlate with cocaine-dependent regulation of gene expression, including those involving pre-mRNA alternative splicing. Through bioinformatic prediction and biological validation, we identify one particular splicing factor, A2BP1(Rbfox1/Fox-1), which is enriched at genes that display certain chromatin signatures and contributes to drug-induced behavioral abnormalities. Together, this delineation of the cocaine-induced epigenome in the nucleus accumbens reveals several novel modes of regulation by which cocaine alters the brain.
Conclusions
We establish combinatorial chromatin and transcriptional profiles in mouse nucleus accumbens after repeated cocaine treatment. These results serve as an important resource for the field and provide a template for the analysis of other systems to reveal new transcriptional and epigenetic mechanisms of neuronal regulation.
doi:10.1186/gb-2014-15-4-r65
PMCID: PMC4073058  PMID: 24758366
16.  Cocaine-mediated induction of microglial activation involves the ER stress-TLR2 axis 
Background
Neuroinflammation associated with advanced human immunodeficiency virus (HIV)-1 infection is often exacerbated by chronic cocaine abuse. Cocaine exposure has been demonstrated to mediate up-regulation of inflammatory mediators in in vitro cultures of microglia. The molecular mechanisms involved in this process, however, remain poorly understood. In this study, we sought to explore the underlying signaling pathways involved in cocaine-mediated activation of microglial cells.
Methods
BV2 microglial cells were exposed to cocaine and assessed for toll-like receptor (TLR2) expression by quantitative polymerase chain reaction (qPCR), western blot, flow cytometry, and immunofluorescence staining. The mRNA and protein levels of cytokines (TNFα, IL-6, MCP-1) were detected by qPCR and ELISA, respectively; level of reactive oxygen species (ROS) production was examined by the Image-iT LIVE Green ROS detection kit; activation of endoplasmic reticulum (ER)-stress pathways were detected by western blot. Chromatin immunoprecipitation (ChIP) assay was employed to discern the binding of activating transcription factor 4 (ATF4) with the TLR2 promoter. Immunoprecipitation followed by western blotting with tyrosine antibody was used to determine phosphorylation of TLR2. Cocaine-mediated up-regulation of TLR2 expression and microglial activation was validated in cocaine-injected mice.
Results
Exposure of microglial cells to cocaine resulted in increased expression of TLR2 with a concomitant induction of microglial activation. Furthermore, this effect was mediated by NADPH oxidase-mediated rapid accumulation of ROS with downstream activation of the ER-stress pathways as evidenced by the fact that cocaine exposure led to up-regulation of pPERK/peIF2α/ATF4 and TLR2. The novel role of ATF4 in the regulation of TLR2 expression was confirmed using genetic and pharmacological approaches.
Conclusions
xThe current study demonstrates that cocaine-mediated activation of microglia involves up-regulation of TLR2 through the ROS-ER stress-ATF4-TLR2 axis. Understanding the mechanism(s) involved in cocaine-mediated up-regulation of ROS-ER stress/TLR2 expression and microglial activation could have implications for the development of potential therapeutic targets aimed at resolving neuroinflammation in cocaine abusers.
Electronic supplementary material
The online version of this article (doi:10.1186/s12974-016-0501-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s12974-016-0501-2
PMCID: PMC4748483  PMID: 26860188
Neuroinflammation; Cocaine; ER stress; Microglial activation; TLR2; ATF4
17.  Forced Abstinence from Cocaine Self-Administration is Associated with DNA Methylation Changes in Myelin Genes in the Corpus Callosum: a Preliminary Study 
Background: Human cocaine abuse is associated with alterations in white matter integrity revealed upon brain imaging, an observation that is recapitulated in an animal model of continuous cocaine exposure. The mechanism through which cocaine may affect white matter is unknown and the present study tested the hypothesis that cocaine self-administration results in changes in DNA methylation that could result in altered expression of several myelin genes that could contribute to the effects of cocaine on white matter integrity. Methods: In the present study, we examined the impact of forced abstinence from cocaine self-administration on chromatin associated changes in white matter. To this end, rats were trained to self-administer cocaine (0.75 mg/kg/0.1 mL infusion) for 14 days followed by forced abstinence for 1 day (n = 6) or 30 days (n = 6) before sacrifice. Drug-free, sham surgery controls (n = 7) were paired with the experimental groups. Global DNA methylation and DNA methylation at specific CpG sites in the promoter regions ofmyelin basic protein (Mbp), proteolipid protein-1 (Plp1), and SRY-related HMG-box-10 (Sox10) genes were analyzed in DNA extracted from corpus callosum. Results: Significant differences in the overall methylation patterns of the Sox10 promoter region were observed in the corpus callosum of rats at 30 days of forced abstinence from cocaine self-administration relative to sham controls; the −189, −142, −93, and −62 CpG sites were significantly hypomethylated point-wise at this time point. After correction for multiple comparisons, no differences in global methylation or the methylation patterns of Mbp or Plp1 were found. Conclusion: Forced abstinence from cocaine self-administration was associated with differences in DNA methylation at specific CpG sites in the promoter region of the Sox10 gene in corpus callosum. These changes may be related to reductions in normal age related changes in DNA methylation and could be a factor in white matter alterations seen after withdrawal from repeated cocaine self-administration. Further research is warranted examining the effects of cocaine on DNA methylation in white matter.
doi:10.3389/fpsyt.2012.00060
PMCID: PMC3374938  PMID: 22712019
cocaine; corpus callosum; gene; self-administration; white matter; epigenetics
18.  The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism 
eLife  null;4:e06073.
ISWI family chromatin remodelers typically organize nucleosome arrays, while SWI/SNF family remodelers (RSC) typically disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism and reveal different mechanisms at two different promoter architectures.
DOI: http://dx.doi.org/10.7554/eLife.06073.001
eLife digest
The genome of an organism can contain hundreds to thousands of genes. However, these genes are not all active at the same time. Instead, mechanisms exist that control when genes are switched off or on. One such mechanism alters how tightly DNA is packaged into a structure called chromatin. To form chromatin, DNA is wrapped around histone proteins at different points along its length; these structures are known as nucleosomes. Once formed, chromatin can either adopt a tightly packed form that represses gene activity or a less compact form associated with gene activation.
The proteins that control how chromatin is packed are called ‘chromatin remodelers’. These proteins work in complexes that either disassemble chromatin—for example, by repositioning nucleosomes or removing histones—or organize chromatin by replacing nucleosomes and making it more compact.
Studies in many organisms have identified two key families of chromatin remodelers. In yeast, the ISWI family of complexes assembles chromatin and a protein complex called RSC disassembles chromatin. Parnell, Schlichter et al. used a range of genetic techniques to investigate whether these two chromatin-remodeling complexes work against each other in a species of yeast called Saccharomyces cerevisiae. The results suggest that this is indeed the case.
Both the ISWI complex and the RSC complex bind to regions of DNA called promoters, which are found at the start of a gene and help to regulate its activity. Parnell, Schlichter et al. found that the RSC complex helps to activate genes by establishing or maintaining regions of nucleosome-poor chromatin at a promoter. The chromatin is relaxed in these regions, which allows the proteins that activate genes to access the DNA. This effect is partially counteracted by the ISWI complex, which repositions nucleosomes across the promoters to fill the gaps created by the RSC complex.
In comparison, Parnell, Schlichter et al. found that promoters that do not have regions of nucleosome-poor chromatin contain a larger number of both of the remodeling complexes and have a high turnover of histone proteins. This suggests that at these sites, the RSC proteins are needed to overcome the assembly of nucleosomes by the ISWI complex in order to activate the gene. Thus, these two chromatin remodelers, ISWI and RSC, compete at promoters to determine whether they contain or lack nucleosomes, which helps determine whether the gene is silent or active, respectively. Future work will look further at how the ‘winner’ is determined: how transcription factors or signaling systems within the cell bias the recruitment or activity of RSC or ISWI at particular promoters, to determine gene activity.
DOI: http://dx.doi.org/10.7554/eLife.06073.002
doi:10.7554/eLife.06073
PMCID: PMC4423118  PMID: 25821983
chromatin; remodeler; nucleosome; RSC; ISWI; S. cerevisiae
19.  Discovering chromatin motifs using FAIRE sequencing and the human diploid genome 
BMC Genomics  2013;14:310.
Background
Specific chromatin structures are associated with active or inactive gene transcription. The gene regulatory elements are intrinsically dynamic and alternate between inactive and active states through the recruitment of DNA binding proteins, such as chromatin-remodeling proteins.
Results
We developed a unique genome-wide method to discover DNA motifs associated with chromatin accessibility using formaldehyde-assisted isolation of regulatory elements with high-throughput sequencing (FAIRE-seq). We aligned the FAIRE-seq reads to the GM12878 diploid genome and subsequently identified differential chromatin-state regions (DCSRs) using heterozygous SNPs. The DCSR pairs represent the locations of imbalances of chromatin accessibility between alleles and are ideal to reveal chromatin motifs that may directly modulate chromatin accessibility. In this study, we used DNA 6-10mer sequences to interrogate all DCSRs, and subsequently discovered conserved chromatin motifs with significant changes in the occurrence frequency. To investigate their likely roles in biology, we studied the annotated protein associated with each of the top ten chromatin motifs genome-wide, in the intergenic regions and in genes, respectively. As a result, we found that most of these annotated motifs are associated with chromatin remodeling, reflecting their significance in biology.
Conclusions
Our method is the first one using fully phased diploid genome and FAIRE-seq to discover motifs associated with chromatin accessibility. Our results were collected to construct the first chromatin motif database (CMD), providing the potential DNA motifs recognized by chromatin-remodeling proteins and is freely available at http://syslab.nchu.edu.tw/chromatin.
doi:10.1186/1471-2164-14-310
PMCID: PMC3655836  PMID: 23656909
20.  Epigenetic Readers of Lysine Acetylation Regulate Cocaine-Induced Plasticity 
The Journal of Neuroscience  2015;35(45):15062-15072.
Epigenetic processes that regulate histone acetylation play an essential role in behavioral and molecular responses to cocaine. To date, however, only a small fraction of the mechanisms involved in the addiction-associated acetylome have been investigated. Members of the bromodomain and extraterminal (BET) family of epigenetic “reader” proteins (BRD2, BRD3, BRD4, and BRDT) bind acetylated histones and serve as a scaffold for the recruitment of macromolecular complexes to modify chromatin accessibility and transcriptional activity. The role of BET proteins in cocaine-induced plasticity, however, remains elusive. Here, we used behavioral, pharmacological, and molecular techniques to examine the involvement of BET bromodomains in cocaine reward. Of the BET proteins, BRD4, but not BRD2 or BRD3, was significantly elevated in the nucleus accumbens (NAc) of mice and rats following repeated cocaine injections and self-administration. Systemic and intra-accumbal inhibition of BRD4 with the BET inhibitor, JQ1, attenuated the rewarding effects of cocaine in a conditioned place preference procedure but did not affect conditioned place aversion, nor did JQ1 alone induce conditioned aversion or preference. Investigating the underlying mechanisms, we found that repeated cocaine injections enhanced the binding of BRD4, but not BRD3, to the promoter region of Bdnf in the NAc, whereas systemic injection of JQ1 attenuated cocaine-induced expression of Bdnf in the NAc. JQ1 and siRNA-mediated knockdown of BRD4 in vitro also reduced expression of Bdnf. These findings indicate that disrupting the interaction between BET proteins and their acetylated lysine substrates may provide a new therapeutic avenue for the treatment of drug addiction.
SIGNIFICANCE STATEMENT Proteins involved in the “readout” of lysine acetylation marks, referred to as BET bromodomain proteins (including BRD2, BRD3, BRD4, and BRDT), have been shown to be key regulators of chromatin dynamics and disease, and BET inhibitors are currently being studied in several clinical trials. However, their role in addiction-related phenomena remains unknown. In the current studies, we revealed that BRD4 is elevated in the nucleus accumbens and recruited to promoter regions of addiction-related genes following repeated cocaine administration, and that inhibition of BRD4 attenuates transcriptional and behavioral responses to cocaine. Together, these studies reveal that BET inhibitors may have therapeutic utility in the treatment of cocaine addiction.
doi:10.1523/JNEUROSCI.0826-15.2015
PMCID: PMC4642238  PMID: 26558777
BDNF; BET; BRD4; bromodomain; cocaine; epigenetic
21.  Functional Antagonism between Sas3 and Gcn5 Acetyltransferases and ISWI Chromatin Remodelers 
PLoS Genetics  2012;8(10):e1002994.
Chromatin-modifying enzymes and ATP-dependent remodeling complexes have been intensely studied individually, yet how these activities are coordinated to ensure essential cell functions such as transcription, replication, and repair of damage is not well understood. In this study, we show that the critical loss of Sas3 and Gcn5 acetyltransferases in yeast can be functionally rescued by inactivation of ISWI remodelers. This genetic interaction depends on the ATPase activities of Isw1 and Isw2, suggesting that it involves chromatin remodeling activities driven by the enzymes. Genetic dissection of the Isw1 complexes reveals that the antagonistic effects are mediated specifically by the Isw1a complex. Loss of Sas3 and Gcn5 correlates with defective RNA polymerase II (RNAPII) occupancy at actively transcribed genes, as well as a significant loss of H3K14 acetylation. Inactivation of the Isw1a complex in the acetyltransferase mutants restores RNAPII recruitment at active genes, indicating that transcriptional regulation may be the mechanism underlying suppression. Dosage studies and further genetic dissection reveal that the Isw1b complex may act in suppression through down-regulation of Isw1a. These studies highlight the importance of balanced chromatin modifying and remodeling activities for optimal transcription and cell growth.
Author Summary
In eukaryotes, essential processes such as transcription, replication, and repair of damage occur in the context of chromatin. The structure of chromatin is tightly regulated during the cell cycle by chromatin-modifying enzymes, including acetyltransferases, and ATP-dependent remodeling complexes. Although there has been extensive characterization of their individual functions, little is known about how their activities are coordinated to maintain cell viability. In this study, we show that the critical loss of Sas3 and Gcn5 acetyltransferases can be functionally rescued by inactivation of ISWI remodelers. At a molecular level, the effects on cell viability tightly correlate with the recruitment of RNA polymerase II (RNAPII) at active genes, suggesting that transcriptional regulation may be the mechanism underlying cell viability rescue. Our genetic analyses reveal distinct roles for the two Isw1a and Isw1b complexes; in particular, the antagonistic effects are mediated specifically by the Isw1a complex. These studies highlight the importance of balanced chromatin modifying and remodeling activities for optimal transcription and cell growth.
doi:10.1371/journal.pgen.1002994
PMCID: PMC3464200  PMID: 23055944
22.  Defining the budding yeast chromatin-associated interactome 
We report here the first large-scale affinity purification and mass spectrometry (AP-MS) study of chromatin-associated protein, in which over 100 different baits involved in chromatin biology were studied by modified chromatin immunopurification (mChIP)-MS. In particular, focus was placed on poorly studied chromatin binding proteins, such as transcription factors, which have been underrepresented in previous AP-MS studies.mChIP-MS analysis of transcription factors identified dense networks of protein associated with chromatin that were composed of specific transcriptional co-activators, information not accessible through the use of classical AP-MS methods.Finally, we demonstrate that novel protein–protein interactions identified in study by mChIP have functional implications exemplified by the detailed study of both the ubiquitination of the proline isomerase Cpr1 and of histone chaperones involved in the regulation of the HTA1-HTB1 promoter.Our work demonstrates the value of targeted interactome studies, in which affinity purification methods are adapted to the needs of specific baits, as is the case for chromatin binding proteins.
The maintenance of cellular fitness requires living organisms to integrate multiple signals into coordinated outputs. Central to this process is the regulation of the expression of the genetic information encoded into DNA. As a result, there are numerous constraints imposed on gene expression. The access to DNA is restricted by the formation of nucleosomes, in which DNA is wrapped around histone octamers to form chromatin wherein the volume of DNA is considerably reduced. As such, nucleosome positioning is critical and must be defined precisely, particularly during transcription (Workman, 2006). Furthermore, nucleosomes can be actively assembled/disassembled by histone chaperones and can be made to ‘slide' along DNA by the actions of chromatin remodelers. Moreover, the histone proteins are heavily regulated at the expression level and by extensive post-translational modifications (PTMs) (Campos and Reinberg, 2009). Histone PTMs have also been shown to help recruit numerous chromatin-associated factors in accordance with the histone code (Strahl and Allis, 2000). Although our understanding of chromatin and its roles has improved, we still have limited knowledge of the chromatin-associated protein complexes and their interactions.
The characterization of biological systems and of specific subdomain within them, such as chromatin, remains a difficult task. An efficient approach to gain insight in the function of protein is to define its interactome. The underlying principle of protein interaction mapping is that proteins found to interact must be involved in common processes and localization, i.e., guilt by association. The large-scale mapping of proteins interactions allows to annotate protein of unknown functions, implicate protein of known functions in different processes and derive new hypothesis. This is possible because most proteins do not act in isolation but rather as part of complexes, and thus possess interaction partners that can now be detected with the right tools. AP-MS has emerged as a powerful tool for characterizing protein–protein interactions and biological systems in general (Gingras et al, 2007; Gstaiger and Aebersold, 2009).
Recently, we reported the development of a novel affinity purification approach termed mChIP, which was designed to improve the characterization of DNA binding proteins interactome (Lambert et al, 2009). The mChIP method consists of a single affinity purification step, whereby chromatin-associated proteins are isolated from mildly sonicated and gently clarified cellular extracts using magnetic beads coated with antibodies (Lambert et al, 2009; Figure 1A). As such, the mChIP approach maintains chromatin fragments in solution enabling their specific purification, something not previously possible in classical AP-MS methods (Lambert et al, 2009).
In this study, we report the utilization of mChIP followed by MS for the characterization of more than 100 proteins and their associated protein networks (Figure 1B). We initially focused on DNA-associated proteins that had been poorly characterized in past AP-MS studies, such as transcription factors. In addition, many histone modifiers, such as lysine acetyl transferases (KAT) and lysine methyl transferases, critical components of chromatin function and regulation, were also studied by mChIP. This resulted in raw non-redundant mChIP-MS data containing ∼9000 protein–protein interactions between ∼900 proteins. Following a two-step curation process designed to remove common contaminants and protein not specifically associated with the baits under study, a high confidence mChIP-MS data set was produced containing 2966 protein–protein interactions between 724 proteins (Figure 1B). It is important to note that our curation strategy was capable of maintaining the majority of the protein–protein interaction identified in previous AP-MS studies, while removing the bulk of protein–protein interaction not related to chromatin biology. Further analysis of the mChIP-MS data set revealed that for most bait tested, mChIP-MS resulted in the identification of more interaction partners than classical TAP-MS.
Visualization of the mChIP-MS data set was achieved by generating heat maps from two-dimensional hierarchical clustering of the bait–prey interactions. This revealed numerous clusters within our data set supporting functional relationship. For instance, mChIP analysis of the highly homologous heat-shock-inducible transcription factors Msn2 and Msn4 clustered with different transcriptional co-activators. Importantly, our analysis also revealed key differences in the co-activators associated with Msn2 and Msn4 relevant to their function. Another example that we explore in greater details is the Cpr1 proline isomerase, a known member of the Set3 complex (Pijnappel et al, 2001). mChIP-MS analysis of Cpr1 revealed an extended network of associated proteins, including the E3 ubiquitin ligase Bre1 and its association partner Lge1 (Figure 5A). This association raised the possibility of a direct action of Bre1/Lge1 on Cpr1 to ubiquitinate it. In targeted experiments, we observed that Cpr1 is in fact ubiquitinated in a process involving Bre1/Lge1 (Figure 5E), confirming their functional relationship. As such, mChIP is capable of uncovering novel protein–protein interactions with physiological impacts.
In this study, we report how the use of an AP-MS method designed for a given class of protein (chromatin-associated proteins) can help uncover numerous novel protein–protein interactions. Furthermore, our work detected dense chromatin-associated protein networks being co-purified with multiple transcription factors and other DNA binding proteins. The fact that even in the best-characterized model organism Saccharomyces cerevisiae, thousands of novel protein–protein interactions can be detected supports our view that targeted interactome studies are worthwhile and desirable. As such, the budding yeast interactome can still be consider incomplete and warrant further study.
We previously reported a novel affinity purification (AP) method termed modified chromatin immunopurification (mChIP), which permits selective enrichment of DNA-bound proteins along with their associated protein network. In this study, we report a large-scale study of the protein network of 102 chromatin-related proteins from budding yeast that were analyzed by mChIP coupled to mass spectrometry. This effort resulted in the detection of 2966 high confidence protein associations with 724 distinct preys. mChIP resulted in significantly improved interaction coverage as compared with classical AP methodology for ∼75% of the baits tested. Furthermore, mChIP successfully identified novel binding partners for many lower abundance transcription factors that previously failed using conventional AP methodologies. mChIP was also used to perform targeted studies, particularly of Asf1 and its associated proteins, to allow for a understanding of the physical interplay between Asf1 and two other histone chaperones, Rtt106 and the HIR complex, to be gained.
doi:10.1038/msb.2010.104
PMCID: PMC3018163  PMID: 21179020
affinity purification; chromatin-associated protein networks; mass spectrometry; nucleosome assembly factor Asf1; protein–DNA interaction
23.  Drug experience epigenetically primes Fosb gene inducibility in rat nucleus accumbens 
ΔFosB, a Fosb gene product, is induced in nucleus accumbens (NAc) and caudate putamen (CPu) by repeated exposure to drugs of abuse such as cocaine. This induction contributes to aberrant patterns of gene expression and behavioral abnormalities seen with repeated drug exposure. Here, we assessed whether a remote history of drug exposure in rats might alter inducibility of the Fosb gene elicited by subsequent cocaine exposure. We show that prior chronic cocaine administration, followed by extended withdrawal, increases inducibility of Fosb in NAc as evidenced by greater acute induction of ΔFosB mRNA and faster accumulation of ΔFosB protein after repeated cocaine re-exposure. No such primed Fosb induction was observed in CPu, in fact, subsequent acute induction of ΔFosB mRNA was suppressed in CPu. These abnormal patterns of Fosb expression are associated with chromatin modifications at the Fosb gene promoter. Prior chronic cocaine administration induces a long-lasting increase in RNA polymerase II (Pol II) binding at the Fosb promoter in NAc only, suggesting that Pol II “stalling” primes Fosb for induction in this region upon re-exposure to cocaine. A cocaine challenge then triggers the release of Pol II from the gene promoter, allowing for more rapid Fosb transcription. A cocaine challenge also decreases repressive histone modifications at the Fosb promoter in NAc, but increases such repressive marks and decreases activating marks in CPu. These results provide new insight into the chromatin dynamics at the Fosb promoter and reveal a novel mechanism for primed Fosb induction in NAc upon re-exposure to cocaine.
doi:10.1523/JNEUROSCI.1290-12.2012
PMCID: PMC3417057  PMID: 22836260
24.  DNA Methylation Regulates Cocaine-Induced Behavioral Sensitization in Mice 
Neuropsychopharmacology  2010;35(12):2450-2461.
The behavioral sensitization produced by repeated cocaine treatment represents the neural adaptations underlying some of the features of addiction in humans. Cocaine administrations induce neural adaptations through regulation of gene expression. Several studies suggest that epigenetic modifications, including DNA methylation, are the critical regulators of gene expression in the adult central nervous system. DNA methylation is catalyzed by DNA methyltransferases (DNMTs) and consequent promoter region hypermethylation is associated with transcriptional silencing. In this study a potential role for DNA methylation in a cocaine-induced behavioral sensitization model in mice was explored. We report that acute cocaine treatment caused an upregulation of DNMT3A and DNMT3B gene expression in the nucleus accumbens (NAc). Using methylated DNA immunoprecipitation, DNA bisulfite modification, and chromatin immunoprecipitation assays, we observed that cocaine treatment resulted in DNA hypermethylation and increased binding of methyl CpG binding protein 2 (MeCP2) at the protein phosphatase-1 catalytic subunit (PP1c) promoter. These changes are associated with transcriptional downregulation of PP1c in NAc. In contrast, acute and repeated cocaine administrations induced hypomethylation and decreased binding of MeCP2 at the fosB promoter, and these are associated with transcriptional upregulation of fosB in NAc. We also found that pharmacological inhibition of DNMT by zebularine treatment decreased cocaine-induced DNA hypermethylation at the PP1c promoter and attenuated PP1c mRNA downregulation in NAc. Finally, zebularine and cocaine co-treatment delayed the development of cocaine-induced behavioral sensitization. Together, these results suggest that dynamic changes of DNA methylation may be an important gene regulation mechanism underlying cocaine-induced behavioral sensitization.
doi:10.1038/npp.2010.128
PMCID: PMC3055323  PMID: 20720536
DNA methylation; DNA methyltransferase; cocaine; behavioral sensitization; nucleus accumbens; zebularine; psychostimulants; addiction & substance abuse; molecular & cellular neurobiology; plasticity; DNA methylation; DNA methyltransferase; cocaine; behavioural sensitization; nucleus accumbens
25.  NFκB Signaling Regulates Neuronal Morphology and Cocaine Reward 
While chronic cocaine-induced changes in dendritic spines on nucleus accumbens (NAc) neurons have been correlated with behavioral sensitization, the molecular pathways governing these structural changes, and their resulting behavioral effects, are poorly understood. The transcription factor, nuclear factor kappa B (NFκB), is rapidly activated by diverse stimuli and regulates expression of many genes known to maintain cell structure. Therefore, we evaluated the role of NFκB in regulating cocaine-induced dendritic spine changes on medium spiny neurons of the NAc and the rewarding effects of cocaine. We show that chronic cocaine induces NFκB-dependent transcription in the NAc of NFκB-LacZ transgenic mice. This induction of NFκB activity is accompanied by increased expression of several NFκB genes, the promoters of which show chromatin modifications after chronic cocaine exposure consistent with their transcriptional activation. To study the functional significance of this induction, we used viral-mediated gene transfer to express either a constitutively active or dominant negative mutant of I kappa kinase (IKKca or IKKdn), which normally activates NFκB signaling, in the NAc. We found that activation of NFκB by IKKca increases the number of dendritic spines on NAc neurons, while inhibition of NFκB by IKKdn decreases basal dendritic spine number and blocks the increase in dendritic spines after chronic cocaine. Moreover, inhibition of NFκB blocks the rewarding effects of cocaine and the ability of prior cocaine exposure to increase an animal’s preference for cocaine. Together, these studies establish a direct role for NFκB pathways in the NAc to regulate structural and behavioral plasticity to cocaine.
doi:10.1523/JNEUROSCI.6173-08.2009
PMCID: PMC2677656  PMID: 19295158
chromatin; dendritic spines; drug addiction; epigenetic; mesolimbic dopamine; neurotrophic factor; medium spiny neuron (MSN)

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