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1.  An RNAi-Based Dimorphic Genetic Screen Identified the Double Bromodomain Protein BET-1 as a Sumo-Dependent Attenuator of RAS-Mediated Signalling 
PLoS ONE  2013;8(12):e83659.
Attenuation of RAS/RAF/MAPK signalling is essential to prevent hyperactivation of this oncogenic pathway. In C. elegans, the sumoylation pathway and a combination of histone tail modifications regulate gene expression to attenuate the LET-60 (RAS) signalling pathway. We hypothesised that a number of chromatin regulators are likely to depend on sumoylation to attenuate the pathway. To reveal these, we designed an RNAi-based dimorphic genetic screen that selects candidates based on their ability to act as enhancers of a sumo mutant phenotype, such interactions would suggest that the candidates may be physically associated with sumoylation. We found 16 enhancers, one of which BET-1, is a conserved double bromodomain containing protein. We further characterised BET-1 and showed that it can physically associate with SMO-1 and UBC-9, and that it can be sumoylated in vitro within the second bromodomain at lysine 252. Previous work has shown that BET-1 can bind acetyl-lysines on histone tails to influence gene expression. In conclusion, our screening approach has identified BET-1 as a Sumo-dependent attenuator of LET-60-mediated signalling and our characterisation suggests that BET-1 can be sumoylated.
doi:10.1371/journal.pone.0083659
PMCID: PMC3862036  PMID: 24349540
2.  Widespread Misinterpretable ChIP-seq Bias in Yeast 
PLoS ONE  2013;8(12):e83506.
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to detect genome-wide interactions between a protein of interest and DNA in vivo. Loci showing strong enrichment over adjacent background regions are typically considered to be sites of binding. Insufficient attention has been given to systematic artifacts inherent to the ChIP-seq procedure that might generate a misleading picture of protein binding to certain loci. We show here that unrelated transcription factors appear to consistently bind to the gene bodies of highly transcribed genes in yeast. Strikingly, several types of negative control experiments, including a protein that is not expected to bind chromatin, also showed similar patterns of strong binding within gene bodies. These false positive signals were evident across sequencing platforms and immunoprecipitation protocols, as well as in previously published datasets from other labs. We show that these false positive signals derive from high rates of transcription, and are inherent to the ChIP procedure, although they are exacerbated by sequencing library construction procedures. This expression bias is strong enough that a known transcriptional repressor like Tup1 can erroneously appear to be an activator. Another type of background bias stems from the inherent nucleosomal structure of chromatin, and can potentially make it seem like certain factors bind nucleosomes even when they don't. Our analysis suggests that a mock ChIP sample offers a better normalization control for the expression bias, whereas the ChIP input is more appropriate for the nucleosomal periodicity bias. While these controls alleviate the effect of the biases to some extent, they are unable to eliminate it completely. Caution is therefore warranted regarding the interpretation of data that seemingly show the association of various transcription and chromatin factors with highly transcribed genes in yeast.
doi:10.1371/journal.pone.0083506
PMCID: PMC3857294  PMID: 24349523
3.  Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution 
PLoS Computational Biology  2013;9(11):e1003373.
Nucleosomes, the basic repeat units of eukaryotic chromatin, have been suggested to influence the evolution of eukaryotic genomes, both by altering the propensity of DNA to mutate and by selection acting to maintain or exclude nucleosomes in particular locations. Contrary to the popular idea that nucleosomes are unique to eukaryotes, histone proteins have also been discovered in some archaeal genomes. Archaeal nucleosomes, however, are quite unlike their eukaryotic counterparts in many respects, including their assembly into tetramers (rather than octamers) from histone proteins that lack N- and C-terminal tails. Here, we show that despite these fundamental differences the association between nucleosome footprints and sequence evolution is strikingly conserved between humans and the model archaeon Haloferax volcanii. In light of this finding we examine whether selection or mutation can explain concordant substitution patterns in the two kingdoms. Unexpectedly, we find that neither the mutation nor the selection model are sufficient to explain the observed association between nucleosomes and sequence divergence. Instead, we demonstrate that nucleosome-associated substitution patterns are more consistent with a third model where sequence divergence results in frequent repositioning of nucleosomes during evolution. Indeed, we show that nucleosome repositioning is both necessary and largely sufficient to explain the association between current nucleosome positions and biased substitution patterns. This finding highlights the importance of considering the direction of causality between genetic and epigenetic change.
Author Summary
Genome sequences as well as epigenetic states, such as DNA methylation or nucleosome binding patterns, change during evolution. But what is the causal relationship between the two? We already know that nucleotide variation within and between species is distributed unevenly around nucleosome footprints, but does this mean that sequence evolution follows a biased course because the presence of nucleosomes affects mutation and DNA repair dynamics? Or is it, in fact, the other way around, i.e. changes happen at the DNA level and prompt shifts in nucleosome positioning? To investigate the direction of causality in genetic versus epigenetic evolution, we analyze substitutions patterns in eukaryotes as well as the archaeon Haloferax volcanii in the context of genome-wide nucleosome binding maps. We demonstrate that the relationship between nucleosome positions and between-species divergence patterns, strikingly similar in eukaryotes and archaea, can be explained in large parts by nucleosomes shifting positions in response to substitution, although both mutation and selection biases might still exist. Our results illustrate that it is important to consider the direction of causality between epigenetic and genetic change when analyzing patterns of sequence divergence and using sequence conservation to infer selection on epigenetic states.
doi:10.1371/journal.pcbi.1003373
PMCID: PMC3836710  PMID: 24278010
4.  Electrostatic Mis-Interactions Cause Overexpression Toxicity of Proteins in E. coli 
PLoS ONE  2013;8(5):e64893.
A majority of E. coli proteins when overexpressed inhibit its growth, but the reasons behind overexpression toxicity of proteins remain unknown. Understanding the mechanism of overexpression toxicity is important from evolutionary, biotechnological and possibly clinical perspectives. Here we study sequence and functional features of cytosolic proteins of E. coli associated with overexpression toxicity to understand its mechanism. We find that number of positively charged residues is significantly higher in proteins showing overexpression toxicity. Very long proteins also show high overexpression toxicity. Among the functional classes, transcription factors and regulatory proteins are enriched in toxic proteins, while catalytic proteins are depleted. Overexpression toxicity could be predicted with reasonable accuracy using these few properties. The importance of charged residues in overexpression toxicity indicates that nonspecific electrostatic interactions resulting from protein overexpression cause toxicity of these proteins and suggests ways to improve the expression level of native and foreign proteins in E. coli for basic research and biotechnology. These results might also be applicable to other bacterial species.
doi:10.1371/journal.pone.0064893
PMCID: PMC3667126  PMID: 23734225
5.  Epigenetic epistatic interactions constrain the evolution of gene expression 
Harmful epistatic (genetic) interactions not only occur between mutations, but also when genes change in expression. Gene expression dynamics in yeast suggests that this ‘epigenetic' epistasis constrains evolution, with the tight regulation of network hubs promoting a robust, ‘canalized' phenotype.
Yeast genes with many negative genetic interaction partners tend to have expression that is stable between cells, across conditions, and through evolution.This low expression variation is linked to the use of alternative promoter architectures.The stable expression of genetic interaction network hubs suggests that epigenetic epistasis confers a constraint on evolution.
Reduced activity of two genes in combination often has a more detrimental effect than expected. Such epistatic interactions not only occur when genes are mutated but also due to variation in gene expression, including among isogenic individuals in a controlled environment. We hypothesized that these ‘epigenetic' epistatic interactions could place important constraints on the evolution of gene expression. Consistent with this, we show here that yeast genes with many epistatic interaction partners typically show low expression variation among isogenic individuals and low variation across different conditions. In addition, their expression tends to remain stable in response to the accumulation of mutations and only diverges slowly between strains and species. Yeast promoter architectures, the retention of gene duplicates, and the divergence of expression between humans and chimps are also consistent with selective pressure to reduce the likelihood of harmful epigenetic epistatic interactions. Based on these and previous analyses, we propose that the tight regulation of epistatic interaction network hubs makes an important contribution to the maintenance of a robust, ‘canalized' phenotype. Moreover, that epigenetic epistatic interactions may contribute substantially to fitness defects when single genes are deleted.
doi:10.1038/msb.2013.2
PMCID: PMC3588906  PMID: 23423319
epigenetics; epistasis; evolution; gene expression; genetic interaction
6.  Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner 
PLoS Computational Biology  2012;8(12):e1002846.
The binding of proteins can shield DNA from mutagenic processes but also interfere with efficient repair. How the presence of DNA-binding proteins shapes intra-genomic differences in mutability and, ultimately, sequence variation in natural populations, however, remains poorly understood. In this study, we examine sequence evolution in Escherichia coli in relation to the binding of four abundant nucleoid-associated proteins: Fis, H-NS, IhfA, and IhfB. We find that, for a subset of mutations, protein occupancy is associated with both increased and decreased mutability in the underlying sequence depending on when the protein is bound during the bacterial growth cycle. On average, protein-bound DNA exhibits reduced mutability compared to protein-free DNA. However, this net protective effect is weak and can be abolished or even reversed during stages of colony growth where binding coincides – and hence likely interferes with – DNA repair activity. We suggest that the four nucleoid-associated proteins analyzed here have played a minor but significant role in patterning extant sequence variation in E. coli.
Author Summary
Mutations can be more or less likely to occur depending on whether DNA is naked or bound by proteins. On the one hand, DNA-binding proteins can shield the DNA from certain mutagenic processes. On the other hand, the very same proteins can interfere with efficient DNA repair. In this study, we reconstruct the history of mutations across 54 E. coli genomes and ask whether mutation risk is higher or lower in regions occupied by proteins that help organize bacterial DNA into chromatin. Intriguingly, we find that the effect of binding depends on its timing. When we consider genomic regions bound during stationary phase, we observe that binding is associated with lower mutation risk for some mutation classes compared to naked DNA, albeit weakly. However, when binding occurs during exponential phase, bound regions actually experience more mutations on average. We argue that this is because, during exponential phase, the major effect of binding is that it interferes with efficient DNA repair, whereas in stationary phase – when many repair pathways are inactive – the protective effect of binding dominates. Our results suggest that the four DNA-binding proteins considered here have a small but significant growth phase-specific effect on mutation dynamics in E. coli.
doi:10.1371/journal.pcbi.1002846
PMCID: PMC3527292  PMID: 23284284
7.  Human genes with CpG island promoters have a distinct transcription-associated chromatin organization 
Genome Biology  2012;13(11):R110.
Background
More than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. These genes show differences in their patterns of transcription initiation, and have been reported to have higher levels of some activation-associated chromatin modifications.
Results
Here we report that genes with CpG island promoters have a characteristic transcription-associated chromatin organization. This signature includes high levels of the transcription elongation-associated histone modifications H4K20me1, H2BK5me1 and H3K79me1/2/3 in the 5' end of the gene, depletion of the activation marks H2AK5ac, H3K14ac and H3K23ac immediately downstream of the transcription start site (TSS), and characteristic epigenetic asymmetries around the TSS. The chromosome organization factor CTCF may be bound upstream of RNA polymerase in most active CpG island promoters, and an unstable nucleosome at the TSS may be specifically marked by H4K20me3, the first example of such a modification. H3K36 monomethylation is only detected as enriched in the bodies of active genes that have CpG island promoters. Finally, as expression levels increase, peak modification levels of the histone methylations H3K9me1, H3K4me1, H3K4me2 and H3K27me1 shift further away from the TSS into the gene body.
Conclusions
These results suggest that active genes with CpG island promoters have a distinct step-like series of modified nucleosomes after the TSS. The identity, positioning, shape and relative ordering of transcription-associated histone modifications differ between genes with and without CpG island promoters. This supports a model where chromatin organization reflects not only transcription activity but also the type of promoter in which transcription initiates.
doi:10.1186/gb-2012-13-11-r110
PMCID: PMC3580500  PMID: 23186133
8.  Directional Selection Causes Decanalization in a Group I Ribozyme 
PLoS ONE  2012;7(9):e45351.
A canalized genotype is robust to environmental or genetic perturbations. Canalization is expected to result from stabilizing selection on a well-adapted phenotype. Decanalization, the loss of robustness, might follow periods of directional selection toward a new optimum. The evolutionary forces causing decanalization are still unknown, in part because it is difficult to determine the fitness effects of mutations in populations of organisms with complex genotypes and phenotypes. Here, we report direct experimental measurements of robustness in a system with a simple genotype and phenotype, the catalytic activity of an RNA enzyme. We find that the robustness of a population of RNA enzymes decreases during a period of directional selection in the laboratory. The decrease in robustness is primarily caused by the selective sweep of a genotype that is decanalized relative to the wild-type, both in terms of mutational robustness and environmental robustness (thermodynamic stability). Our results experimentally demonstrate that directional selection can cause decanalization on short time scales, and demonstrate co-evolution of mutational and environmental robustness.
doi:10.1371/journal.pone.0045351
PMCID: PMC3445466  PMID: 23028955
9.  Cellular Plasticity Enables Adaptation to Unforeseen Cell-Cycle Rewiring Challenges 
PLoS ONE  2012;7(9):e45184.
The fundamental dynamics of the cell cycle, underlying cell growth and reproduction, were previously found to be robust under a wide range of environmental and internal perturbations. This property was commonly attributed to its network structure, which enables the coordinated interactions among hundreds of proteins. Despite significant advances in deciphering the components and autonomous interactions of this network, understanding the interfaces of the cell cycle with other major cellular processes is still lacking. To gain insight into these interfaces, we used the process of genome-rewiring in yeast by placing an essential metabolic gene HIS3 from the histidine biosynthesis pathway, under the exclusive regulation of different cell-cycle promoters. In a medium lacking histidine and under partial inhibition of the HIS3p, the rewired cells encountered an unforeseen multitasking challenge; the cell-cycle regulatory genes were required to regulate the essential histidine-pathway gene in concert with the other metabolic demands, while simultaneously driving the cell cycle through its proper temporal phases. We show here that chemostat cell populations with rewired cell-cycle promoters adapted within a short time to accommodate the inhibition of HIS3p and stabilized a new phenotypic state. Furthermore, a significant fraction of the population was able to adapt and grow into mature colonies on plates under such inhibiting conditions. The adapted state was shown to be stably inherited across generations. These adaptation dynamics were accompanied by a non-specific and irreproducible genome-wide transcriptional response. Adaptation of the cell-cycle attests to its multitasking capabilities and flexible interface with cellular metabolic processes and requirements. Similar adaptation features were found in our previous work when rewiring HIS3 to the GAL system and switching cells from galactose to glucose. Thus, at the basis of cellular plasticity is the emergence of a yet-unknown general, non-specific mechanism allowing fast inherited adaptation to unforeseen challenges.
doi:10.1371/journal.pone.0045184
PMCID: PMC3445480  PMID: 23028834
10.  WormScan: A Technique for High-Throughput Phenotypic Analysis of Caenorhabditis elegans 
PLoS ONE  2012;7(3):e33483.
Background
There are four main phenotypes that are assessed in whole organism studies of Caenorhabditis elegans; mortality, movement, fecundity and size. Procedures have been developed that focus on the digital analysis of some, but not all of these phenotypes and may be limited by expense and limited throughput. We have developed WormScan, an automated image acquisition system that allows quantitative analysis of each of these four phenotypes on standard NGM plates seeded with E. coli. This system is very easy to implement and has the capacity to be used in high-throughput analysis.
Methodology/Principal Findings
Our system employs a readily available consumer grade flatbed scanner. The method uses light stimulus from the scanner rather than physical stimulus to induce movement. With two sequential scans it is possible to quantify the induced phototactic response. To demonstrate the utility of the method, we measured the phenotypic response of C. elegans to phosphine gas exposure. We found that stimulation of movement by the light of the scanner was equivalent to physical stimulation for the determination of mortality. WormScan also provided a quantitative assessment of health for the survivors. Habituation from light stimulation of continuous scans was similar to habituation caused by physical stimulus.
Conclusions/Significance
There are existing systems for the automated phenotypic data collection of C. elegans. The specific advantages of our method over existing systems are high-throughput assessment of a greater range of phenotypic endpoints including determination of mortality and quantification of the mobility of survivors. Our system is also inexpensive and very easy to implement. Even though we have focused on demonstrating the usefulness of WormScan in toxicology, it can be used in a wide range of additional C. elegans studies including lifespan determination, development, pathology and behavior. Moreover, we have even adapted the method to study other species of similar dimensions.
doi:10.1371/journal.pone.0033483
PMCID: PMC3311640  PMID: 22457766
11.  Epistasis for Growth Rate and Total Metabolic Flux in Yeast 
PLoS ONE  2012;7(3):e33132.
Studies of interactions between gene deletions repeatedly show that the effect of epistasis on the growth of yeast cells is roughly null or barely positive. These observations relate generally to the pace of growth, its costs in terms of required metabolites and energy are unknown. We measured the maximum rate at which yeast cultures grow and amounts of glucose they consume per synthesized biomass for strains with none, single, or double gene deletions. Because all strains were maintained under a fermentative mode of growth and thus shared a common pattern of metabolic processes, we used the rate of glucose uptake as a proxy for the total flux of metabolites and energy. In the tested sample, the double deletions showed null or slightly positive epistasis both for the mean growth and mean flux. This concordance is explained by the fact that average efficiency of converting glucose into biomass was nearly constant, that is, it did not change with the strength of growth effect. Individual changes in the efficiency caused by gene deletions did have a genetic basis as they were consistent over several environments and transmitted between single and double deletion strains indicating that the efficiency of growth, although independent of its rate, was appreciably heritable. Together, our results suggest that data on the rate of growth can be used as a proxy for the rate of total metabolism when the goal is to find strong individual interactions or estimate the mean epistatic effect. However, it may be necessary to assay both growth and flux in order to detect smaller individual effects of epistasis.
doi:10.1371/journal.pone.0033132
PMCID: PMC3295780  PMID: 22412994
12.  Multiple Phenotypes Resulting from a Mutagenesis Screen for Pharynx Muscle Mutations in Caenorhabditis elegans 
PLoS ONE  2011;6(11):e26594.
We describe a novel screen to isolate pharyngeal cell morphology mutants in Caenorhabditis elegans using myo-2::GFP to rapidly identify abnormally shaped pharynxes in EMS (Ethyl Methanesulfonate) mutagenized worms. We observed over 83 C. elegans lines with distinctive pharyngeal phenotypes in worms surviving to the L1 larval stage, with phenotypes ranging from short pharynx, unattached pharynx, missing cells, asymmetric morphology, and non-adherent pharynx cells. Thirteen of these mutations have been chromosomally mapped using Single Nucleotide Polymorphisms (SNPs) and deficiency strain complementation. Our studies have focused on genetically mapping and functionally testing two phenotypes, the short pharynx and the loss of muscle cohesion phenotypes. We have also identified new alleles of sma-1, and our screen suggests many genes directing pharynx assembly and structure may be either pharynx specific or less critical in other tissues.
doi:10.1371/journal.pone.0026594
PMCID: PMC3206800  PMID: 22073173
13.  Identification of QTLs for Arsenic Accumulation in Maize (Zea mays L.) Using a RIL Population 
PLoS ONE  2011;6(10):e25646.
The Arsenic (As) concentration in different tissues of maize was analyzed using a set of RIL populations derived from an elite hybrid, Nongda108. The results showed that the trend of As concentration in the four measured tissues was leaves>stems>bracts>kernels. Eleven QTLs for As concentration were detected in the four tissues. Three QTLs for As concentration in leaves were mapped on chromosomes 1, 5, and 8, respectively. For As concentration in the bracts, two QTLs were identified, with 9.61% and 10.03% phenotypic variance. For As concentration in the stems, three QTLs were detected with 8.24%, 14.86%, and 15.23% phenotypic variance. Three QTLs were identified for kernels on chromosomes 3, 5, and 7, respectively, with 10.73%, 8.52%, and 9.10% phenotypic variance. Only one common chromosomal region between SSR marker bnlg1811 and umc1243 was detected for QTLs qLAV1 and qSAC1. The results implied that the As accumulation in different tissues in maize was controlled by different molecular mechanism. The study demonstrated that maize could be a useful plant for phytoremediation of As-contaminated paddy soil, and the QTLs will be useful for selecting inbred lines and hybrids with low As concentration in their kernels.
doi:10.1371/journal.pone.0025646
PMCID: PMC3196502  PMID: 22028786
14.  Acute Drug Treatment in the Early C. elegans Embryo 
PLoS ONE  2011;6(9):e24656.
Genetic and genome-wide RNAi approaches available in C. elegans, combined with tools for visualizing subcellular events with high-resolution, have led to increasing adoption of the early C. elegans embryo as a model for mechanistic and functional genomic analysis of cellular processes. However, a limitation of this system has been the impermeability of the embryo eggshell, which has prevented the routine use of small molecule inhibitors. Here, we present a method to permeabilize and immobilize embryos for acute inhibitor treatment in conjunction with live imaging. To identify a means to permeabilize the eggshell, we used a dye uptake assay to screen a set of 310 candidate genes defined by a combination of bioinformatic criteria. This screen identified 20 genes whose inhibition resulted in >75% eggshell permeability, and 3 that permeabilized embryos with minimal deleterious effects on embryo production and early embryonic development. To mount permeabilized embryos for acute drug addition in conjunction with live imaging, we combined optimized inhibition of one of these genes with the use of a microfabricated chamber that we designed. We demonstrate that these two developments enable the temporally controlled introduction of inhibitors for mechanistic studies. This method should also open new avenues of investigation by allowing profiling and specificity-testing of inhibitors through comparison with genome-wide phenotypic datasets.
doi:10.1371/journal.pone.0024656
PMCID: PMC3173474  PMID: 21935434
15.  Functional Analysis of Conserved Non-Coding Regions Around the Short Stature hox Gene (shox) in Whole Zebrafish Embryos 
PLoS ONE  2011;6(6):e21498.
Background
Mutations in the SHOX gene are responsible for Leri-Weill Dyschondrosteosis, a disorder characterised by mesomelic limb shortening. Recent investigations into regulatory elements surrounding SHOX have shown that deletions of conserved non-coding elements (CNEs) downstream of the SHOX gene produce a phenotype indistinguishable from Leri-Weill Dyschondrosteosis. As this gene is not found in rodents, we used zebrafish as a model to characterise the expression pattern of the shox gene across the whole embryo and characterise the enhancer domains of different CNEs associated with this gene.
Methodology/Principal Findings
Expression of the shox gene in zebrafish was identified using in situ hybridization, with embryos showing expression in the blood, putative heart, hatching gland, brain pharyngeal arch, olfactory epithelium, and fin bud apical ectodermal ridge. By identifying sequences showing 65% identity over at least 40 nucleotides between Fugu, human, dog and opossum we uncovered 35 CNEs around the shox gene. These CNEs were compared with CNEs previously discovered by Sabherwal et al., resulting in the identification of smaller more deeply conserved sub-sequence. Sabherwal et al.'s CNEs were assayed for regulatory function in whole zebrafish embryos resulting in the identification of additional tissues under the regulatory control of these CNEs.
Conclusion/Significance
Our results using whole zebrafish embryos have provided a more comprehensive picture of the expression pattern of the shox gene, and a better understanding of its regulation via deeply conserved noncoding elements. In particular, we identify additional tissues under the regulatory control of previously identified SHOX CNEs. We also demonstrate the importance of these CNEs in evolution by identifying duplicated shox CNEs and more deeply conserved sub-sequences within already identified CNEs.
doi:10.1371/journal.pone.0021498
PMCID: PMC3123344  PMID: 21731768
16.  Integrated Genome-Scale Prediction of Detrimental Mutations in Transcription Networks 
PLoS Genetics  2011;7(5):e1002077.
A central challenge in genetics is to understand when and why mutations alter the phenotype of an organism. The consequences of gene inhibition have been systematically studied and can be predicted reasonably well across a genome. However, many sequence variants important for disease and evolution may alter gene regulation rather than gene function. The consequences of altering a regulatory interaction (or “edge”) rather than a gene (or “node”) in a network have not been as extensively studied. Here we use an integrative analysis and evolutionary conservation to identify features that predict when the loss of a regulatory interaction is detrimental in the extensively mapped transcription network of budding yeast. Properties such as the strength of an interaction, location and context in a promoter, regulator and target gene importance, and the potential for compensation (redundancy) associate to some extent with interaction importance. Combined, however, these features predict quite well whether the loss of a regulatory interaction is detrimental across many promoters and for many different transcription factors. Thus, despite the potential for regulatory diversity, common principles can be used to understand and predict when changes in regulation are most harmful to an organism.
Author Summary
The genomes of individuals differ in sequence at thousands of base pairs. Some of these polymorphisms affect the sequence of proteins, but many are likely to alter how genes are regulated. When are changes in gene regulation detrimental to an organism? We have used an integrative analysis of transcription factor binding site conservation in budding yeast to address the extent to which different features predict when potential changes in gene regulation are detrimental. We found that, despite the diversity of transcription factors and regulatory regions in a genome, a few simple properties can be used to predict and understand when changes in regulation are most harmful.
doi:10.1371/journal.pgen.1002077
PMCID: PMC3102745  PMID: 21637788
17.  A Gene-Phenotype Network for the Laboratory Mouse and Its Implications for Systematic Phenotyping 
PLoS ONE  2011;6(5):e19693.
The laboratory mouse is the pre-eminent model organism for the dissection of human disease pathways. With the advent of a comprehensive panel of gene knockouts, projects to characterise the phenotypes of all knockout lines are being initiated. The range of genotype-phenotype associations can be represented using the Mammalian Phenotype ontology. Using publicly available data annotated with this ontology we have constructed gene and phenotype networks representing these associations. These networks show a scale-free, hierarchical and modular character and community structure. They also exhibit enrichment for gene coexpression, protein-protein interactions and Gene Ontology annotation similarity. Close association between gene communities and some high-level ontology terms suggests that systematic phenotyping can provide a direct insight into underlying pathways. However some phenotypes are distributed more diffusely across gene networks, likely reflecting the pleiotropic roles of many genes. Phenotype communities show a many-to-many relationship to human disease communities, but stronger overlap at more granular levels of description. This may suggest that systematic phenotyping projects should aim for high granularity annotations to maximise their relevance to human disease.
doi:10.1371/journal.pone.0019693
PMCID: PMC3098258  PMID: 21625554
18.  A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans 
PLoS ONE  2011;6(5):e19055.
While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bacterial and fungal infection. Using tiling arrays and/or RNA-sequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (Serratia marcescens, Enterococcus faecalis and otorhabdus luminescens) and two fungal pathogens (Drechmeria coniospora and Harposporium sp.). We developed a flexible tool, the WormBase Converter (available at http://wormbasemanager.sourceforge.net/), to allow cross-study comparisons. The new data sets provided more extensive lists of differentially regulated genes than previous studies. Annotation analysis confirmed that genes commonly up-regulated by bacterial infections are related to stress responses. We found substantial overlaps between the genes regulated upon intestinal infection by the bacterial pathogens and Harposporium, and between those regulated by Harposporium and D. coniospora, which infects the epidermis. Among the fungus-regulated genes, there was a significant bias towards genes that are evolving rapidly and potentially encode small proteins. The results obtained using new methods reveal that the response to infection in C. elegans is determined by the nature of the pathogen, the site of infection and the physiological imbalance provoked by infection. They form the basis for future functional dissection of innate immune signaling. Finally, we also propose alternative methods to identify differentially regulated genes that take into account the greater variability in lowly expressed genes.
doi:10.1371/journal.pone.0019055
PMCID: PMC3094335  PMID: 21602919
19.  Computational Integration of Homolog and Pathway Gene Module Expression Reveals General Stemness Signatures 
PLoS ONE  2011;6(4):e18968.
The stemness hypothesis states that all stem cells use common mechanisms to regulate self-renewal and multi-lineage potential. However, gene expression meta-analyses at the single gene level have failed to identify a significant number of genes selectively expressed by a broad range of stem cell types. We hypothesized that stemness may be regulated by modules of homologs. While the expression of any single gene within a module may vary from one stem cell type to the next, it is possible that the expression of the module as a whole is required so that the expression of different, yet functionally-synonymous, homologs is needed in different stem cells. Thus, we developed a computational method to test for stem cell-specific gene expression patterns from a comprehensive collection of 49 murine datasets covering 12 different stem cell types. We identified 40 individual genes and 224 stemness modules with reproducible and specific up-regulation across multiple stem cell types. The stemness modules included families regulating chromatin remodeling, DNA repair, and Wnt signaling. Strikingly, the majority of modules represent evolutionarily related homologs. Moreover, a score based on the discovered modules could accurately distinguish stem cell-like populations from other cell types in both normal and cancer tissues. This scoring system revealed that both mouse and human metastatic populations exhibit higher stemness indices than non-metastatic populations, providing further evidence for a stem cell-driven component underlying the transformation to metastatic disease.
doi:10.1371/journal.pone.0018968
PMCID: PMC3084730  PMID: 21559491
20.  Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome 
PLoS Genetics  2011;7(4):e1002036.
Chromatin in sperm is different from that in other cells, with most of the genome packaged by protamines not nucleosomes. Nucleosomes are, however, retained at some genomic sites, where they have the potential to transmit paternal epigenetic information. It is not understood how this retention is specified. Here we show that base composition is the major determinant of nucleosome retention in human sperm, predicting retention very well in both genic and non-genic regions of the genome. The retention of nucleosomes at GC-rich sequences with high intrinsic nucleosome affinity accounts for the previously reported retention at transcription start sites and at genes that regulate development. It also means that nucleosomes are retained at the start sites of most housekeeping genes. We also report a striking link between the retention of nucleosomes in sperm and the establishment of DNA methylation-free regions in the early embryo. Taken together, this suggests that paternal nucleosome transmission may facilitate robust gene regulation in the early embryo. We propose that chromatin organization in the male germline, rather than in somatic cells, is the major functional consequence of fine-scale base composition variation in the human genome. The selective pressure driving base composition evolution in mammals could, therefore, be the need to transmit paternal epigenetic information to the zygote.
Author Summary
In most cells, DNA is packaged by protein complexes called nucleosomes. In sperm, however, nucleosomes are only retained at a small fraction of the genome, particularly at the start sites of genes. In this work, we show that the sites at which nucleosomes are retained in sperm are specified by variation in the base composition of the human genome. At a fine scale, the human genome varies extensively in the content of GC versus AT base pairs, and we find that in both genic and non-genic regions this predicts very well where nucleosomes are retained in mature sperm. These regions include transcription start sites, especially for genes that are expressed in all cells and for genes that regulate development. We also report that regions that retain nucleosomes in sperm are likely to be protected from DNA methylation in the early embryo, suggesting a further connection between the presence of nucleosomes on the paternal genome and the establishment of gene regulation in the embryo. Based on these results, we propose that an important selective pressure on base composition evolution in mammalian genomes may be the requirement to organize chromatin in sperm in a way that facilitates gene regulation in the early embryo.
doi:10.1371/journal.pgen.1002036
PMCID: PMC3072381  PMID: 21490963
21.  Fluctuation and response in biology 
Cellular and Molecular Life Sciences  2010;68(6):1005-1010.
In 1905, Albert Einstein proposed that the forces that cause the random Brownian motion of a particle also underlie the resistance to macroscopic motion when a force is applied. This insight, of a coupling between fluctuation (stochastic behavior) and responsiveness (non-stochastic behavior), founded an important branch of physics. Here we argue that his insight may also be relevant for understanding evolved biological systems, and we present a ‘fluctuation–response relationship’ for biology. The relationship is consistent with the idea that biological systems are similarly canalized to stochastic, environmental, and genetic perturbations. It is also supported by in silico evolution experiments, and by the observation that ‘noisy’ gene expression is often both more responsive and more ‘evolvable’. More generally, we argue that in biology there is (and always has been) an important role for macroscopic theory that considers the general behavior of systems without concern for their intimate molecular details.
Electronic supplementary material
The online version of this article (doi:10.1007/s00018-010-0589-y) contains supplementary material, which is available to authorized users.
doi:10.1007/s00018-010-0589-y
PMCID: PMC3043249  PMID: 21116679
Noise; Plasticity; Canalization; Evolvability; Fluctuation; Response; Genetic assimilation; Gene expression
22.  Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. elegans 
PLoS ONE  2010;5(11):e13922.
Defining the mutational landscape when individuals of a species grow separately and diverge over many generations can provide insights into trait evolution. A specific example of this involves studying changes associated with domestication where different lines of the same wild stock have been cultivated independently in different standard environments. Whole genome sequence comparison of such lines permits estimation of mutation rates, inference of genes' ancestral states and ancestry of existing strains, and correction of sequencing errors in genome databases. Here we study domestication of the C. elegans Bristol strain as a model, and report the genome sequence of LSJ1 (Bristol), a sibling of the standard C. elegans reference wild type N2 (Bristol). The LSJ1 and N2 lines were cultivated separately from shortly after the Bristol strain was isolated until methods to freeze C. elegans were developed. We find that during this time the two strains have accumulated 1208 genetic differences. We describe phenotypic variation between N2 and LSJ1 in the rate at which embryos develop, the rate of production of eggs, the maturity of eggs at laying, and feeding behavior, all the result of post-isolation changes. We infer the ancestral alleles in the original Bristol isolate and highlight 2038 likely sequencing errors in the original N2 reference genome sequence. Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication.
doi:10.1371/journal.pone.0013922
PMCID: PMC2978686  PMID: 21085631
23.  Conflict between Noise and Plasticity in Yeast 
PLoS Genetics  2010;6(11):e1001185.
Gene expression responds to changes in conditions but also stochastically among individuals. In budding yeast, both expression responsiveness across conditions (“plasticity”) and cell-to-cell variation (“noise”) have been quantified for thousands of genes and found to correlate across genes. It has been argued therefore that noise and plasticity may be strongly coupled and mechanistically linked. This is consistent with some theoretical ideas, but a strong coupling between noise and plasticity also has the potential to introduce cost–benefit conflicts during evolution. For example, if high plasticity is beneficial (genes need to respond to the environment), but noise is detrimental (fluctuations are harmful), then strong coupling should be disfavored. Here, evidence is presented that cost–benefit conflicts do occur and that they constrain the evolution of gene expression and promoter usage. In contrast to recent assertions, coupling between noise and plasticity is not a general property, but one associated with particular mechanisms of transcription initiation. Further, promoter architectures associated with coupling are avoided when noise is most likely to be detrimental, and noise and plasticity are largely independent traits for core cellular components. In contrast, when genes are duplicated noise–plasticity coupling increases, consistent with reduced detrimental affects of expression variation. Noise–plasticity coupling is, therefore, an evolvable trait that may constrain the emergence of highly responsive gene expression and be selected against during evolution. Further, the global quantitative data in yeast suggest that one mechanism that relieves the constraints imposed by noise–plasticity coupling is gene duplication, providing an example of how duplication can facilitate escape from adaptive conflicts.
Author Summary
Gene expression needs to respond to changes in conditions, but also varies stochastically among cells in a homogenous environment. It has been argued that these two levels of expression variation may be coupled, relating to the same underlying molecular mechanisms. However, such a strong coupling between expression “plasticity” and expression “noise” may introduce cost–benefit conflicts during evolution. For example, if plasticity is beneficial, but noise is detrimental, then coupling will be disfavored. In this work, evidence is presented that such cost–benefit conflicts do occur and that they constrain the evolution of gene expression in yeast. In contrast to recent conclusions, it is shown that noise–plasticity coupling is not a general result, but rather one associated with particular mechanisms of transcription initiation. Promoter architectures associated with coupling are avoided when noise is detrimental, and noise and plasticity are not coupled for core cellular components. Noise–plasticity coupling is therefore not a general property of gene expression, but an evolvable trait that may constrain the evolution of gene expression and be selected against during evolution. Further, gene duplication may facilitate escape from the adaptive conflict imposed by coupling.
doi:10.1371/journal.pgen.1001185
PMCID: PMC2973811  PMID: 21079670
24.  High-Content, Image-Based Screening for Drug Targets in Yeast 
PLoS ONE  2010;5(4):e10177.
Background
Drug discovery and development are predicated on elucidation of the potential mechanisms of action and cellular targets of candidate chemical compounds. Recent advances in high-content imaging techniques allow simultaneous analysis of a range of cellular events. In this study, we propose a novel strategy to identify drug targets by combining genetic screening and high-content imaging in yeast.
Methodology
In this approach, we infer the cellular functions affected by candidate drugs by comparing morphologic changes induced by the compounds with the phenotypes of yeast mutants.
Conclusions
Using this method and four well-characterized reagents, we successfully identified previously known target genes of the compounds as well as other genes involved with functionally related cellular pathways. This is the first demonstration of a genetic high-content assay that can be used to identify drug targets based on morphologic phenotypes of a reference mutant panel.
doi:10.1371/journal.pone.0010177
PMCID: PMC2854693  PMID: 20418956
25.  Phenotypic Covariance of Longevity, Immunity and Stress Resistance in the Caenorhabditis Nematodes 
PLoS ONE  2010;5(4):e9978.
Background
Ageing, immunity and stresstolerance are inherent characteristics of all organisms. In animals, these traits are regulated, at least in part, by forkhead transcription factors in response to upstream signals from the Insulin/Insulin–like growth factor signalling (IIS) pathway. In the nematode Caenorhabditis elegans, these phenotypes are molecularly linked such that activation of the forkhead transcription factor DAF-16 both extends lifespan and simultaneously increases immunity and stress resistance. It is known that lifespan varies significantly among the Caenorhabditis species but, although DAF-16 signalling is highly conserved, it is unclear whether this phenotypic linkage occurs in other species. Here we investigate this phenotypic covariance by comparing longevity, stress resistance and immunity in four Caenorhabditis species.
Methodology/Principal Findings
We show using phenotypic analysis of DAF-16 influenced phenotypes that among four closely related Caenorhabditis nematodes, the gonochoristic species (Caenorhabditis remanei and Caenorhabditis brenneri) have diverged significantly with a longer lifespan, improved stress resistance and higher immunity than the hermaphroditic species (C. elegans and Caenorhabditis briggsae). Interestingly, we also observe significant differences in expression levels between the daf-16 homologues in these species using Real-Time PCR, which positively correlate with the observed phenotypes. Finally, we provide additional evidence in support of a role for DAF-16 in regulating phenotypic coupling by using a combination of wildtype isolates, constitutively active daf-16 mutants and bioinformatic analysis.
Conclusions
The gonochoristic species display a significantly longer lifespan (p<0.0001) and more robust immune and stress response (p<0.0001, thermal stress; p<0.01, heavy metal stress; p<0.0001, pathogenic stress) than the hermaphroditic species. Our data suggests that divergence in DAF-16 mediated phenotypes may underlie many of the differences observed between these four species of Caenorhabditis nematodes. These findings are further supported by the correlative higher daf-16 expression levels among the gonochoristic species and significantly higher lifespan, immunity and stress tolerance in the constitutively active daf-16 hermaphroditic mutants.
doi:10.1371/journal.pone.0009978
PMCID: PMC2848519  PMID: 20369008

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