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1.  Sema3F downregulates p53 expression leading to axonal growth cone collapse in primary hippocampal neurons 
Hippocampal nerve growth is regulated by the coordinated action of numerous external stimuli, including positively acting neurotrophin-derived growth cues and restrictive semaphorin cues, however the underlying cellular mechanisms remain largely unclear. We examined the potential cellular mechanism of Semaphorin3F (Sema3F) in cultured primary hippocampal neurons. We show that Sema3F can down-regulate p53 expression in primary hippocampal neurons, thereby contributing to growth cone collapse. Sema3F suppressed p53-induced pathways, which we show to be required to maintain growth cone structure. Sema3F-induced growth cone collapse was partially reversed by overexpression of p53, which promoted growth cone extension. Inhibition of p53 function by inhibitor, siRNAs, induced axonal growth cone collapse, whereas p53 over-expression led to larger growth cones in cultured primary hippocampal neurons.These data reveal a novel mechanism by which Sema3F can induce hippocampal neuron growth cone collapse and provide evidence for an intracellular mechanism for cross talk between positive and negative axon growth cues.
PMCID: PMC3438774  PMID: 22977659
Sema3F; p53; hippocampal neurons; collapse; transfection; growth cone
2.  PICH and BLM limit histone association with anaphase centromeric DNA threads and promote their resolution 
The EMBO Journal  2011;30(16):3309-3321.
PICH and BLM limit histone association with anaphase centromeric DNA threads and promote their resolution
The helicase proteins PICH and BLM localize to ultrafine DNA threads between separating sister chromatids. It now appears they cooperate to remove histones from these anaphase DNA bridges, to allow their stretching and unravelling without breakage.
Centromeres nucleate the formation of kinetochores and are vital for chromosome segregation during mitosis. The SNF2 family helicase PICH (Plk1-interacting checkpoint helicase) and the BLM (the Bloom's syndrome protein) helicase decorate ultrafine histone-negative DNA threads that link the segregating sister centromeres during anaphase. The functions of PICH and BLM at these threads are not understood, however. Here, we show that PICH binds to BLM and enables BLM localization to anaphase centromeric threads. PICH- or BLM-RNAi cells fail to resolve these threads in anaphase. The fragmented threads form centromeric-chromatin-containing micronuclei in daughter cells. Anaphase threads in PICH- and BLM-RNAi cells contain histones and centromere markers. Recombinant purified PICH has nucleosome remodelling activities in vitro. We propose that PICH and BLM unravel centromeric chromatin and keep anaphase DNA threads mostly free of nucleosomes, thus allowing these threads to span long distances between rapidly segregating centromeres without breakage and providing a spatiotemporal window for their resolution.
doi:10.1038/emboj.2011.226
PMCID: PMC3160651  PMID: 21743438
centromere; chromatin remodelling; DNA repair; mitosis
3.  A novel acetylation of β-tubulin by San modulates microtubule polymerization via down-regulating tubulin incorporation 
Molecular Biology of the Cell  2011;22(4):448-456.
We report that San, an acetyltransferase required for sister chromatid cohesion, also acetylates β-tubulin at lysine 252. The acetylation happens only on free tubulin heterodimers, and it delays the incorporation of modified tubulins into microtubules in vivo.
Dynamic instability is a critical property of microtubules (MTs). By regulating the rate of tubulin polymerization and depolymerization, cells organize the MT cytoskeleton to accommodate their specific functions. Among many processes, posttranslational modifications of tubulin are implicated in regulating MT functions. Here we report a novel tubulin acetylation catalyzed by acetyltransferase San at lysine 252 (K252) of β-tubulin. This acetylation, which is also detected in vivo, is added to soluble tubulin heterodimers but not tubulins in MTs. The acetylation-mimicking K252A/Q mutants were incorporated into the MT cytoskeleton in HeLa cells without causing any obvious MT defect. However, after cold-induced catastrophe, MT regrowth is accelerated in San-siRNA cells while the incorporation of acetylation-mimicking mutant tubulins is severely impeded. K252 of β-tubulin localizes at the interface of α-/β-tubulins and interacts with the phosphate group of the α-tubulin-bound GTP. We propose that the acetylation slows down tubulin incorporation into MTs by neutralizing the positive charge on K252 and allowing tubulin heterodimers to adopt a conformation that disfavors tubulin incorporation.
doi:10.1091/mbc.E10-03-0203
PMCID: PMC3038643  PMID: 21177827
4.  MS/MS/MS reveals false positive identification of histone serine methylation 
Journal of proteome research  2010;9(1):585-594.
Methylation of lysine and arginine residues is known to play a key role in regulating histone structure and function. However, methylation of other amino acid residues in histones has not been previously described. Using exhaustive nano-HPLC/MS/MS and blind protein sequence database searches, we tentatively assigned methylation to serine 28 of histone H3 from calf thymus. The assignment was in agreement with our stringent manual verification rules, co-elution in HPLC/MS/MS with its corresponding synthetic peptide, the dynamic nature of such methylation in distinct cell lines, and isotopic labeling. However, careful inspection of the MS/MS and MS/MS/MS spectra of a series of synthetic peptides confirmed that methylation actually occurs on K27 rather than on S28. The misassignment was caused by the fact that the (y9 + 14) of the putative S28-methylated peptide and (b9 + 18) ions of the K27 methylated peptide share the same m/z value (m/z 801). This MS/MS peak was used as the major evidence to assign methylation to S28 (consecutive y8 and (y9 + 14) ions). MS/MS/MS analysis revealed the false positive nature of serine methylation: the ambiguous ion at m/z 801 is indeed (b9 + 18), an ion resulting from an in vitro reaction in the gas phase during collisionally activated dissociation (CAD). When lysine (K27) was acetylated, the degree of such in vitro reactions was greatly reduced, and such reactions were completely eliminated when the C-terminus was blocked by carboxylic group derivatization. Moreover, such side-chain assisted C-terminal rearrangement was found to be charge dependent. In aggregate, these results suggest that extra caution should be taken in interpretation of post-translational modification (PTM) data and that MS/MS as well as MS/MS/MS of synthetic peptides are needed for verifying the identity of peptides bearing a novel PTM.
doi:10.1021/pr900864s
PMCID: PMC2801770  PMID: 19877717
MS/MS/MS analysis; false positive identification; protein methylation; charge dependence; side-chain assisted C-terminal rearrangement; C-terminal elimination; loss of C-terminal; histone modifications
5.  CHD7 cooperates with PBAF to control multipotent neural crest formation 
Nature  2010;463(7283):958-962.
Summary
Heterozygous mutations in the gene encoding CHD7, an ATP-dependent chromatin remodeler result in a complex constellation of congenital anomalies called CHARGE syndrome. Here we show that in humans and in Xenopus, CHD7 is essential for the formation of multipotent migratory neural crest cells, a transient cell population that is ectodermal in origin, but undergoes a major gene expression reprogramming to acquire a remarkably broad differentiation potential and ability to migrate throughout the body to give rise to bones, cartilages, nerves, and cardiac structures. We demonstrate that CHD7 function is essential for activation of core components of neural crest transcriptional circuitry, including Sox9, Twist and Slug. Moreover, the major features of CHARGE are recapitulated in Xenopus embryo by the downregulation of CHD7 levels or overexpression of its catalytically inactive ATP-ase mutant. We further show that in human multipotent neural crest cells, CHD7 associates with a BRG1-containing complex PBAF, and both factors co-occupy a neural crest-specific distal SOX9 enhancer, as well as a novel genomic element located upstream from TWIST1 gene and marked by H3K4me1. Furthermore, in the embryo CHD7 and PBAF act synergistically to promote neural crest gene expression and cell migration. Our work identifies an evolutionary conserved role for CHD7 in orchestrating neural crest gene expression programs, provides insights into the synergistic regulation of distal genomic elements by two distinct chromatin remodelers, and illuminates the patho-embryology of CHARGE syndrome.
doi:10.1038/nature08733
PMCID: PMC2890258  PMID: 20130577
6.  Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells 
Cell  2009;139(7):1290-1302.
SUMMARY
Polycomb Repressive Complex 2 (PRC2) regulates key developmental genes in embryonic stem(ES) cells and during development. Here we show that Jarid2/Jumonji, a protein enriched in pluripotent cells and a founding member of the Jumonji C (JmjC) domain protein family, is a PRC2 subunit in ES cells. Genome-wide ChIP-seq analyses of Jarid2, Ezh2, and Suz12 binding reveal that Jarid2 and PRC2 occupy the same genomic regions. We further show that Jarid2 promotes PRC2 recruitment to the target genes while inhibiting PRC2 histone methyltransferase activity, suggesting that it acts as a “molecular rheostat” that finely calibrates PRC2 functions at developmental genes. Using Xenopus laevis as a model we demonstrate that Jarid2 knockdown impairs the induction of gastrulation genes in blastula embryos and results in failure of differentiation. Our findings illuminate a mechanism of histone methylation regulation in pluripotent cells and during early cell-fate transitions.
doi:10.1016/j.cell.2009.12.002
PMCID: PMC2911953  PMID: 20064375
7.  Identification of Four Novel Types of in Vitro Protein Modifications 
Journal of proteome research  2008;7(10):4603-4608.
In vitro chemical modifications in proteins, introduced during sample preparation, can complicate mass spectra and increase the potential for false-positive identifications. While several in vitro protein modifications have been described previously, additional types of such modifications may exist. Here, we report discovery of four types of in vitro protein modifications, identified by HPLC/ MS/MS analysis and nonrestrictive protein sequence alignment by PTMap, an algorithm recently developed in our laboratory. These novel in vitro modifications included ethylation of aspartate and glutamate (+28 Da), esterification of aspartate and glutamate by glycerol (+74 Da), loss of 19 Da from lysine, and addition of 108 Da to cysteine. We confirmed that these modifications occurred in vitro and not in vivo in control experiments designed to avoid conditions likely to induce the modifications. We propose a plausible molecular mechanism for the −19 Da modification of lysine. Our study therefore conclusively identifies several novel in vitro protein modifications, suggests ways to avoid these modifications, and highlights the possibility of misidentification of peptides because of in vitro modifications.
doi:10.1021/pr800456q
PMCID: PMC2911956  PMID: 18767873
protein modifications; PTMap; automated database searching
8.  Mascot-derived False Positive Peptide Identifications Revealed by Manual Analysis of Tandem Mass Spectra 
Journal of proteome research  2009;8(6):3141-3147.
False positives that arise when MS/MS data are used to search protein sequence databases remain a concern in proteomics research. Here we present five types of false positives identified when aligning sequences to MS/MS spectra by Mascot database searching software. False positives arise because of 1) enzymatic digestion at abnormal sites; 2) misinterpretation of charge states; 3) misinterpretation of protein modifications; 4) incorrect assignment of the protein modification site; and 5) incorrect use of isotopic peaks. We present examples, clearly identified as false positives by manual inspection, that nevertheless were assigned high scores by Mascot sequence alignment algorithm. In some examples, the sequence assigned to the MS/MS spectrum explains more than 80% of the fragment ions present. Because of high sequence similarity between the false positives and their corresponding true hits, the false positive rate cannot be evaluated by the common method of using a reversed or scrambled sequence database. A common feature of the false positives is the presence of unmatched peaks in the MS/MS spectra. Our studies highlight the importance of using unmatched peaks to remove false positives and offer direction to aid development of better sequence alignment algorithms for peptide and PTM identification.
doi:10.1021/pr900172v
PMCID: PMC2720604  PMID: 19368407
protein identification; manual verification; automated database search
9.  Protein Acetylation Microarray Reveals NuA4 Controls Key Metabolic Target Regulating Gluconeogenesis 
Cell  2009;136(6):1073-1084.
SUMMARY
Histone acetyltransferases (HATs) and histone deacetylases (HDACs) conduct many critical functions through nonhistone substrates in metazoans, but only chromatin-associated nonhistone substrates are known in Saccharomyces cerevisiae. Using yeast proteome microarrays, we identified and validated many nonchromatin substrates of the essential nucleosome acetyltransferase of H4 (NuA4) complex. Among these, acetylation sites (Lys 19 and 514) of phosphoenolpyruvate carboxykinase (Pck1p) were determined by tandem mass spectrometry. Acetylation at Lys 514 was crucial for enzymatic activity and the ability of yeast cells to grow on non-fermentable carbon sources. Loss of Pck1p activity blocked the extension of yeast chronological life span caused by water starvation. In human hepatocellular carcinoma (HepG2) cells, human Pck1 acetylation and glucose production was dependent on TIP60, the human homolog of ESA1. Our results demonstrate a novel regulatory function for the NuA4 complex in glucose metabolism and life span by acetylating a critical metabolic enzyme.
doi:10.1016/j.cell.2009.01.033
PMCID: PMC2696288  PMID: 19303850
10.  Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex 
Nucleic Acids Research  2008;37(1):96-110.
Eukaryotic RNase H2 is a heterotrimeric enzyme. Here, we show that the biochemical composition and stoichiometry of the human RNase H2 complex is consistent with the properties previously deduced from genetic studies. The catalytic subunit of eukaryotic RNase H2, RNASEH2A, is well conserved and similar to the monomeric prokaryotic RNase HII. In contrast, the RNASEH2B and RNASEH2C subunits from human and Saccharomyces cerevisiae share very little homology, although they both form soluble B/C complexes that may serve as a nucleation site for the addition of RNASEH2A to form an active RNase H2, or for interactions with other proteins to support different functions. The RNASEH2B subunit has a PIP-box and confers PCNA binding to human RNase H2. Unlike Escherichia coli RNase HII, eukaryotic RNase H2 acts processively and hydrolyzes a variety of RNA/DNA hybrids with similar efficiencies, suggesting multiple cellular substrates. Moreover, of five analyzed mutations in human RNASEH2B and RNASEH2C linked to Aicardi-Goutières Syndrome (AGS), only one, R69W in the RNASEH2C protein, exhibits a significant reduction in specific activity, revealing a role for the C subunit in enzymatic activity. Near-normal activity of four AGS-related mutant enzymes was unexpected in light of their predicted impairment causing the AGS phenotype.
doi:10.1093/nar/gkn913
PMCID: PMC2615623  PMID: 19015152
11.  Wwp2-Mediated Ubiquitination of the RNA Polymerase II Large Subunit in Mouse Embryonic Pluripotent Stem Cells▿  
Molecular and Cellular Biology  2007;27(15):5296-5305.
Ubiquitination and the degradation of the large subunit of RNA polymerase II, Rpb1, is not only involved in DNA damage-induced arrest but also in other transcription-obstructing events. However, the ubiquitin ligases responsible for DNA damage-independent processes in mammalian cells remain to be identified. Here, we identified Wwp2, a mouse HECT domain ubiquitin E3 ligase, as a novel ubiquitin ligase of Rpb1. We found that Wwp2 specifically interacted with mouse Rpb1 and targeted it for ubiquitination both in vitro and in vivo. Interestingly, the interaction with and ubiquitination of Rpb1 was dependent neither on its phosphorylation state nor on DNA damage. However, the enzymatic activity of Wwp2 was absolutely required for its ubiquitin modification of Rpb1. Furthermore, our study indicates that the interaction between Wwp2 and Rpb1 was mediated through WW domain of Wwp2 and C-terminal domain of Rpb1, respectively. Strikingly, downregulation of Wwp2 expression compromised Rpb1 ubiquitination and elevated its intracellular steady-state protein level significantly. Importantly, we identified six lysine residues in the C-terminal domain of Rpb1 as ubiquitin acceptor sites mediated by Wwp2. These results indicate that Wwp2 plays an important role in regulating expression of Rpb1 in normal physiological conditions.
doi:10.1128/MCB.01667-06
PMCID: PMC1952083  PMID: 17526739

Results 1-11 (11)