32 results on '"Swaminathan, Venkatesh"'
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2. Methods to Study Histone Chaperone Function in Nucleosome Assembly and Chromatin Transcription
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Senapati, Parijat, primary, Sudarshan, Deepthi, additional, Gadad, Shrikanth S., additional, Shandilya, Jayasha, additional, Swaminathan, Venkatesh, additional, and Kundu, Tapas K., additional
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- 2015
- Full Text
- View/download PDF
3. Histone Chaperone as Coactivator of Chromatin Transcription: Role of Acetylation
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Gadad, Shrikanth S., primary, Shandilya, Jayasha, additional, Swaminathan, Venkatesh, additional, and Kundu, Tapas K., additional
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- 2009
- Full Text
- View/download PDF
4. Swi/Snf dynamics on stress-responsive genes is governed by competitive bromodomain interactions
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Swaminathan Venkatesh, Madelaine Gogol, Jerry L. Workman, Jeong Hoon Kim, Laurence Florens, Michael P. Washburn, Joshua M. Gilmore, Michaela Smolle, and Arnob Dutta
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Saccharomyces cerevisiae Proteins ,cells ,genetic processes ,Saccharomyces cerevisiae ,macromolecular substances ,Biology ,Chromatin remodeling ,Stress, Physiological ,Genetics ,Nucleosome ,Chromatin structure remodeling (RSC) complex ,Transcription factor ,Adenosine Triphosphatases ,Acetylation ,SWI/SNF ,Nucleosomes ,Bromodomain ,Cell biology ,enzymes and coenzymes (carbohydrates) ,Histone ,Biochemistry ,biology.protein ,biological phenomena, cell phenomena, and immunity ,Research Paper ,Protein Binding ,Transcription Factors ,Developmental Biology - Abstract
The Swi/Snf chromatin remodeling complex functions to alter nucleosome positions by either sliding nucleosomes on DNA or the eviction of histones. The presence of histone acetylation and activator-dependent recruitment and retention of Swi/Snf is important for its efficient function. It is not understood, however, why such mechanisms are required to enhance Swi/Snf activity on nucleosomes. Snf2, the catalytic subunit of the Swi/Snf remodeling complex, has been shown to be a target of the Gcn5 acetyltransferase. Our study found that acetylation of Snf2 regulates both recruitment and release of Swi/Snf from stress-responsive genes. Also, the intramolecular interaction of the Snf2 bromodomain with the acetylated lysine residues on Snf2 negatively regulates binding and remodeling of acetylated nucleosomes by Swi/Snf. Interestingly, the presence of transcription activators mitigates the effects of the reduced affinity of acetylated Snf2 for acetylated nucleosomes. Supporting our in vitro results, we found that activator-bound genes regulating metabolic processes showed greater retention of the Swi/Snf complex even when Snf2 was acetylated. Our studies demonstrate that competing effects of (1) Swi/Snf retention by activators or high levels of histone acetylation and (2) Snf2 acetylation-mediated release regulate dynamics of Swi/Snf occupancy at target genes.
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- 2014
5. Phosphorylation by Casein Kinase 2 Facilitates Psh1 Protein-assisted Degradation of Cse4 Protein
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Jennifer L. Gerton, Jerry L. Workman, Mark Mattingly, Swaminathan Venkatesh, Laurence Florens, Geetha S. Hewawasam, and Ying Zhang
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Proteasome Endopeptidase Complex ,Saccharomyces cerevisiae Proteins ,Chromosomal Proteins, Non-Histone ,CK2 ,Ubiquitin-Protein Ligases ,Proteolysis ,Protein subunit ,Centromere ,Saccharomyces cerevisiae ,DNA and Chromosomes ,Biology ,Psh1 ,Biochemistry ,Catalysis ,medicine ,E3 Ubiquitin Ligase ,Phosphorylation ,Casein Kinase II ,Kinetochores ,Molecular Biology ,medicine.diagnostic_test ,Strain (chemistry) ,Ubiquitin ,food and beverages ,Cse4/CENP-A ,Cell Biology ,Peptide Elongation Factors ,Yeast ,Recombinant Proteins ,Ubiquitin ligase ,DNA-Binding Proteins ,biology.protein ,Casein kinase 2 ,Gene Deletion - Abstract
Background: Psh1 is an E3 ubiquitin ligase that controls CenH3/Cse4 levels through proteolysis in budding yeast. Results: Psh1 is phosphorylated in vivo by CK2, and its E3 ligase activity is promoted. Conclusion: Phosphorylation is crucial in Psh1-assisted control of Cse4 levels, and the Psh1-Cse4 association itself functions to prevent Cse4 misincorporation. Significance: This work reports a previously unknown function of CK2 in CenH3/Cse4 regulation., Cse4 is the centromeric histone H3 variant in budding yeast. Psh1 is an E3 ubiquitin ligase that controls Cse4 levels through proteolysis. Here we report that Psh1 is phosphorylated by the Cka2 subunit of casein kinase 2 (CK2) to promote its E3 activity for Cse4. Deletion of CKA2 significantly stabilized Cse4. Consistent with phosphorylation promoting the activity of Psh1, Cse4 was stabilized in a Psh1 phosphodepleted mutant strain in which the major phosphorylation sites were changed to alanines. Phosphorylation of Psh1 did not control Psh1-Cse4 or Psh1-Ubc3(E2) interactions. Although Cse4 was highly stabilized in a cka2Δ strain, mislocalization of Cse4 was mild, suggesting that Cse4 misincorporation was prevented by the intact Psh1-Cse4 association. Supporting this idea, Psh1 was also stabilized in a cka2Δ strain. Collectively our data suggest that phosphorylation is crucial in Psh1-assisted control of Cse4 levels and that the Psh1-Cse4 association itself functions to prevent Cse4 misincorporation.
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- 2014
6. Selective suppression of antisense transcription by Set2-mediated H3K36 methylation
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Madelaine Gogol, Jerry L. Workman, Hua Li, and Swaminathan Venkatesh
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0301 basic medicine ,Saccharomyces cerevisiae Proteins ,Transcription, Genetic ,Science ,RNA Stability ,General Physics and Astronomy ,Saccharomyces cerevisiae ,Biology ,Methylation ,Article ,General Biochemistry, Genetics and Molecular Biology ,Histones ,Open Reading Frames ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Gene Expression Regulation, Fungal ,Sense (molecular biology) ,RNA, Antisense ,RNA, Messenger ,Gene ,Genetics ,Regulation of gene expression ,Multidisciplinary ,Lysine ,Reproducibility of Results ,RNA ,Methyltransferases ,General Chemistry ,Chromatin ,030104 developmental biology ,Histone methyltransferase ,Genome, Fungal ,Gene Deletion ,030217 neurology & neurosurgery - Abstract
Maintenance of a regular chromatin structure over the coding regions of genes occurs co-transcriptionally via the ‘chromatin resetting' pathway. One of the central players in this pathway is the histone methyltransferase Set2. Here we show that the loss of Set2 in yeast, Saccharomyces cerevisiae, results in transcription initiation of antisense RNAs embedded within body of protein-coding genes. These RNAs are distinct from the previously identified non-coding RNAs and cover 11% of the yeast genome. These RNA species have been named Set2-repressed antisense transcripts (SRATs) since the co-transcriptional addition of the H3K36 methyl mark by Set2 over their start sites results in their suppression. Interestingly, loss of chromatin resetting factor Set2 or the subsequent production of SRATs does not affect the abundance of the sense transcripts. This difference in transcriptional outcomes of overlapping transcripts due to a strand-independent addition of H3K36 methylation is a key regulatory feature of interleaved transcriptomes., Maintenance of chromatin structure in coding regions is partially dependent on transcription, with histone methyltransferase Set2 playing a role in this process. Here, the authors provide evidence that Set2 regulates repression of a specific set of antisense RNAs embedded within the coding genes.
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- 2016
7. Set2 mediated H3 lysine 36 methylation: regulation of transcription elongation and implications in organismal development
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Swaminathan Venkatesh and Jerry L. Workman
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Regulation of gene expression ,Genetics ,Histone methyltransferase ,EZH2 ,Histone methylation ,Histone code ,Cell Biology ,Methylation ,Histone exchange ,Biology ,Molecular Biology ,Developmental Biology ,Epigenomics - Abstract
Set2 is a RNA Polymerase II (RNAPII) associated histone methyltransferase involved in the co-transcriptional methylation of the H3 K36 residue (H3K36me). It is responsible for multiple degrees of methylation (mono-, di-, tri-), each of which has a distinct functional consequence. The extent of methylation and its genomic distribution is determined by different factors that co-ordinate to achieve a functional outcome. In yeast, the Set2-mediated H3K36me is involved in suppressing histone exchange, preventing hyperacetylation and promoting maintenance of well-spaced chromatin structure over the coding regions. In metazoans, separation of this enzymatic activity affords greater functional diversity extending beyond the control of transcription elongation to developmental gene regulation. This review focuses on the molecular aspects of the Set2 distribution and function, and discusses the role played by H3 K36 methyl mark in organismal development.
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- 2013
8. reSETting chromatin during transcription elongation
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Jerry L. Workman, Michaela Smolle, and Swaminathan Venkatesh
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Genetics ,Cancer Research ,Transcription Elongation, Genetic ,Pioneer factor ,Histone Deacetylase 1 ,Histone-Lysine N-Methyltransferase ,Biology ,Chromatin Assembly and Disassembly ,Chromatin ,Chromatin remodeling ,Cell biology ,Histones ,Histone H1 ,Histone methyltransferase ,Histone methylation ,Histone H2A ,Animals ,Humans ,Histone code ,Point of View ,Molecular Biology - Abstract
Maintenance of ordered chromatin structure over the body of genes is vital for the regulation of transcription. Increased access to the underlying DNA sequence results in the recruitment of RNA polymerase II to inappropriate, promoter-like sites within genes, resulting in unfettered transcription. Two new papers show how the Set2-mediated methylation of histone H3 on Lys36 (H3K36me) maintains chromatin structure by limiting histone dynamics over gene bodies, either by recruiting chromatin remodelers that preserve ordered nucleosomal distribution or by lowering the binding affinity of histone chaperones for histones, preventing their removal.
- Published
- 2013
9. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange
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Laurence Florens, Ying Zhang, Michael P. Washburn, Hua Li, Michaela Smolle, Jerry L. Workman, Swaminathan Venkatesh, and Madelaine Gogol
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Genetics ,0303 health sciences ,030302 biochemistry & molecular biology ,Histone exchange ,Biology ,Article ,Chromatin remodeling ,Chromatin ,03 medical and health sciences ,Histone H1 ,Structural Biology ,Histone methyltransferase ,Histone H2A ,Histone methylation ,Histone code ,Molecular Biology ,030304 developmental biology - Abstract
Set2-mediated methylation of histone H3 Lys36 (H3K36) is a mark associated with the coding sequences of actively transcribed genes, yet plays a negative role during transcription elongation. It prevents trans-histone exchange over coding regions and signals for histone deacetylation in the wake of RNA polymerase II (RNAPII) passage. We have found that in Saccharomyces cerevisiae the Isw1b chromatin-remodeling complex is specifically recruited to open reading frames (ORFs) by H3K36 methylation through the PWWP domain of its Ioc4 subunit in vivo and in vitro. Isw1b acts in conjunction with Chd1 to regulate chromatin structure by preventing trans-histone exchange from taking place over coding regions and thus maintains chromatin integrity during transcription elongation by RNA polymerase II.
- Published
- 2012
10. Rtr1 Is a CTD Phosphatase that Regulates RNA Polymerase II during the Transition from Serine 5 to Serine 2 Phosphorylation
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Swaminathan Venkatesh, Laurence Florens, Samantha G. Pattenden, Jerry L. Workman, Amber L. Mosley, Joshua M. Gilmore, Michael P. Washburn, and Michael Carey
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Chromatin Immunoprecipitation ,Saccharomyces cerevisiae Proteins ,Transcription, Genetic ,RNA polymerase II ,Saccharomyces cerevisiae ,Biology ,environment and public health ,Article ,Serine ,03 medical and health sciences ,Open Reading Frames ,Transcription (biology) ,Protein Interaction Mapping ,Phosphoprotein Phosphatases ,Phosphorylation ,Transcription factor ,RNA polymerase II holoenzyme ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Messenger RNA ,Models, Genetic ,030302 biochemistry & molecular biology ,Cell Biology ,Molecular biology ,Proton-Translocating ATPases ,biology.protein ,RNA Polymerase II ,Transcription factor II D ,Transcription Factors - Abstract
Messenger RNA processing is coupled to RNA Polymerase II (RNAPII) transcription through coordinated recruitment of accessory proteins to the Rpb1 C-terminal domain (CTD). Dynamic changes in CTD phosphorylation during transcription elongation are responsible for their recruitment, with serine 5 phosphorylation (S5-P) occurring towards the 5’ end of genes and serine 2 phosphorylation (S2-P) occurring towards the 3’ end. The proteins responsible for regulation of the transition state between S5-P and S2-P CTD remain elusive. We show that a conserved protein of unknown function, Rtr1, localizes within coding regions, with maximum levels of enrichment occurring between the peaks of S5-P and S2-P RNAPII. Upon deletion of Rtr1, the S5-P form of RNAPII accumulates in both whole cell extracts and throughout coding regions; additionally, RNAPII transcription is decreased and termination defects are observed. Functional characterization of Rtr1 reveals its role as a CTD phosphatase essential for the S5- to S2- P transition.
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- 2009
- Full Text
- View/download PDF
11. Histone exchange, chromatin structure and the regulation of transcription
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Jerry L. Workman and Swaminathan Venkatesh
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RNA, Untranslated ,Transcription, Genetic ,Chromatin remodeling ,Histones ,Histone H1 ,Histone methylation ,Histone H2A ,Nucleosome ,Histone code ,Animals ,Humans ,RNA, Messenger ,Molecular Biology ,Genome ,Chemistry ,Eukaryotic transcription ,Cell Biology ,DNA ,Chromatin Assembly and Disassembly ,Cell biology ,Chromatin ,Nucleosomes ,Eukaryotic Cells ,Gene Expression Regulation ,RNA Polymerase II ,Transcription Factors - Abstract
The packaging of DNA into strings of nucleosomes is one of the features that allows eukaryotic cells to tightly regulate gene expression. The ordered disassembly of nucleosomes permits RNA polymerase II (Pol II) to access the DNA, whereas nucleosomal reassembly impedes access, thus preventing transcription and mRNA synthesis. Chromatin modifications, chromatin remodellers, histone chaperones and histone variants regulate nucleosomal dynamics during transcription. Disregulation of nucleosome dynamics results in aberrant transcription initiation, producing non-coding RNAs. Ongoing research is elucidating the molecular mechanisms that regulate chromatin structure during transcription by preventing histone exchange, thereby limiting non-coding RNA expression.
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- 2015
12. Histone acetyltransferase Enok regulates oocyte polarization by promoting expression of the actin nucleation factor spire
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Michaela Smolle, Ariel Paulson, Fu Huang, Arnob Dutta, Susan M. Abmayr, Jerry L. Workman, and Swaminathan Venkatesh
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Chromatin Immunoprecipitation ,Embryo, Nonmammalian ,Histones ,Histone H3 ,Genetics ,Transcriptional regulation ,Animals ,Drosophila Proteins ,Protein Isoforms ,Actin nucleation ,Histone Acetyltransferases ,biology ,Microfilament Proteins ,Ovary ,Gene Expression Regulation, Developmental ,Acetylation ,Histone acetyltransferase ,Cell biology ,Histone ,Drosophila melanogaster ,Mutation ,biology.protein ,Oocytes ,Female ,Chromatin immunoprecipitation ,Developmental Biology ,Research Paper - Abstract
KAT6 histone acetyltransferases (HATs) are highly conserved in eukaryotes and have been shown to play important roles in transcriptional regulation. Here, we demonstrate that the Drosophila KAT6 Enok acetylates histone H3 Lys 23 (H3K23) in vitro and in vivo. Mutants lacking functional Enok exhibited defects in the localization of Oskar (Osk) to the posterior end of the oocyte, resulting in loss of germline formation and abdominal segments in the embryo. RNA sequencing (RNA-seq) analysis revealed that spire (spir) and maelstrom (mael), both required for the posterior localization of Osk in the oocyte, were down-regulated in enok mutants. Chromatin immunoprecipitation showed that Enok is localized to and acetylates H3K23 at the spir and mael genes. Furthermore, Gal4-driven expression of spir in the germline can largely rescue the defective Osk localization in enok mutant ovaries. Our results suggest that the Enok-mediated H3K23 acetylation (H3K23Ac) promotes the expression of spir, providing a specific mechanism linking oocyte polarization to histone modification.
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- 2014
13. Histone modification and exchange during gene transcription: signals and mechanisms (108.1)
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Swaminathan Venkatesh, Jerry L. Workman, and Mihaela Smolle
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Genetics ,Chemistry ,Pioneer factor ,Biochemistry ,Chromatin ,Cell biology ,Histone H3 ,Histone H1 ,Histone methyltransferase ,Histone methylation ,Histone H2A ,Histone code ,Molecular Biology ,Biotechnology - Abstract
Maintenance of ordered chromatin structure over the body of genes is vital for the regulation of transcription. Increased access to the underlying DNA sequence results in the recruitment of RNA polymerase II to inappropriate, promoter-like sites within genes, resulting in unfettered transcription. Our recent studies show how Set2-mediated methylation of histone H3 on Lys36 (H3K36me) maintains chromatin structure by limiting histone dynamics over gene bodies, either by recruiting chromatin remodelers that preserve ordered nucleosomal distribution or by lowering the binding affinity of histone chaperones for histones, preventing their removal.
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- 2014
14. Transcription Through Chromatin
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Michaela Smolle and Swaminathan Venkatesh
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biology ,General transcription factor ,Transcription (biology) ,Eukaryotic transcription ,biology.protein ,RNA polymerase II ,Transcription coregulator ,RNA polymerase II holoenzyme ,Chromatin remodeling ,Chromatin ,Cell biology - Abstract
All nuclear processes, including transcription by RNA polymerase II, take place in the context of the higher-order packaging of DNA into chromatin. Controlled gene expression requires first unimpeded access to the DNA by the transcriptional machinery and subsequent reformation of DNA into chromatin to avoid aberrant transcription. We will discuss the regulatory mechanisms that promote and limit RNA polymerase II transcription in cells.
- Published
- 2013
15. Non-coding transcription SETs up regulation
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Swaminathan Venkatesh and Jerry L. Workman
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Regulation of gene expression ,Genetics ,biology ,RNA ,Cell Biology ,Computational biology ,Non-coding RNA ,Research Highlight ,Chromatin ,Histones ,Histone ,Gene Expression Regulation ,Transcription (biology) ,Gene expression ,biology.protein ,Transcriptional regulation ,Humans ,RNA, Long Noncoding ,Molecular Biology - Abstract
An abundance of long non-coding RNA (lncRNA) present in most species from yeast to human are involved in transcriptional regulation, dosage compensation and imprinting. This underscores the importance of lncRNA as functional RNA despite the fact that they do not produce proteins. Two recent papers in Cell have demonstrated that transcription of the non-conserved lncRNAs, but not the RNAs themselves, is necessary to introduce co-transcriptional regulatory histone marks to regulate gene expression.
- Published
- 2012
16. Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro
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Michael Carey, Benjamin G. Kuryan, Sarah Lombardo, Nancy Tran, Jerry L. Workman, Swaminathan Venkatesh, and Jessica J. Kim
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Multidisciplinary ,Nucleosome Assembly Protein 1 ,biology ,Cell-Free System ,Transcription, Genetic ,Saccharomyces cerevisiae ,Biological Sciences ,Chromatin Assembly and Disassembly ,Molecular biology ,Cell biology ,Histones ,Histone H1 ,Histone methyltransferase ,Multiprotein Complexes ,Histone methylation ,Histone H2A ,biology.protein ,Nucleosome ,Histone code ,Histone octamer ,Chromatin structure remodeling (RSC) complex ,RNA Polymerase II ,Transcription Factors - Abstract
ATPases and histone chaperones facilitate RNA polymerase II (pol II) elongation on chromatin. In vivo, the coordinated action of these enzymes is necessary to permit pol II passage through a nucleosome while restoring histone density afterward. We have developed a biochemical system recapitulating this basic process. Transcription through a nucleosome in vitro requires the ATPase remodels structure of chromatin (RSC) and the histone chaperone nucleosome assembly protein 1 (NAP1). In the presence of NAP1, RSC generates a hexasome. Despite the propensity of RSC to evict histones, NAP1 reprograms the reaction such that the hexasome is retained on the template during multiple rounds of transcription. This work has implications toward understanding the mechanism of pol II elongation on chromatin.
- Published
- 2012
17. Characterization of a Highly Conserved Histone Related Protein, Ydl156w, and Its Functional Associations Using Quantitative Proteomic Analyses*
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Chris Seidel, Laurence Florens, Jerry L. Workman, Joshua M. Gilmore, Allison Peak, Mihaela E. Sardiu, Brent Stutzman, Swaminathan Venkatesh, and Michael P. Washburn
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Genetics ,Proteomics ,Saccharomyces cerevisiae Proteins ,biology ,Transcription, Genetic ,In silico ,Research ,Quantitative proteomics ,RNA Polymerase III ,Saccharomyces cerevisiae ,Biochemistry ,DNA-binding protein ,Chromatin remodeling ,Analytical Chemistry ,Protein–protein interaction ,DNA-Binding Proteins ,Histones ,Histone ,Non-histone protein ,biology.protein ,Molecular Biology - Abstract
A significant challenge in biology is to functionally annotate novel and uncharacterized proteins. Several approaches are available for deducing the function of proteins in silico based upon sequence homology and physical or genetic interaction, yet this approach is limited to proteins with well-characterized domains, paralogs and/or orthologs in other species, as well as on the availability of suitable large-scale data sets. Here, we present a quantitative proteomics approach extending the protein network of core histones H2A, H2B, H3, and H4 in Saccharomyces cerevisiae, among which a novel associated protein, the previously uncharacterized Ydl156w, was identified. In order to predict the role of Ydl156w, we designed and applied integrative bioinformatics, quantitative proteomics and biochemistry approaches aiming to infer its function. Reciprocal analysis of Ydl156w protein interactions demonstrated a strong association with all four histones and also to proteins strongly associated with histones including Rim1, Rfa2 and 3, Yku70, and Yku80. Through a subsequent combination of the focused quantitative proteomics experiments with available large-scale genetic interaction data and Gene Ontology functional associations, we provided sufficient evidence to associate Ydl156w with multiple processes including chromatin remodeling, transcription and DNA repair/replication. To gain deeper insights into the role of Ydl156w in histone biology we investigated the effect of the genetic deletion of ydl156w on H4 associated proteins, which lead to a dramatic decrease in the association of H4 with RNA polymerase III proteins. The implication of a role for Ydl156w in RNA Polymerase III mediated transcription was consequently verified by RNA-Seq experiments. Finally, using these approaches we generated a refined network of Ydl156w-associated proteins.
- Published
- 2011
18. Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes
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Krishnamurthy Natarajan, Shambhu Kumar, Hua Li, Swaminathan Venkatesh, Jerry L. Workman, Michaela Smolle, Malika Saint, and Madelaine Gogol
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Multidisciplinary ,Saccharomyces cerevisiae Proteins ,Transcription, Genetic ,Lysine ,Genes, Fungal ,Acetylation ,Cell Cycle Proteins ,Histone exchange ,Methyltransferases ,Saccharomyces cerevisiae ,Biology ,Methylation ,Histones ,Histone H3 ,Open Reading Frames ,Phenotype ,Biochemistry ,Histone H1 ,Histone methyltransferase ,Histone H2A ,Histone methylation ,Histone code ,Histone octamer ,RNA Polymerase II ,Molecular Chaperones - Abstract
In yeast, histone H3 lysine 36 methylation can suppress the incorporation of acetylated histones by inhibiting histone exchange in transcribed genes, thus preventing spurious cryptic transcripts from initiating within open reading frames. The accuracy of RNA polymerase II transcription through the coding region of genes is maintained in part by Set2-mediated methylation of histone H3K36 (H3K36me), a modification that suppresses histone acetylation and so prevents spurious cryptic transcripts from initiating within open-reading frames (ORFs). Here, in yeast, Jerry Workman and colleagues show that histones can become acetylated during transcription owing to histone exchange over ORFs, and Set2-mediated H3K36 methylation suppresses this histone exchange by preventing interactions with histone chaperones. Thus, Set2 can suppress the incorporation of acetylated histones, as well as lead to deacetylation of such histones in transcribed genes. Set2-mediated methylation of histone H3 at Lys 36 (H3K36me) is a co-transcriptional event that is necessary for the activation of the Rpd3S histone deacetylase complex, thereby maintaining the coding region of genes in a hypoacetylated state1,2. In the absence of Set2, H3K36 or Rpd3S acetylated histones accumulate on open reading frames (ORFs), leading to transcription initiation from cryptic promoters within ORFs1,3. Although the co-transcriptional deacetylation pathway is well characterized, the factors responsible for acetylation are as yet unknown. Here we show that, in yeast, co-transcriptional acetylation is achieved in part by histone exchange over ORFs. In addition to its function of targeting and activating the Rpd3S complex, H3K36 methylation suppresses the interaction of H3 with histone chaperones, histone exchange over coding regions and the incorporation of new acetylated histones. Thus, Set2 functions both to suppress the incorporation of acetylated histones and to signal for the deacetylation of these histones in transcribed genes. By suppressing spurious cryptic transcripts from initiating within ORFs, this pathway is essential to maintain the accuracy of transcription by RNA polymerase II.
- Published
- 2011
19. Recognizing methylated histone variant H3.3 to prevent tumors
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Swaminathan Venkatesh and Jerry L. Workman
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Genetics ,Transcription Elongation, Genetic ,Lysine ,Breast Neoplasms ,Cell Biology ,Biology ,Research Highlight ,Article ,Cell biology ,Histones ,Histone ,Histone H1 ,Histone methyltransferase ,Histone H2A ,Histone methylation ,biology.protein ,Animals ,Humans ,Histone code ,Female ,RNA Polymerase II ,Histone octamer ,Carrier Proteins ,Molecular Biology ,Chromatin immunoprecipitation - Abstract
Recognition of modified histones by “reader” proteins plays a critical role in the regulation of chromatin1. H3K36 trimethylation (H3K36me3) is deposited onto the nucleosomes in the transcribed regions following RNA polymerase II (Pol II) elongation. In yeast, this mark in turn recruits epigenetic regulators to reset the chromatin to a relatively repressive state thus suppressing cryptic transcription2. However, much less is known about the role of H3K36me3 in transcription regulation in mammals. This is further complicated by the transcription-coupled incorporation of the histone variant H3.3 in gene bodies3. Here we show that the candidate tumor suppressor ZMYND11 specifically recognizes H3K36me3 on H3.3 (H3.3K36me3) and regulates Pol II elongation. Structural studies reveal that in addition to the trimethyl-lysine binding by an aromatic cage within the PWWP domain, the H3.3-dependent recognition is mediated by the encapsulation of the H3.3-specific “Ser31” residue in a composite pocket formed by the tandem bromo-PWWP domains of ZMYND11. ChIP-sequencing analyses reveal a genome-wide colocalization of ZMYND11 with H3K36me3 and H3.3 in gene bodies, and its occupancy requires the pre-deposition of H3.3K36me3. Although ZMYND11 is associated with highly expressed genes, it functions as an unconventional transcription corepressor via modulating Pol II at the elongation stage. ZMYND11 is critical for the repression of a transcriptional program that is essential for tumor cell growth; low expression level of ZMYND11 in breast cancer patients correlates with worse prognosis. Consistently, overexpression of ZMYND11 suppresses cancer cell growth in vitro and tumor formation in mice. Together, this study identifies ZMYND11 as an H3.3-specific reader of H3K36me3 that links the histone variant-mediated transcription elongation control to tumor suppression.
- Published
- 2014
20. Psh1 is an E3 ubiquitin ligase that targets the centromeric histone variant Cse4
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Laurence Florens, Jerry L. Workman, Skylar Martin-Brown, Manjunatha Shivaraju, Geetha S. Hewawasam, Jennifer L. Gerton, Mark Mattingly, and Swaminathan Venkatesh
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Zinc finger ,biology ,Cell Biology ,DNA-binding protein ,Article ,Ubiquitin ligase ,Histone H3 ,Histone ,Ubiquitin ,Biochemistry ,Chaperone (protein) ,biology.protein ,Nucleosome ,Molecular Biology - Abstract
Cse4 is a variant of histone H3 that is incorporated into a single nucleosome at each centromere in budding yeast. We have discovered an E3 ubiquitin ligase, called Psh1, which controls the cellular level of Cse4 via ubiquitylation and proteolysis. The activity of Psh1 is dependent on both its RING and zinc finger domains. We demonstrate the specificity of the ubiquitylation activity of Psh1 toward Cse4 in vitro and map the sites of ubiquitylation. Mutation of key lysines prevents ubiquitylation of Cse4 by Psh1 in vitro and stabilizes Cse4 in vivo. While deletion of Psh1 stabilizes Cse4, elimination of the Cse4-specific chaperone Scm3 destabilizes Cse4, and the addition of Scm3 to the Psh1-Cse4 ubiquitylation reaction prevents Cse4 ubiquitylation, together suggesting Scm3 may protect Cse4 from ubiquitylation. Without Psh1, Cse4 overexpression is toxic and Cse4 is found at ectopic locations. Our results suggest Psh1 functions to prevent the mislocalization of Cse4.
- Published
- 2010
21. Molecular secrets of a parasite
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Mats Wahlgren, Maria Teresa Bejarano, Jerry L. Workman, and Swaminathan Venkatesh
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Regulation of gene expression ,Multidisciplinary ,biology ,Plasmodium falciparum ,medicine.disease ,biology.organism_classification ,Virology ,Histone H3 ,Immune system ,parasitic diseases ,biology.protein ,medicine ,Gene silencing ,Antibody ,Gene ,Malaria - Abstract
Research shows how the malaria parasite Plasmodium falciparum manipulates the expression of its var genes to avoid recognition by the host immune system. Four experts comment on the implications of these results for our understanding of gene regulation in general and the development of antimalaria vaccines. See Letter p.223 When the malaria parasite Plasmodium falciparum infects red blood cells, it escapes immune detection by expressing just one of 60 antigenically distinct var genes at a time, then switching to express a new gene during the course of infection. Here, Louis Miller and colleagues show that the histone H3 modification lysine 36 trimethylation (H3K36me3) is present at the transcription start site and along the gene body of silenced var genes. Knockout of the P. falciparum variant-silencing SET gene (PfSETvs) results in concurrent transcription of all 60 var genes, each one coding for a different version of the PfEMP1 membrane protein. PfSETvs therefore has a key role in var gene silencing. In addition, the PfSETvs knockout parasite generated in this work has potential as an antimalarial vaccine owing to its ability to express all PfEMP1 proteins, which should generate a broad repertoire of antibodies to protect against malaria.
- Published
- 2013
22. Innate immune responses of exfoliated epithelial cells. (P4165)
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Srinivasan, Mythily, primary, Swaminathan, Venkatesh, additional, Negrini, Thais, additional, and Arthur, Rodrigo, additional
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- 2013
- Full Text
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23. Chromatin reassembly following RNA polymerase II transcription
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Michael P. Washburn, Hua Li, Ying Zhang, Madelaine Gogol, Florence Laurens, Swaminathan Venkatesh, Michaela Smolle, and Jerry L. Workman
- Subjects
Histone-modifying enzymes ,Biology ,Molecular biology ,Chromatin remodeling ,Chromatin ,Cell biology ,Histone H1 ,Histone methyltransferase ,Histone H2A ,Histone methylation ,Genetics ,Histone code ,Oral Presentation ,Molecular Biology - Abstract
During the process of transcription elongation, the chromatin structure of transcribed sequences can be perturbed, exposing cryptic promoter-like sequences within the body of transcribed genes to function as initiation sites. Re-establishing a stable repressive structure of open reading frames requires histone chaperones, methyltransferases, deacetylases and chromatin remodeling complexes. The Set2/Rpd3S pathway is used by elongating RNA polymerase II to signal for histone deacetylation in its wake. Set2 associates with the elongating form of RNA polymerase II and co-transcriptionally methylates histone H3K36. H3K36 is recognized by the Rpd3S deacetylase complex to deacetylate histones in transcribed sequences. In recent work, we have found that a major source of cotranscriptional histone acetylation is the incorporation of soluble, Rtt109 H3K56-acetylated histones by the Asf1 histone chaperone. Set2 methylation of H3K36 promotes retention of the original histones and suppresses the incorporation of soluble histones by Asf1. By identifying factors that interact with H3K36 methylated nucleosomes, we have found that chromatin remodeling is also required to stabilize the chromatin structures of open reading frames following transcription elongation. Our studies identified the ATP-dependent chromatin remodelers Isw1 and Chd1 as two factors involved in this pathway as deletion of ISW1 and CHD1 enhanced the cryptic transcript phenotype caused by set2. Moreover, loss of ISW1 and CHD1 also enhanced the incorporation of new histones from the soluble pool into chromatin. Thus, retention of original histones, deacetylation of any new ones and their organization by chromatin remodeling are all required to re-establish stable chromatin resistant to cryptic transcription initiation.
- Published
- 2013
24. Differential expression of TLR-2 and TLR-4 in the epithelial cells in oral lichen planus
- Author
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Janardhanam, Srihari B., primary, Prakasam, Sivaraman, additional, Swaminathan, Venkatesh T., additional, Kodumudi, Krithika N., additional, Zunt, Susan L., additional, and Srinivasan, Mythily, additional
- Published
- 2012
- Full Text
- View/download PDF
25. The Multifunctional Protein Nucleophosmin (NPM1) Is a Human Linker Histone H1 Chaperone
- Author
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Gadad, Shrikanth S., primary, Senapati, Parijat, additional, Syed, Sajad Hussain, additional, Rajan, Roshan Elizabeth, additional, Shandilya, Jayasha, additional, Swaminathan, Venkatesh, additional, Chatterjee, Snehajyoti, additional, Colombo, Emanuela, additional, Dimitrov, Stefan, additional, Pelicci, Pier Giuseppe, additional, Ranga, Udaykumar, additional, and Kundu, Tapas K., additional
- Published
- 2011
- Full Text
- View/download PDF
26. Phosphorylated Pol II CTD Recruits Multiple HDACs, Including Rpd3C(S), for Methylation-Dependent Deacetylation of ORF Nucleosomes
- Author
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Govind, Chhabi K., primary, Qiu, Hongfang, additional, Ginsburg, Daniel S., additional, Ruan, Chun, additional, Hofmeyer, Kimberly, additional, Hu, Cuihua, additional, Swaminathan, Venkatesh, additional, Workman, Jerry L., additional, Li, Bing, additional, and Hinnebusch, Alan G., additional
- Published
- 2010
- Full Text
- View/download PDF
27. Acetylated NPM1 Localizes in the Nucleoplasm and Regulates Transcriptional Activation of Genes Implicated in Oral Cancer Manifestation
- Author
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Shandilya, Jayasha, primary, Swaminathan, Venkatesh, additional, Gadad, Shrikanth S., additional, Choudhari, Ramesh, additional, Kodaganur, Gopinath S., additional, and Kundu, Tapas K., additional
- Published
- 2009
- Full Text
- View/download PDF
28. Curcumin, a Novel p300/CREB-binding Protein-specific Inhibitor of Acetyltransferase, Represses the Acetylation of Histone/Nonhistone Proteins and Histone Acetyltransferase-dependent Chromatin Transcription
- Author
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Balasubramanyam, Karanam, primary, Varier, Radhika A., additional, Altaf, Mohammed, additional, Swaminathan, Venkatesh, additional, Siddappa, Nagadenahalli B., additional, Ranga, Udaykumar, additional, and Kundu, Tapas K., additional
- Published
- 2004
- Full Text
- View/download PDF
29. Histone chaperone as coactivator of chromatin transcription: role of acetylation
- Author
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Gadad, S. S., Shandilya, J., Swaminathan Venkatesh, and Kundu, T. K.
30. UpSETing chromatin during non-coding RNA production
- Author
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Jerry L. Workman, Michaela Smolle, and Swaminathan Venkatesh
- Subjects
Cryptic transcription ,Genetics ,0303 health sciences ,biology ,RNA ,RNA polymerase II ,Eukaryotic DNA replication ,Review ,Non-coding RNA ,Chromatin ,DNA sequencing ,Cell biology ,03 medical and health sciences ,0302 clinical medicine ,Gene expression ,biology.protein ,Nucleosome ,Nucleosomal organization ,Molecular Biology ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
The packaging of eukaryotic DNA into nucleosomal arrays permits cells to tightly regulate and fine-tune gene expression. The ordered disassembly and reassembly of these nucleosomes allows RNA polymerase II (RNAPII) conditional access to the underlying DNA sequences. Disruption of nucleosome reassembly following RNAPII passage results in spurious transcription initiation events, leading to the production of non-coding RNA (ncRNA). We review the molecular mechanisms involved in the suppression of these cryptic initiation events and discuss the role played by ncRNAs in regulating gene expression.
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- View/download PDF
31. Methods to study histone chaperone function in nucleosome assembly and chromatin transcription.
- Author
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Senapati P, Sudarshan D, Gadad SS, Shandilya J, Swaminathan V, and Kundu TK
- Subjects
- Animals, Cell Line, Chromatin metabolism, Chromatin Assembly and Disassembly, Humans, In Vitro Techniques, Mice, Nucleophosmin, Nucleosomes metabolism, Chromatin genetics, Histone Chaperones metabolism, Histones metabolism, Nucleosomes genetics, Transcription, Genetic
- Abstract
Histone chaperones are histone interacting proteins that are involved in various stages of histone metabolism in the cell such as histone storage, transport, nucleosome assembly and disassembly. Histone assembly and disassembly are essential processes in certain DNA-templated phenomena such as replication, repair and transcription in eukaryotes. Since the first histone chaperone Nucleoplasmin was discovered in Xenopus, a plethora of histone chaperones have been identified, characterized and their functional significance elucidated in the last 35 years or so. Some of the histone chaperone containing complexes such as FACT have been described to play a significant role in nucleosome disassembly during transcription elongation. We have reported earlier that human Nucleophosmin (NPM1), a histone chaperone belonging to the Nucleoplasmin family, is a co-activator of transcription. In this chapter, we describe several methods that are used to study the histone chaperone activity of proteins and their role in transcription.
- Published
- 2015
- Full Text
- View/download PDF
32. Histone chaperone as coactivator of chromatin transcription: role of acetylation.
- Author
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Gadad SS, Shandilya J, Swaminathan V, and Kundu TK
- Subjects
- Acetylation, Animals, Biological Assay, Cell Extracts, Cell Nucleus metabolism, Chromatin Assembly and Disassembly, DNA Topoisomerases, Type I isolation & purification, Drosophila melanogaster, HeLa Cells, Histones isolation & purification, Humans, Membrane Proteins isolation & purification, Membrane Proteins metabolism, Mice, Micrococcal Nuclease metabolism, Nuclear Proteins isolation & purification, Nuclear Proteins metabolism, Nucleophosmin, Plasmids isolation & purification, Protein Binding, Templates, Genetic, Chromatin genetics, Histones metabolism, Molecular Biology methods, Molecular Chaperones metabolism, Transcription, Genetic
- Abstract
Histone chaperones are a group of histone-interacting proteins, involved in several important cellular functions. These chaperones are essential to facilitate ordered assembly of nucleosomes, both in replication dependent and independent manner. Replication independent function of histone chaperone is necessary for histone eviction during transcriptional initiation and elongation. In this chapter we have discussed a method to evaluate the role of histone chaperone NPM1 (the only known chaperone to get acetylated with functional consequence) in the transcriptional activation which is acetylation dependent.
- Published
- 2009
- Full Text
- View/download PDF
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