15 results on '"Swaminathan, Venkatesh"'
Search Results
2. Histone acetyltransferase Enok regulates oocyte polarization by promoting expression of the actin nucleation factor spire
- Author
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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.
- Published
- 2014
3. 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
4. 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.
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- 2010
5. Methods to Study Histone Chaperone Function in Nucleosome Assembly and Chromatin Transcription.
- Author
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Senapati, Parijat, Sudarshan, Deepthi, Gadad, Shrikanth S., Shandilya, Jayasha, Swaminathan, Venkatesh, and Kundu, Tapas K.
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- 2015
- Full Text
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6. 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
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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
7. Histone Chaperone as Coactivator of Chromatin Transcription: Role of Acetylation.
- Author
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Gadad, Shrikanth S., Shandilya, Jayasha, Swaminathan, Venkatesh, and Kundu, Tapas K.
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- 2009
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8. The Multifunctional Protein Nucleophosmin (NPM1) Is a Human Linker Histone H1 Chaperone.
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Gadad, Shrikanth S., Senapati, Parijat, Hussain Syed, Sajad, Rajan, Roshan Elizabeth, Shandilya, Jayasha, Swaminathan, Venkatesh, Chatterjee, Snehajyoti, Colombo, Emanuela, Dimitrov, Stefan, Giuseppe Pelicci, Pier, Ranga, Udaykumar, and Kundu, Tapas K.
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- 2011
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9. Acetylated NPM1 Localizes in the Nucleoplasm and Regulates Transcriptional Activation of Genes Implicated in Oral Cancer Manifestation.
- Author
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Shandilya, Jayasha, Swaminathan, Venkatesh, Gadad, Shrikanth S., Choudhari, Ramesh, Kodaganur, Gopinath S., and Kundu, Tapas K.
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NUCLEOPHILIC reactions , *CELL proliferation , *ORIGIN of life , *SQUAMOUS cell carcinoma , *RNA polymerases , *CARCINOGENESIS - Abstract
Nucleophosmin (NPM1) is a multifunctional protein involved in the regulation of centrosome duplication, ribosome biogenesis, genomic stability, histone chaperone function, and transcription. Overexpression of NPM1 is associated with cancers of diverse histological origins. Here, we have found that p300-mediated acetylation of NPM1 modulates its subcellular localization and augments its oncogenic potential. Acetylated NPM1 is predominantly localized in the nucleoplasm, where it associates with transcriptionally active RNA polymerase II. Deacetylation of NPM1 is brought about by human SIRT1 and reduces its transcriptional activation potential. Remarkably, increased levels of acetylated NPM1 were found in grade II and III oral squamous cell carcinoma (OSCC) patient samples. Small interfering RNA (siRNA)-mediated knockdown of NPM1 in an OSCC cell line, followed by microarray analysis and chromatin immunoprecipitation experiments, revealed that some of the genes involved in oral cancer malignancy are regulated by NPM1 and have acetylated NPM1 localized at their promoters. Either suppression of p300 by siRNA or mutation of acetylatable lysine residues of NPM1 resulted in reduced occupancy of acetylated NPM1 on the target gene promoter concomitant with its decreased transcript levels. These observations suggest that acetylated NPM1 transcriptionally regulates genes involved in cell survival and proliferation during carcinogenesis. [ABSTRACT FROM AUTHOR]
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- 2009
- Full Text
- View/download PDF
10. UpSETing chromatin during non-coding RNA production
- Author
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Jerry L. Workman, Michaela Smolle, and Swaminathan Venkatesh
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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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11. Differential expression of TLR-2 and TLR-4 in the epithelial cells in oral lichen planus
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Janardhanam, Srihari B., Prakasam, Sivaraman, Swaminathan, Venkatesh T., Kodumudi, Krithika N., Zunt, Susan L., and Srinivasan, Mythily
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EPITHELIAL cells , *LICHEN planus , *GENE expression , *KERATINOCYTES , *LYMPHOCYTES , *TOLL-like receptors - Abstract
Abstract: Objective: Oral lichen planus (OLP) is a chronic inflammatory condition of the mucosa mediated by a complex signalling network between the keratinocytes and the sub-epithelial lymphocytes. Since OLP occurs in constantly renewing epithelium continuously exposed to commensals, we hypothesised that the epithelial cell microflora interactions may mediate the persistent inflammation. By virtue of their ability to respond to most oral commensal microorganisms, the toll like receptor-2 (TLR-2) and TLR-4 are the most widely investigated receptors in oral diseases. The overall objective of this study was to investigate the role of TLR-2 and TLR-4 in OLP. Design: Systemically healthy OLP and control subjects were recruited after obtaining the institutional review board approval. Expression of TLR-2 and TLR-4 proteins and transcripts in the tissue epithelium and in the epithelial cells isolated from saliva were determined by immunohistochemistry and quantitative real-time polymerase chain reaction respectively. Results: The tissue epithelium and the salivary epithelial cells expressed reduced TLR-2 and increased TLR-4 proteins and transcripts in OLP. The salivary epithelial cells from OLP subjects secreted elevated IL-12. However, upon stimulation with bacterial lipopolysaccharide the epithelial cells from OLP exhibited a mixed Th1 (IL-12) and Th2 (IL-4) response. Presence of dexamethasone significantly reduced inflammatory cytokines in the in vitro stimulated cultures of salivary epithelial cells from OLP subjects. Conclusion: Collectively, our data support a critical role for the host–microbial interactions in the OLP pathogenesis. The potential use of exfoliated oral epithelial cells in saliva for functional analysis exponentially increases its value as biological specimen for clinical research. [Copyright &y& Elsevier]
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- 2012
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12. Phosphorylated Pol II CTD Recruits Multiple HDACs, Including Rpd3C(S), for Methylation-Dependent Deacetylation of ORF Nucleosomes
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Govind, Chhabi K., Qiu, Hongfang, Ginsburg, Daniel S., Ruan, Chun, Hofmeyer, Kimberly, Hu, Cuihua, Swaminathan, Venkatesh, Workman, Jerry L., Li, Bing, and Hinnebusch, Alan G.
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PHOSPHORYLATION , *HISTONE deacetylase , *METHYLATION , *TRANSCRIPTION factors , *GENETIC mutation , *MOLECULAR biology - Abstract
Summary: Methylation of histone H3 by Set1 and Set2 is required for deacetylation of nucleosomes in coding regions by histone deacetylase complexes (HDACs) Set3C and Rpd3C(S), respectively. We report that Set3C and Rpd3C(S) are cotranscriptionally recruited in the absence of Set1 and Set2, but in a manner stimulated by Pol II CTD kinase Cdk7/Kin28. Consistently, Rpd3C(S) and Set3C interact with Ser5-phosphorylated Pol II and histones in extracts, but only the histone interactions require H3 methylation. Moreover, reconstituted Rpd3C(S) binds specifically to Ser5-phosphorylated CTD peptides in vitro. Hence, whereas interaction with methylated H3 residues is required for Rpd3C(S) and Set3C deacetylation activities, their cotranscriptional recruitment is stimulated by the phosphorylated CTD. We further demonstrate that Rpd3, Hos2, and Hda1 have overlapping functions in deacetylating histones and suppressing cotranscriptional histone eviction. A strong correlation between increased acetylation and lower histone occupancy in HDA mutants implies that histone acetylation is important for nucleosome eviction. [ABSTRACT FROM AUTHOR]
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- 2010
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13. Curcumin, a Novel p300/CREB-binding Protein-specific Inhibitor of Acetyltransferase, Represses the Acetylation of Histone/Nonhistone...
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Balasubramanyam, Karanam, Varier, Radhika A., Altaf, Mohammed, Swaminathan, Venkatesh, Siddappa, Nagadenahalli B., Ranga, Udaykumar, and Kundu, Tapas K.
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ACETYLTRANSFERASES , *CARRIER proteins , *HIV , *CHROMATIN , *NUCLEIC acids , *GENETIC translation , *GENE expression , *GENETIC regulation , *HUMAN chromosomes , *HUMAN gene mapping , *HUMAN genome - Abstract
Acetylation of histones and non-histone proteins is an important post-translational modification involved in the regulation of gene expression in eukaryotes and all viral DNA that integrates into the human genome (e.g. the human immunodeficiency virus). Dysfunction of histone acetyltransferases (HATs) is often associated with the manifestation of several diseases. In this respect, HATs are the new potential targets for the design of therapeutics. In this study, we report that curcumin (diferuloylmethane), a major curcumanoid in the spice turmeric, is a specific inhibitor of the p300/CREB-bindlng protein (CBP) HAT activity but not of p300/CBPassociated factor, in vitro and in vivo. Furthermore, curcumin could also inhibit the p300-mediated acetylation of p53 in vivo. It specifically represses the p300/CBP HAT activity-dependent transcriptional activation from chromatin but not a DNA template. It is significant that curcumin could inhibit the acetylation of HIV-Tat protein in vitro by p300 as well as proliferation of the virus, as revealed by the repression in syncytia formation upon curcumin treatment in SupT1 cells. Thus, nontoxic curcumin, which targets p300/CBP, may serve as a lead compound in combinatorial HIV therapeutics. [ABSTRACT FROM AUTHOR]
- Published
- 2004
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14. Methods to study histone chaperone function in nucleosome assembly and chromatin transcription.
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Senapati P, Sudarshan D, Gadad SS, Shandilya J, Swaminathan V, and Kundu TK
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- 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.
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- 2015
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15. Histone chaperone as coactivator of chromatin transcription: role of acetylation.
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Gadad SS, Shandilya J, Swaminathan V, and Kundu TK
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- 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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