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https://www.readbyqxmd.com/read/27601353/identification-of-set-domain-containing-proteins-in-gossypium-raimondii-and-their-response-to-high-temperature-stress
#1
Yong Huang, Yijia Mo, Pengyun Chen, Xiaoling Yuan, Funing Meng, Shengwei Zhu, Zhi Liu
SET (Su(var), E(z), and Trithorax) domain-containing proteins play an important role in plant development and stress responses through modifying lysine methylation status of histone. Gossypium raimondii may be the putative contributor of the D-subgenome of economical crops allotetraploid G. hirsutum and G. barbadense and therefore can potentially provide resistance genes. In this study, we identified 52 SET domain-containing genes from G. raimondii genome. Based on conserved sequences, these genes are grouped into seven classes and are predicted to catalyze the methylation of different substrates: GrKMT1 for H3K9me, GrKMT2 and GrKMT7 for H3K4me, GrKMT3 for H3K36me, GrKMT6 for H3K27me, but GrRBCMT and GrS-ET for nonhistones substrate-specific methylation...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27317772/setd2-and-dnmt3a-screen-in-the-sotos-like-syndrome-french-cohort
#2
Camille Tlemsani, Armelle Luscan, Nicolas Leulliot, Eric Bieth, Alexandra Afenjar, Geneviève Baujat, Martine Doco-Fenzy, Alice Goldenberg, Didier Lacombe, Laetitia Lambert, Sylvie Odent, Jérôme Pasche, Sabine Sigaudy, Alexandre Buffet, Céline Violle-Poirsier, Audrey Briand-Suleau, Ingrid Laurendeau, Magali Chin, Pascale Saugier-Veber, Dominique Vidaud, Valérie Cormier-Daire, Michel Vidaud, Eric Pasmant, Lydie Burglen
BACKGROUND: Heterozygous NSD1 mutations were identified in 60%-90% of patients with Sotos syndrome. Recently, mutations of the SETD2 and DNMT3A genes were identified in patients exhibiting only some Sotos syndrome features. Both NSD1 and SETD2 genes encode epigenetic 'writer' proteins that catalyse methylation of histone 3 lysine 36 (H3K36me). The DNMT3A gene encodes an epigenetic 'reader' protein of the H3K36me chromatin mark. METHODS: We aimed at confirming the implication of DNMT3A and SETD2 mutations in an overgrowth phenotype, through a comprehensive targeted-next generation sequencing (NGS) screening in 210 well-phenotyped index cases with a Sotos-like phenotype and no NSD1 mutation, from a French cohort...
June 17, 2016: Journal of Medical Genetics
https://www.readbyqxmd.com/read/27268234/both-h4k20-mono-methylation-and-h3k56-acetylation-mark-transcription-dependent-histone-turnover-in-fission-yeast
#3
Hanna Yang, Chang Seob Kwon, Yoonjung Choi, Daeyoup Lee
Nucleosome dynamics facilitated by histone turnover is required for transcription as well as DNA replication and repair. Histone turnover is often associated with various histone modifications such as H3K56 acetylation (H3K56Ac), H3K36 methylation (H3K36me), and H4K20 methylation (H4K20me). In order to correlate histone modifications and transcription-dependent histone turnover, we performed genome wide analyses for euchromatic regions in G2/M-arrested fission yeast. The results show that transcription-dependent histone turnover at 5' promoter and 3' termination regions is directly correlated with the occurrence of H3K56Ac and H4K20 mono-methylation (H4K20me1) in actively transcribed genes...
August 5, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/26747610/homodimeric-phd-domain-containing-rco1-subunit-constitutes-a-critical-interaction-hub-within-the-rpd3s-histone-deacetylase-complex
#4
Chun Ruan, Haochen Cui, Chul-Hwan Lee, Sheng Li, Bing Li
Recognition of histone post-translational modifications is pivotal for directing chromatin-modifying enzymes to specific genomic regions and regulating their activities. Emerging evidence suggests that other structural features of nucleosomes also contribute to precise targeting of downstream chromatin complexes, such as linker DNA, the histone globular domain, and nucleosome spacing. However, how chromatin complexes coordinate individual interactions to achieve high affinity and specificity remains unclear...
March 4, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26275777/functional-interaction-of-rpb1-and-spt5-c-terminal-domains-in-co-transcriptional-histone-modification
#5
Jean Mbogning, Viviane Pagé, Jillian Burston, Emily Schwenger, Robert P Fisher, Beate Schwer, Stewart Shuman, Jason C Tanny
Transcription by RNA polymerase II (RNAPII) is accompanied by a conserved pattern of histone modifications that plays important roles in regulating gene expression. The establishment of this pattern requires phosphorylation of both Rpb1 (the largest RNAPII subunit) and the elongation factor Spt5 on their respective C-terminal domains (CTDs). Here we interrogated the roles of individual Rpb1 and Spt5 CTD phospho-sites in directing co-transcriptional histone modifications in the fission yeast Schizosaccharomyces pombe...
November 16, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25746793/mesenchyme-specific-overexpression-of-nucleolar-protein-66-in-mice-inhibits-skeletal-growth-and-bone-formation
#6
Qin Chen, Liping Zhang, Benoit de Crombrugghe, Ralf Krahe
Previous studies showed that nucleolar protein 66 (NO66), the Jumonji C-domain-containing histone demethylase for methylated histone H3K4 and H3K36 (H3K36me), negatively regulates osteoblast differentiation in vitro by inhibiting the activity of transcription factor osterix (Osx). However, whether NO66 affects mammalian skeletogenesis in vivo is not yet known. Here, we generated transgenic (TG) mice overexpressing a flag-tagged NO66 transgene driven by the Prx1 (paired related homeobox 1) promoter. We found that NO66 overexpression in Prx1-expressing mesenchymal cells inhibited skeletal growth and bone formation...
June 2015: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/25578729/nucleosome-contact-triggers-conformational-changes-of-rpd3s-driving-high-affinity-h3k36me-nucleosome-engagement
#7
Chun Ruan, Chul-Hwan Lee, Haochen Cui, Sheng Li, Bing Li
The Rpd3S histone deacetylase complex utilizes two subunits, Eaf3 and Rco1, to recognize nucleosomes methylated at H3K36 (H3K36me) with high affinity and strong specificity. However, the chromobarrel domain of Eaf3 (CHD) that is responsible for H3K36me recognition only binds weakly and with little specificity to histone peptides. Here, using deuterium exchange mass spectrometry (DXMS), we detected conformational changes of Rpd3S upon its contact with chromatin. Interestingly, we found that the Sin3-interacting domain of Rco1 (SID) allosterically stimulates preferential binding of Eaf3 to H3K36-methylated peptides...
January 13, 2015: Cell Reports
https://www.readbyqxmd.com/read/25300486/rad9-interacts-with-aft1-to-facilitate-genome-surveillance-in-fragile-genomic-sites-under-non-dna-damage-inducing-conditions-in-s-cerevisiae
#8
Christos Andreadis, Christoforos Nikolaou, George S Fragiadakis, Georgia Tsiliki, Despina Alexandraki
DNA damage response and repair proteins are centrally involved in genome maintenance pathways. Yet, little is known about their functional role under non-DNA damage-inducing conditions. Here we show that Rad9 checkpoint protein, known to mediate the damage signal from upstream to downstream essential kinases, interacts with Aft1 transcription factor in the budding yeast. Aft1 regulates iron homeostasis and is also involved in genome integrity having additional iron-independent functions. Using genome-wide expression and chromatin immunoprecipitation approaches, we found Rad9 to be recruited to 16% of the yeast genes, often related to cellular growth and metabolism, while affecting the transcription of ∼2% of the coding genome in the absence of exogenously induced DNA damage...
November 10, 2014: Nucleic Acids Research
https://www.readbyqxmd.com/read/25016215/a-developmental-genetic-analysis-of-the-lysine-demethylase-kdm2-mutations-in-drosophila-melanogaster
#9
Yani Zheng, Fu-Ning Hsu, Wu Xu, Xiao-Jun Xie, Xinjie Ren, Xinsheng Gao, Jian-Quan Ni, Jun-Yuan Ji
Post-translational modification of histones plays essential roles in the transcriptional regulation of genes in eukaryotes. Methylation on basic residues of histones is regulated by histone methyltransferases and histone demethylases, and misregulation of these enzymes has been linked to a range of diseases such as cancer. Histone lysine demethylase 2 (KDM2) family proteins have been shown to either promote or suppress tumorigenesis in different human malignancies. However, the roles and regulation of KDM2 in development are poorly understood, and the exact roles of KDM2 in regulating demethylation remain controversial...
August 2014: Mechanisms of Development
https://www.readbyqxmd.com/read/24987060/molecular-pathways-deregulation-of-histone-h3-lysine-27-methylation-in-cancer-different-paths-same-destination
#10
REVIEW
Teresa Ezponda, Jonathan D Licht
Methylation of lysine 27 on histone H3 (H3K27me), a modification associated with gene repression, plays a critical role in regulating the expression of genes that determine the balance between cell differentiation and proliferation. Alteration of the level of this histone modification has emerged as a recurrent theme in many types of cancer, demonstrating that either excess or lack of H3K27 methylation can have oncogenic effects. Cancer genome sequencing has revealed the genetic basis of H3K27me deregulation, including mutations of the components of the H3K27 methyltransferase complex PRC2 and accessory proteins, and deletions and inactivating mutations of the H3K27 demethylase UTX in a wide variety of neoplasms...
October 1, 2014: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/24910128/an-rna-polymerase-ii-coupled-function-for-histone-h3k36-methylation-in-checkpoint-activation-and-dsb-repair
#11
Deepak Kumar Jha, Brian D Strahl
Histone modifications are major determinants of DNA double-strand break (DSB) response and repair. Here we elucidate a DSB repair function for transcription-coupled Set2 methylation at H3 lysine 36 (H3K36me). Cells devoid of Set2/H3K36me are hypersensitive to DNA-damaging agents and site-specific DSBs, fail to properly activate the DNA-damage checkpoint, and show genetic interactions with DSB-sensing and repair machinery. Set2/H3K36me3 is enriched at DSBs, and loss of Set2 results in altered chromatin architecture and inappropriate resection during G1 near break sites...
2014: Nature Communications
https://www.readbyqxmd.com/read/24281426/opposing-activities-of-drm-and-mes-4-tune-gene-expression-and-x-chromosome-repression-in-caenorhabditis-elegans-germ-cells
#12
Tomoko M Tabuchi, Andreas Rechtsteiner, Susan Strome, Kirsten A Hagstrom
During animal development, gene transcription is tuned to tissue-appropriate levels. Here we uncover antagonistic regulation of transcript levels in the germline of Caenorhabditis elegans hermaphrodites. The histone methyltransferase MES-4 (Maternal Effect Sterile-4) marks genes expressed in the germline with methylated lysine on histone H3 (H3K36me) and promotes their transcription; MES-4 also represses genes normally expressed in somatic cells and genes on the X chromosome. The DRM transcription factor complex, named for its Dp/E2F, Retinoblastoma-like, and MuvB subunits, affects germline gene expression and prevents excessive repression of X-chromosome genes...
January 2014: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/24055344/chromatin-remodelers-fine-tune-h3k36me-directed-deacetylation-of-neighbor-nucleosomes-by-rpd3s
#13
Chul-Hwan Lee, Jun Wu, Bing Li
Chromatin remodelers have been implicated in the regulation of histone-modifying complexes. However, the underlying mechanism remains poorly understood. The Rpd3S histone deacetylase complex is recruited by elongating RNA polymerase II to remove histone acetylation at coding regions in a manner that is dependent on methylation of lysine 36 on histone 3 (H3K36me), and Rpd3S prefers dinucleosomes. Here, we show that the binding of Rpd3S to dinucleosomes and its catalytic activity are sensitive to the length of nucleosomal linker in a nonlinear fashion...
October 24, 2013: Molecular Cell
https://www.readbyqxmd.com/read/24014454/set2-mediated-h3-lysine-36-methylation-regulation-of-transcription-elongation-and-implications-in-organismal-development
#14
REVIEW
Swaminathan Venkatesh, Jerry L Workman
Set2 is a RNA polymerase II (RNAPII) associated histone methyltransferase involved in the cotranscriptional methylation of the H3 K36 residue (H3K36me). It is responsible for multiple degrees of methylation (mono-, di-, and trimethylation), each of which has a distinct functional consequence. The extent of methylation and its genomic distribution is determined by different factors that coordinate 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...
September 2013: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/23656834/nucleosomal-dna-binding-drives-the-recognition-of-h3k36-methylated-nucleosomes-by-the-psip1-pwwp-domain
#15
Rick van Nuland, Frederik Ma van Schaik, Marieke Simonis, Sebastiaan van Heesch, Edwin Cuppen, Rolf Boelens, Ht Marc Timmers, Hugo van Ingen
BACKGROUND: Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. Here, we provide the structural and thermodynamic basis for the recognition of H3K36-methylated (H3K36me) nucleosomes by the PSIP1-PWWP domain, based on extensive mutational analysis, advanced nuclear magnetic resonance (NMR), and computational approaches...
2013: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/23508102/quantitative-dissection-and-stoichiometry-determination-of-the-human-set1-mll-histone-methyltransferase-complexes
#16
Rick van Nuland, Arne H Smits, Paschalina Pallaki, Pascal W T C Jansen, Michiel Vermeulen, H T Marc Timmers
Methylation of lysine 4 on histone H3 (H3K4) at promoters is tightly linked to transcriptional regulation in human cells. At least six different COMPASS-like multisubunit (SET1/MLL) complexes that contain methyltransferase activity for H3K4 have been described, but a comprehensive and quantitative analysis of these SET1/MLL complexes is lacking. We applied label-free quantitative mass spectrometry to determine the subunit composition and stoichiometry of the human SET1/MLL complexes. We identified both known and novel, unique and shared interactors and determined their distribution and stoichiometry over the different SET1/MLL complexes...
May 2013: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/23257840/resetting-chromatin-during-transcription-elongation
#17
REVIEW
Michaela Smolle, Jerry L Workman, Swaminathan Venkatesh
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...
January 2013: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/23124068/mechanism-for-epigenetic-variegation-of-gene-expression-at-yeast-telomeric-heterochromatin
#18
Tasuku Kitada, Benjamin G Kuryan, Nancy Nga Huynh Tran, Chunying Song, Yong Xue, Michael Carey, Michael Grunstein
Yeast contains heterochromatin at telomeres and the silent mating-type loci (HML/HMR). Genes positioned within the telomeric heterochromatin of Saccharomyces cerevisiae switch stochastically between epigenetically bistable ON and OFF expression states. Important aspects of the mechanism of variegated gene expression, including the chromatin structure of the natural ON state and the mechanism by which it is maintained, are unknown. To address this issue, we developed approaches to select cells in the ON and OFF states...
November 1, 2012: Genes & Development
https://www.readbyqxmd.com/read/23104054/phf19-links-methylated-lys36-of-histone-h3-to-regulation-of-polycomb-activity
#19
Cecilia Ballaré, Martin Lange, Audrone Lapinaite, Gloria Mas Martin, Lluis Morey, Gloria Pascual, Robert Liefke, Bernd Simon, Yang Shi, Or Gozani, Teresa Carlomagno, Salvador Aznar Benitah, Luciano Di Croce
Polycomb-group proteins are transcriptional repressors with essential roles in embryonic development. Polycomb repressive complex 2 (PRC2) contains the methyltransferase activity for Lys27. However, the role of other histone modifications in regulating PRC2 activity is just beginning to be understood. Here we show that direct recognition of methylated histone H3 Lys36 (H3K36me), a mark associated with activation, by the PRC2 subunit Phf19 is required for the full enzymatic activity of the PRC2 complex. Using NMR spectroscopy, we provide structural evidence for this interaction...
December 2012: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/22962860/integrative-analysis-of-chromatin-states-in-arabidopsis-identified-potential-regulatory-mechanisms-for-natural-antisense-transcript-production
#20
Chongyuan Luo, David J Sidote, Yi Zhang, Randall A Kerstetter, Todd P Michael, Eric Lam
Genome-wide analyses of epigenomic and transcriptomic profiles provide extensive resources for discovering epigenetic regulatory mechanisms. However, the construction of functionally relevant hypotheses from correlative patterns and the rigorous testing of these hypotheses may be challenging. We combined bioinformatics-driven hypothesis building with mutant analyses to identify potential epigenetic mechanisms using the model plant Arabidopsis thaliana. Genome-wide maps of nine histone modifications produced by ChIP-seq were used together with a strand-specific RNA-seq dataset to profile the epigenome and transcriptome of Arabidopsis...
January 2013: Plant Journal: for Cell and Molecular Biology
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