keyword
MENU ▼
Read by QxMD icon Read
search

H3K36me3

keyword
https://www.readbyqxmd.com/read/27892458/modulation-of-mrna-and-lncrna-expression-dynamics-by-the-set2-rpd3s-pathway
#1
Ji Hyun Kim, Bo Bae Lee, Young Mi Oh, Chenchen Zhu, Lars M Steinmetz, Yookyeong Lee, Wan Kyu Kim, Sung Bae Lee, Stephen Buratowski, TaeSoo Kim
H3K36 methylation by Set2 targets Rpd3S histone deacetylase to transcribed regions of mRNA genes, repressing internal cryptic promoters and slowing elongation. Here we explore the function of this pathway by analysing transcription in yeast undergoing a series of carbon source shifts. Approximately 80 mRNA genes show increased induction upon SET2 deletion. A majority of these promoters have overlapping lncRNA transcription that targets H3K36me3 and deacetylation by Rpd3S to the mRNA promoter. We previously reported a similar mechanism for H3K4me2-mediated repression via recruitment of the Set3C histone deacetylase...
November 28, 2016: Nature Communications
https://www.readbyqxmd.com/read/27806100/transcriptional-activation-of-pericentromeric-satellite-repeats-and-disruption-of-centromeric-clustering-upon-proteasome-inhibition
#2
Theona Natisvili, Cihangir Yandim, Raquel Silva, Giulia Emanuelli, Felix Krueger, Sathiji Nageshwaran, Richard Festenstein
Heterochromatinisation of pericentromeres, which in mice consist of arrays of major satellite repeats, are important for centromere formation and maintenance of genome stability. The dysregulation of this process has been linked to genomic stress and various cancers. Here we show in mice that the proteasome binds to major satellite repeats and proteasome inhibition by MG132 results in their transcriptional de-repression; this de-repression is independent of cell-cycle perturbation. The transcriptional activation of major satellite repeats upon proteasome inhibition is accompanied by delocalisation of heterochromatin protein 1 alpha (HP1α) from chromocentres, without detectable change in the levels of histone H3K9me3, H3K4me3, H3K36me3 and H3 acetylation on the major satellite repeats...
2016: PloS One
https://www.readbyqxmd.com/read/27793787/dynamic-and-antagonistic-allele-specific-epigenetic-modifications-controlling-the-expression-of-imprinted-genes-in-maize-endosperm
#3
Xiaomei Dong, Mei Zhang, Jian Chen, Lizeng Peng, Nan Zhang, Xin Wang, Jinsheng Lai
Genomic imprinting is often associated with allele-specific epigenetic modifications. Although there are many reports suggesting the potential roles of DNA methylation and H3K27me3 in regulation of genomic imprinting, research about the contributions of allele-specific active histone modifications to imprinting has been highly limited in plant. Here we reported the identification of 337 high-stringency allele-specific H3K4me3 and H3K36me3 peaks in maize endosperm. Paternally preferred H3K4me3 and H3K36me3 peaks mostly co-localized at paternally expressed genes (PEGs), while endosperm-specific maternally expressed genes (endo-MEGs) were associated with maternally preferred H3K4me3 and H3K36me3 peaks...
October 25, 2016: Molecular Plant
https://www.readbyqxmd.com/read/27791097/stable-caenorhabditis-elegans-chromatin-domains-separate-broadly-expressed-and-developmentally-regulated-genes
#4
Kenneth J Evans, Ni Huang, Przemyslaw Stempor, Michael A Chesney, Thomas A Down, Julie Ahringer
Eukaryotic genomes are organized into domains of differing structure and activity. There is evidence that the domain organization of the genome regulates its activity, yet our understanding of domain properties and the factors that influence their formation is poor. Here, we use chromatin state analyses in early embryos and third-larval stage (L3) animals to investigate genome domain organization and its regulation in Caenorhabditis elegans At both stages we find that the genome is organized into extended chromatin domains of high or low gene activity defined by different subsets of states, and enriched for H3K36me3 or H3K27me3, respectively...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27777628/high-throughput-assessment-of-context-dependent-effects-of-chromatin-proteins
#5
Laura Brueckner, Joris van Arensbergen, Waseem Akhtar, Ludo Pagie, Bas van Steensel
BACKGROUND: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein but has also been linked to transcriptional activation...
2016: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/27765800/sex-specific-associations-between-one-carbon-metabolism-indices-and-posttranslational-histone-modifications-in-arsenic-exposed-bangladeshi-adults
#6
Caitlin G Howe, Xinhua Liu, Megan N Hall, Vesna Ilievski, Marie A Caudill, Olga Malysheva, Angela M Lomax-Luu, Faruque Parvez, Abu B Siddique, Hasan Shahriar, Mohammad N Uddin, Tariqul Islam, Joseph H Graziano, Max Costa, Mary V Gamble
BACKGROUND: Posttranslational histone modifications (PTHMs) are altered by arsenic, an environmental carcinogen. PTHMs are also influenced by nutritional methyl donors involved in one-carbon metabolism (OCM), which may protect against epigenetic dysregulation. METHODS: We measured global levels of three PTHMs, which are dysregulated in cancers (H3K36me2, H3K36me3, H3K79me2), in peripheral blood mononuclear cells (PBMCs) from 324 participants enrolled in the Folic Acid and Creatine Trial, a randomized trial in arsenic-exposed Bangladeshi adults...
October 20, 2016: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/27716056/histone-modifications-facilitate-the-coexpression-of-bidirectional-promoters-in-rice
#7
Yuan Fang, Lei Wang, Ximeng Wang, Qi You, Xiucai Pan, Jin Xiao, Xiu-E Wang, Yufeng Wu, Zhen Su, Wenli Zhang
BACKGROUND: Bidirectional gene pairs are highly abundant and mostly co-regulated in eukaryotic genomes. The structural features of bidirectional promoters (BDPs) have been well studied in yeast, humans and plants. However, the underlying mechanisms responsible for the coexpression of BDPs remain understudied, especially in plants. RESULTS: Here, we characterized chromatin features associated with rice BDPs. Several unique chromatin features were present in rice BDPs but were missing from unidirectional promoters (UDPs), including overrepresented active histone marks, canonical nucleosomes and underrepresented H3K27me3...
September 30, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27713408/mutually-exclusive-sense-antisense-transcription-at-flc-facilitates-environmentally-induced-gene-repression
#8
Stefanie Rosa, Susan Duncan, Caroline Dean
Antisense transcription through genic regions is pervasive in most genomes; however, its functional significance is still unclear. We are studying the role of antisense transcripts (COOLAIR) in the cold-induced, epigenetic silencing of Arabidopsis FLOWERING LOCUS C (FLC), a regulator of the transition to reproduction. Here we use single-molecule RNA FISH to address the mechanistic relationship of FLC and COOLAIR transcription at the cellular level. We demonstrate that while sense and antisense transcripts can co-occur in the same cell they are mutually exclusive at individual loci...
October 7, 2016: Nature Communications
https://www.readbyqxmd.com/read/27669212/prenatal-dexamethasone-and-postnatal-high-fat-diet-decrease-interferon-gamma-production-through-an-age-dependent-histone-modification-in-male-sprague-dawley-rats
#9
Hong-Ren Yu, You-Lin Tain, Jiunn-Ming Sheen, Mao-Meng Tiao, Chih-Cheng Chen, Ho-Chang Kuo, Pi-Lien Hung, Kai-Sheng Hsieh, Li-Tung Huang
Overexposure to prenatal glucocorticoid (GC) disturbs hypothalamic-pituitary-adrenocortical axis-associated neuroendocrine metabolism and susceptibility to metabolic syndrome. A high-fat (HF) diet is a major environmental factor that can cause metabolic syndrome. We aimed to investigate whether prenatal GC plus a postnatal HF diet could alter immune programming in rat offspring. Pregnant Sprague-Dawley rats were given intraperitoneal injections of dexamethasone or saline at 14-21 days of gestation. Male offspring were then divided into four groups: vehicle, prenatal dexamethasone exposure, postnatal HF diet (VHF), and prenatal dexamethasone exposure plus a postnatal HF diet (DHF)...
2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27660665/neonatal-monocytes-exhibit-a-unique-histone-modification-landscape
#10
Jennifer R Bermick, Nathalie J Lambrecht, Aaron D denDekker, Steven L Kunkel, Nicholas W Lukacs, Cory M Hogaboam, Matthew A Schaller
BACKGROUND: Neonates have dampened expression of pro-inflammatory cytokines and difficulty clearing pathogens. This makes them uniquely susceptible to infections, but the factors regulating neonatal-specific immune responses are poorly understood. Epigenetics, including histone modifications, can activate or silence gene transcription by modulating chromatin structure and stability without affecting the DNA sequence itself and are potentially modifiable. Histone modifications are known to regulate immune cell differentiation and function in adults but have not been well studied in neonates...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27638467/structural-studies-on-mrg701-chromodomain-reveal-a-novel-dimerization-interface-of-mrg-proteins-in-green-plants
#11
Yanchao Liu, Hong Wu, Yu Yu, Ying Huang
MRG proteins are conserved during evolution in fungi, flies, mammals and plants, and they can exhibit diversified functions. The animal MRGs were found to form various complexes to activate gene expression. Plant MRG1/2 and MRG702 were reported to be involved in the regulation of flowering time via binding to H3K36me3-marked flowering genes. Herein, we determined the crystal structure of MRG701 chromodomain (MRG701(CD)). MRG701(CD) forms a novel dimerization fold both in crystal and in solution. Moreover, we found that the dimerization of MRG chromodomains is conserved in green plants...
November 2016: Protein & Cell
https://www.readbyqxmd.com/read/27614073/spop-containing-complex-regulates-setd2-stability-and-h3k36me3-coupled-alternative-splicing
#12
Kun Zhu, Pin-Ji Lei, Lin-Gao Ju, Xiang Wang, Kai Huang, Bo Yang, Changwei Shao, Yuan Zhu, Gang Wei, Xiang-Dong Fu, Lianyun Li, Min Wu
Trimethylation of histone H3K36 is a chromatin mark associated with active gene expression, which has been implicated in coupling transcription with mRNA splicing and DNA damage response. SETD2 is a major H3K36 trimethyltransferase, which has been implicated as a tumor suppressor in mammals. Here, we report the regulation of SETD2 protein stability by the proteasome system, and the identification of SPOP, a key subunit of the CUL3 ubiquitin E3 ligase complex, as a SETD2-interacting protein. We demonstrate that SPOP is critically involved in SETD2 stability control and that the SPOP/CUL3 complex is responsible for SETD2 polyubiquitination both in vivo and in vitro ChIP-Seq analysis and biochemical experiments demonstrate that modulation of SPOP expression confers differential H3K36me3 on SETD2 target genes, and induce H3K36me3-coupled alternative splicing events...
September 9, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27573846/mrg15-is-required-for-pre-mrna-splicing-and-spermatogenesis
#13
Naoki Iwamori, Kaoru Tominaga, Tetsuya Sato, Kevin Riehle, Tokuko Iwamori, Yasuyuki Ohkawa, Cristian Coarfa, Etsuro Ono, Martin M Matzuk
Splicing can be epigenetically regulated and involved in cellular differentiation in somatic cells, but the interplay of epigenetic factors and the splicing machinery during spermatogenesis remains unclear. To study these interactions in vivo, we generated a germline deletion of MORF-related gene on chromosome 15 (MRG15), a multifunctional chromatin organizer that binds to methylated histone H3 lysine 36 (H3K36) in introns of transcriptionally active genes and has been implicated in regulation of histone acetylation, homology-directed DNA repair, and alternative splicing in somatic cells...
September 13, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27528705/a-new-chromatin-cytoskeleton-link-in-cancer
#14
Amato J Giaccia
The set domain containing 2 (SETD2) histone methyltransferase, located at 3p2, specifically trimethylates lysine 36 of histone H3 (H3K36me3). H3K36me3 is an active mark involved in transcriptional elongation and RNA processing and a key regulator of DNA repair. In fact, SETD2 is the only methyltransferase that "writes" the H3K36me3 mark. Recent results from Park and colleagues have found a new role for SETD2 in the methylation of K40 of α-tubulin. Loss of SETD2 abolishes methylation of K40 of α-tubulin and results in a dysfunctional mitotic spindle and abnormalities in cytokinesis...
December 2016: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/27528607/structure-function-analysis-of-recurrent-mutations-in-setd2-protein-reveals-a-critical-and-conserved-role-for-a-set-domain-residue-in-maintaining-protein-stability-and-histone-h3-lys-36-trimethylation
#15
Kathryn E Hacker, Catherine C Fahey, Stephen A Shinsky, Yun-Chen J Chiang, Julia V DiFiore, Deepak Kumar Jha, Andy H Vo, Jordan A Shavit, Ian J Davis, Brian D Strahl, W Kimryn Rathmell
The yeast Set2 histone methyltransferase is a critical enzyme that plays a number of key roles in gene transcription and DNA repair. Recently, the human homologue, SETD2, was found to be recurrently mutated in a significant percentage of renal cell carcinomas, raising the possibility that the activity of SETD2 is tumor-suppressive. Using budding yeast and human cell line model systems, we examined the functional significance of two evolutionarily conserved residues in SETD2 that are recurrently mutated in human cancers...
September 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27518565/dual-chromatin-and-cytoskeletal-remodeling-by-setd2
#16
In Young Park, Reid T Powell, Durga Nand Tripathi, Ruhee Dere, Thai H Ho, T Lynne Blasius, Yun-Chen Chiang, Ian J Davis, Catherine C Fahey, Kathryn E Hacker, Kristen J Verhey, Mark T Bedford, Eric Jonasch, W Kimryn Rathmell, Cheryl Lyn Walker
Posttranslational modifications (PTMs) of tubulin specify microtubules for specialized cellular functions and comprise what is termed a "tubulin code." PTMs of histones comprise an analogous "histone code," although the "readers, writers, and erasers" of the cytoskeleton and epigenome have heretofore been distinct. We show that methylation is a PTM of dynamic microtubules and that the histone methyltransferase SET-domain-containing 2 (SETD2), which is responsible for H3 lysine 36 trimethylation (H3K36me3) of histones, also methylates α-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules...
August 11, 2016: Cell
https://www.readbyqxmd.com/read/27496019/elucidating-combinatorial-chromatin-states-at-single-nucleosome-resolution
#17
Ronen Sadeh, Roee Launer-Wachs, Hava Wandel, Ayelet Rahat, Nir Friedman
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP-seq is an ensemble measurement reporting the average occupancy of individual marks in a cell population. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on correlation between the genomic distributions of individual marks...
September 15, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27476967/dnmt3a-and-dnmt3b-associate-with-enhancers-to-regulate-human-epidermal-stem-cell-homeostasis
#18
Lorenzo Rinaldi, Debayan Datta, Judit Serrat, Lluis Morey, Guiomar Solanas, Alexandra Avgustinova, Enrique Blanco, José Ignacio Pons, David Matallanas, Alex Von Kriegsheim, Luciano Di Croce, Salvador Aznar Benitah
The genome-wide localization and function of endogenous Dnmt3a and Dnmt3b in adult stem cells are unknown. Here, we show that in human epidermal stem cells, the two proteins bind in a histone H3K36me3-dependent manner to the most active enhancers and are required to produce their associated enhancer RNAs. Both proteins prefer super-enhancers associated to genes that either define the ectodermal lineage or establish the stem cell and differentiated states. However, Dnmt3a and Dnmt3b differ in their mechanisms of enhancer regulation: Dnmt3a associates with p63 to maintain high levels of DNA hydroxymethylation at the center of enhancers in a Tet2-dependent manner, whereas Dnmt3b promotes DNA methylation along the body of the enhancer...
October 6, 2016: Cell Stem Cell
https://www.readbyqxmd.com/read/27364684/a-high-resolution-transcriptome-map-of-cell-cycle-reveals-novel-connections-between-periodic-genes-and-cancer
#19
Daniel Dominguez, Yi-Hsuan Tsai, Nicholas Gomez, Deepak Kumar Jha, Ian Davis, Zefeng Wang
Progression through the cell cycle is largely dependent on waves of periodic gene expression, and the regulatory networks for these transcriptome dynamics have emerged as critical points of vulnerability in various aspects of tumor biology. Through RNA-sequencing of human cells during two continuous cell cycles (>2.3 billion paired reads), we identified over 1 000 mRNAs, non-coding RNAs and pseudogenes with periodic expression. Periodic transcripts are enriched in functions related to DNA metabolism, mitosis, and DNA damage response, indicating these genes likely represent putative cell cycle regulators...
August 2016: Cell Research
https://www.readbyqxmd.com/read/27362481/the-meiotic-recombination-activator-prdm9-trimethylates-both-h3k36-and-h3k4-at-recombination-hotspots-in-vivo
#20
Natalie R Powers, Emil D Parvanov, Christopher L Baker, Michael Walker, Petko M Petkov, Kenneth Paigen
In many mammals, including humans and mice, the zinc finger histone methyltransferase PRDM9 performs the first step in meiotic recombination by specifying the locations of hotspots, the sites of genetic recombination. PRDM9 binds to DNA at hotspots through its zinc finger domain and activates recombination by trimethylating histone H3K4 on adjacent nucleosomes through its PR/SET domain. Recently, the isolated PR/SET domain of PRDM9 was shown capable of also trimethylating H3K36 in vitro, raising the question of whether this reaction occurs in vivo during meiosis, and if so, what its function might be...
June 2016: PLoS Genetics
keyword
keyword
66010
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"