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https://www.readbyqxmd.com/read/29027902/independent-manipulation-of-histone-h3-modifications-in-individual-nucleosomes-reveals-the-contributions-of-sister-histones-to-transcription
#1
Zhen Zhou, Yu-Ting Liu, Li Ma, Ting Gong, Yanan Hu, Hong-Tao Li, Chen Cai, Ling-Li Zhang, Gang Wei, Jin-Qiu Zhou
Histone tail modifications can greatly influence chromatin-associated processes. Asymmetrically modified nucleosomes exist in multiple cell types; however, whether modifications on both sister histones contribute equally to chromatin dynamics remains elusive. Here, we devised a bivalent nucleosome system that allowed for the constitutive assembly of asymmetrically modified sister histone H3s in nucleosomes in Saccharomyces cerevisiae. The sister H3K36 methylations independently affected cryptic transcription in gene coding regions, whereas sister H3K79 methylation had cooperative effects on gene silencing near telomeres...
October 13, 2017: ELife
https://www.readbyqxmd.com/read/29027175/multiplexed-chip-seq-using-direct-nucleosome-barcoding-a-tool-for-high-throughput-chromatin-analysis
#2
Christophe D Chabbert, Sophie H Adjalley, Lars M Steinmetz, Vicent Pelechano
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027174/mobe-chip-probing-cell-type-specific-binding-through-large-scale-chromatin-immunoprecipitation
#3
Shenqi Wang, On Sun Lau
In multicellular organisms, the initiation and maintenance of specific cell types often require the activity of cell type-specific transcriptional regulators. Understanding their roles in gene regulation is crucial but probing their DNA targets in vivo, especially in a genome-wide manner, remains a technical challenge with their limited expression. To improve the sensitivity of chromatin immunoprecipitation (ChIP) for detecting the cell type-specific signals, we have developed the Maximized Objects for Better Enrichment (MOBE)-ChIP, where ChIP is performed at a substantially larger experimental scale and under low background conditions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027170/chromatin-immunoprecipitation-of-skeletal-muscle-tissue
#4
Amarjit Saini, Carl Johan Sundberg
Chromatin immunoprecipitation (ChIP) is an invaluable method for studying interactions between histone proteins and genomic DNA regions and transcriptional regulation using antibodies to enrich genomic regions associated with these epitopes. Either to monitor the presence of histones with post-translational modifications at specific genomic locations or to measure transcription factor interactions with a candidate target gene, protein-DNA complexes are most commonly crosslinked using formaldehyde, which stabilizes these transient interactions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027165/chromatin-rna-immunoprecipitation-chrip
#5
Tanmoy Mondal, Santhilal Subhash, Chandrasekhar Kanduri
Researchers have recently had a growing interest in understanding the functional role of long noncoding RNAs (lncRNAs) in chromatin organization. Accumulated evidence suggests lncRNAs could act as interphase molecules between chromatin and chromatin remodelers to define the epigenetic code. However, it is not clear how lncRNAs target chromatin remodelers to specific chromosomal regions in order to establish a functionally distinct epigenetic state of chromatin. We developed and optimized chromatin RNA immunoprecipitation (ChRIP) technology to characterize the lncRNAs associated with active and inactive chromatin compartments...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29026447/epigenome-alterations-in-aortic-valve-stenosis-and-its-related-left-ventricular-hypertrophy
#6
REVIEW
Igor Gošev, Martina Zeljko, Željko Đurić, Ivana Nikolić, Milorad Gošev, Sanja Ivčević, Dino Bešić, Zoran Legčević, Frane Paić
Aortic valve stenosis is the most common cardiac valve disease, and with current trends in the population demographics, its prevalence is likely to rise, thus posing a major health and economic burden facing the worldwide societies. Over the past decade, it has become more than clear that our traditional genetic views do not sufficiently explain the well-known link between AS, proatherogenic risk factors, flow-induced mechanical forces, and disease-prone environmental influences. Recent breakthroughs in the field of epigenetics offer us a new perspective on gene regulation, which has broadened our perspective on etiology of aortic stenosis and other aortic valve diseases...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29025910/protein-arginine-methyltransferase-6-controls-erythroid-gene-expression-and-differentiation-of-human-cd34-progenitor-cells
#7
Stefanie C Herkt, Olga N Kuvardina, Julia Herglotz, Lucas Schneider, Annekarin Meyer, Claudia Pommerenke, Gabriela Salinas-Riester, Erhard Seifried, Halvard Bonig, Jörn Lausen
Hematopoietic differentiation is driven by transcription factors, which orchestrate a fine tuned transcriptional network. At bipotential branching points lineage decisions are made, where key transcription factors initiate cell type specific gene expression programs. These programs are stabilized by the epigenetic activity of recruited chromatin modifying cofactors. An example gives the association of the transcription factor RUNX1 with the protein arginine methyltransferase 6 (PRMT6) at the megakaryocytic/erythroid bifurcation...
October 12, 2017: Haematologica
https://www.readbyqxmd.com/read/29025701/distribution-of-h3k27me3-h3k9me3-and-h3k4me3-along-autophagy-related-genes-highly-expressed-in-starved-zebrafish-myotubes
#8
Peggy R Biga, Mary N Latimer, Jacob Michael Froehlich, Jean-Charles Gabillard, Iban Seiliez
The zebrafish (Danio rerio) remains the teleost fish of choice for biological investigations due to the vast array of molecular tools and resources available. To better understand the epigenetic regulation of autophagy, we utilized a primary myotube culture system generated from isolated myogenic precursor cells (MPCs) from zebrafish grown under starvation conditions using a media devoid of serum and amino acids. Here, we report starvation-induced regulation of several autophagy-related genes (atg) expression and profile the distribution of H3K27me3, H3K9me3, and H3K4me3 marks along lc3b, atg4b and p62/sqstm1 loci...
October 12, 2017: Biology Open
https://www.readbyqxmd.com/read/29025389/chromatin-states-responsible-for-the-regulation-of-differentially-expressed-genes-under-60-co-%C3%AE-ray-radiation-in-rice
#9
Xiucai Pan, Yuan Fang, Xueming Yang, Dongyang Zheng, Lifen Chen, Lei Wang, Jin Xiao, Xiu-E Wang, Kai Wang, Zhukuan Cheng, Hengxiu Yu, Wenli Zhang
BACKGROUND: The role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response. RESULTS: In this study, we used RNA-seq and ChIP-seq to show that differentially expressed genes (DEGs), in response to ionizing radiation (IR), might be involved in different pathways responsible for the DNA damage response...
October 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29025014/reactive-oxygen-species-and-protein-modifications-in-spermatozoa
#10
Cristian O'Flaherty, David Matsushita Fournier
Cellular response to reactive oxygen species (ROS) includes both reversible redox signaling and irreversible non-enzymatic reactions which depend on the nature and concentration of the ROS involved. Changes in thiol/disulfide pairs affect protein conformation, enzymatic activity, ligand binding, and protein-protein interactions. During spermatogenesis and epididymal maturation, there are ROS-dependent modifications of the sperm chromatin and flagellar proteins.The spermatozoon is regulated by redox mechanisms to acquire fertilizing ability...
September 13, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29023412/post-translational-modification-of-human-histone-by-wide-tolerance-of-acetylation
#11
Cuiling Li, Han-Pil Choi, Xiaoyue Wang, Fei Wu, Xinjun Chen, Xin Lü, Ruirui Jing, Hoon Ryu, Xingyuan Wang, Kazem M Azadzoi, Jing-Hua Yang
Histone acetylation adds an acetyl group on the lysine residue commonly found within the N-terminal tail protruding from the histone core of the nucleosome, and is important for chromosome structure and function in gene transcription and chromatin remodeling. Acetylation may also occur on other residues additional to lysine, but have not been thoroughly investigated at the proteomics level. Here we report a wide tolerance acetylation study mimicking the addition of 42 ± 0.5 Da delta mass modification on undefined amino acid residues of histones by shotgun proteomics using liquid chromatography-tandem mass spectrometry...
October 12, 2017: Cells
https://www.readbyqxmd.com/read/29022873/adolescent-thc-exposure-in-female-rats-leads-to-cognitive-deficits-through-a-mechanism-involving-chromatin-modifications-in-the-prefrontal-cortex
#12
Pamela Prini, Franceso Rusconi, Erica Zamberletti, Marina Gabaglio, Federica Penna, Mauro Fasano, Elena Battaglioli, Daniela Parolaro, Tiziana Rubino
BACKGROUND: Increasing cannabis consumption among adolescents, studies that link its early use with mental illnesses, and the political debate on cannabis legalization together call for an urgent need to study molecular underpinnings of adolescent brain vulnerability. The emerging role of epigenetic mechanisms in psychiatric diseases led us to hypothesize that epigenetic alterations could play a role in causes and subsequent development of the depressive/psychotic-like phenotype induced by adolescent, but not adult, Δ9-tetrahydrocannabinol (THC) exposure in female rats...
October 12, 2017: Journal of Psychiatry & Neuroscience: JPN
https://www.readbyqxmd.com/read/29021135/histone-acetyltransferase-kat6a-upregulates-pi3k-akt-signaling-through-trim24-binding
#13
Deguan Lv, Feng Jia, Yanli Hou, Youzhou Sang, Angel A Alvarez, Weiwei Zhang, Wei-Qiang Gao, Bo Hu, Shi-Yuan Cheng, Jianwei Ge, Yanxin Li, Haizhong Feng
Lysine acetyltransferase KAT6A is a chromatin regulator that contributes to histone modification and cancer, but the basis of its actions are not well understood. Here we identify a KAT6A signaling pathway that facilitates glioblastoma (GBM) where it is upregulated. KAT6A expression was associated with GBM patient survival. KAT6A silencing suppressed cell proliferation, cell migration, colony formation and tumor development in an orthotopic mouse xenograft model system. Mechanistic investigations demonstrated that KAT6A acetylates lysine 23 of histone H3 (H3K23), which recruits the nuclear receptor binding protein TRIM24 to activate PIK3CA transcription, thereby enhancing PI3K/AKT signaling and tumorigenesis...
October 11, 2017: Cancer Research
https://www.readbyqxmd.com/read/29020631/covalent-modifications-of-histone-h3k9-promote-binding-of-chd3
#14
Adam H Tencer, Khan L Cox, Luo Di, Joseph B Bridgers, Jie Lyu, Xiaodong Wang, Jennifer K Sims, Tyler M Weaver, Hillary F Allen, Yi Zhang, Jovylyn Gatchalian, Michael A Darcy, Matthew D Gibson, Jinzen Ikebe, Wei Li, Paul A Wade, Jeffrey J Hayes, Brian D Strahl, Hidetoshi Kono, Michael G Poirier, Catherine A Musselman, Tatiana G Kutateladze
Chromatin remodeling is required for genome function and is facilitated by ATP-dependent complexes, such as nucleosome remodeling and deacetylase (NuRD). Among its core components is the chromodomain helicase DNA binding protein 3 (CHD3) whose functional significance is not well established. Here, we show that CHD3 co-localizes with the other NuRD subunits, including HDAC1, near the H3K9ac-enriched promoters of the NuRD target genes. The tandem PHD fingers of CHD3 bind histone H3 tails and posttranslational modifications that increase hydrophobicity of H3K9-methylation or acetylation (H3K9me3 or H3K9ac)-enhance this interaction...
October 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/29017914/the-roles-of-class-i-histone-deacetylases-hdacs-in-memory-learning-and-executive-cognitive-functions-a-review
#15
REVIEW
Claudia Schmauss
Coordinated changes in gene expression are critical for synaptic plasticity supporting learning, memory, and optimal cognitive task performance. These gene expression changes are not only mediated by signaling pathways that activate transcription factors, but also by chromatin modifications that influence the accessibility of the transcriptional machinery to specific genomic regions. During the past decade, evidence accumulated that alterations in chromatin-based epigenetic regulation of gene expression are linked to cognitive dysfunctions in the ageing or neurodegenerating brain as well as to cognitive dysfunctions resulting from chronic stress exposure...
October 7, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28993008/piwi-family-emerging-as-a-decisive-factor-of-cell-fate-an-overview
#16
REVIEW
Murugavel Ponnusamy, Kao-Wen Yan, Cui-Yun Liu, Pei-Feng Li, Kun Wang
PIWI proteins and piRNAs primarily functions as a safeguard of germline cells by activating epigenetic regulations, silencing transposons and maintaining chromatin structure. Increasing evidences reveal that PIWI proteins and piRNAs have broader functions in many vital biological processes including cell proliferation, differentiation and survival. They have been recognized as a crucial factor in the cellular events due their role in controlling mRNA expression, turnover and translation. PIWIs, with or without its partner non-coding RNA (piRNA), govern the expression and activity of many transcription factors and signaling molecules by mastering their expression and/or post-translational modifications by directly interacting with them...
October 2, 2017: European Journal of Cell Biology
https://www.readbyqxmd.com/read/28992434/targeting-epigenetics-in-cancer
#17
Richard L Bennett, Jonathan D Licht
Alterations of genes regulating epigenetic processes are frequently found as cancer drivers and may cause widespread alterations of DNA methylation, histone modification patterns, or chromatin structure that disrupt normal patterns of gene expression. Because of the inherent reversibility of epigenetic changes, inhibitors targeting these processes are promising anticancer strategies. Small molecules targeting epigenetic regulators have been developed recently, and clinical trials of these agents are under way for hematologic malignancies and solid tumors...
October 6, 2017: Annual Review of Pharmacology and Toxicology
https://www.readbyqxmd.com/read/28991910/loss-of-xist-rna-from-the-inactive-x-during-b-cell-development-is-restored-in-a-dynamic-yy1-dependent-two-step-process-in-activated-b-cells
#18
Camille M Syrett, Vishal Sindhava, Suchita Hodawadekar, Arpita Myles, Guanxiang Liang, Yue Zhang, Satabdi Nandi, Michael Cancro, Michael Atchison, Montserrat C Anguera
X-chromosome inactivation (XCI) in female lymphocytes is uniquely regulated, as the inactive X (Xi) chromosome lacks localized Xist RNA and heterochromatin modifications. Epigenetic profiling reveals that Xist RNA is lost from the Xi at the pro-B cell stage and that additional heterochromatic modifications are gradually lost during B cell development. Activation of mature B cells restores Xist RNA and heterochromatin to the Xi in a dynamic two-step process that differs in timing and pattern, depending on the method of B cell stimulation...
October 9, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28991411/structural-insights-into-the-nuclear-import-of-the-histone-acetyltransferase-mof-by-importin-%C3%AE-1
#19
Weili Zheng, Rui Wang, Xi Liu, Siyu Tian, Benqiang Yao, Ang Chen, Shikai Jin, Yong Li
The histone acetyltransferase MOF (males-absent-on-the-first) acetylates the histone H4, a modification important for many biological processes, including chromatin organization, transcriptional regulation, DNA replication, recombination and repair, as well as autophagy. Depletion of MOF induces serious consequences due to the reduction of histone acetylation, such as nuclear morphological defects and cancer. Despite the critical roles of MOF in the nucleus, the structural or functional mechanisms of the nucleocytoplasmic transport of MOF remain elusive...
October 9, 2017: Traffic
https://www.readbyqxmd.com/read/28986581/nucleosome-stability-measured-in-situ-by-automated-quantitative-imaging
#20
László Imre, Zoltán Simándi, Attila Horváth, György Fenyőfalvi, Péter Nánási, Erfaneh Firouzi Niaki, Éva Hegedüs, Zsolt Bacsó, Urbain Weyemi, Rebekka Mauser, Juan Ausio, Albert Jeltsch, William Bonner, László Nagy, Hiroshi Kimura, Gábor Szabó
Current approaches have limitations in providing insight into the functional properties of particular nucleosomes in their native molecular environment. Here we describe a simple and powerful method involving elution of histones using intercalators or salt, to assess stability features dependent on DNA superhelicity and relying mainly on electrostatic interactions, respectively, and measurement of the fraction of histones remaining chromatin-bound in the individual nuclei using histone type- or posttranslational modification- (PTM-) specific antibodies and automated, quantitative imaging...
October 6, 2017: Scientific Reports
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