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chromatin remodeling

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https://www.readbyqxmd.com/read/28213686/the-iswi-remodeler-in-plants-protein-complexes-biochemical-functions-and-developmental-roles
#1
REVIEW
Dongjie Li, Jie Liu, Wu Liu, Guang Li, Zhongnan Yang, Peng Qin, Lin Xu
Imitation Switch (ISWI) is a member of the ATP-dependent chromatin remodeling factor family, whose members move or restructure nucleosomes using energy derived from ATP hydrolysis. ISWI proteins are conserved in eukaryotes and usually form complexes with DDT (DNA-binding homeobox and different transcription factors)-domain proteins. Here, we review recent research on ISWI in the model plant Arabidopsis thaliana (AtISWI). AtISWI forms complexes with AtDDT-domain proteins, many of which have domain structures that differ from those of DDT-domain proteins in yeast and animals...
February 17, 2017: Chromosoma
https://www.readbyqxmd.com/read/28212646/linking-long-non-coding-rnas-and-swi-snf-complexes-to-chromatin-remodeling-in-cancer
#2
REVIEW
Yanyan Tang, Jinpeng Wang, Yu Lian, Chunmei Fan, Ping Zhang, Yingfen Wu, Xiayu Li, Fang Xiong, Xiaoling Li, Guiyuan Li, Wei Xiong, Zhaoyang Zeng
Chromatin remodeling controls gene expression and signaling pathway activation, and aberrant chromatin structure and gene dysregulation are primary characteristics of human cancer progression. Recent reports have shown that long non-coding RNAs (lncRNAs) are tightly associated with chromatin remodeling. In this review, we focused on important chromatin remodelers called the switching defective/sucrose nonfermenting (SWI/SNF) complexes, which use the energy of ATP hydrolysis to control gene transcription by altering chromatin structure...
February 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28212305/epigenetic-landscape-during-coronavirus-infection
#3
Alexandra Schäfer, Ralph S Baric
Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus-host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype...
February 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28212175/advances-in-epilepsy-gene-discovery-and-implications-for-epilepsy-diagnosis-and-treatment
#4
Joseph D Symonds, Sameer M Zuberi, Michael R Johnson
PURPOSE OF REVIEW: Epilepsy genetics is shifting from the academic pursuit of gene discovery to a clinical discipline based on molecular diagnosis and stratified medicine. We consider the latest developments in epilepsy genetics and review how gene discovery in epilepsy is influencing the clinical classification of epilepsy and informing new therapeutic approaches and drug discovery. RECENT FINDINGS: Recent studies highlighting the importance of mutation in GABA receptors, NMDA receptors, potassium channels, G-protein coupled receptors, mammalian target of rapamycin pathway and chromatin remodeling are discussed...
February 15, 2017: Current Opinion in Neurology
https://www.readbyqxmd.com/read/28209301/iswi-atp-dependent-remodeling-of-nucleoplasmic-%C3%AF-speckles-in-the-brain-of-drosophila-melanogaster
#5
Luca Lo Piccolo, Andrea Attardi, Rosa Bonaccorso, Lorenzo Li Greci, Giorgio Giurato, Antonia Maria Rita Ingrassia, Maria Cristina Onorati
Heterogeneous nuclear ribonucleoproteins (hnRNPs) belong to the RNA-binding proteins family. They are involved in processing heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs. These proteins participate in every step of mRNA cycle, such as mRNA export, localization, translation, stability and alternative splicing. At least 14 major hnRNPs, which have structural and functional homologues in mammals, are expressed in Drosophila melanogaster. Until now, six of these hnRNPs are known to be nucleus-localized and associated with the long non-coding RNA (lncRNA) heat shock responsive ω (hsrω) in the omega speckle compartments (ω-speckles)...
December 22, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28205598/lyn-regulates-mucus-secretion-and-muc5ac-via-the-stat6-signaling-pathway-during-allergic-airway-inflammation
#6
Xiaoyun Wang, Yin Li, Deyu Luo, Xing Wang, Yun Zhang, Zhigang Liu, Nanshan Zhong, Min Wu, Guoping Li
Hypersecretion of mucus is an important component of airway remodeling and contributes to the mucus plugs and airflow obstruction associated with severe asthma phenotypes. Lyn has been shown to down-regulate allergen-induced airway inflammation. However, the role of Lyn in mucin gene expression remains unresolved. In this study, we first demonstrate that Lyn overexpression decreased the mucus hypersecretion and levels of the muc5ac transcript in mice exposed to ovalbumin (OVA). Lyn overexpression also decreased the infiltration of inflammatory cells and the levels of IL-13 and IL-4 in OVA-challenged airways...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28202673/molecular-architecture-of-polycomb-repressive-complexes
#7
REVIEW
Emily C Chittock, Sebastian Latwiel, Thomas C R Miller, Christoph W Müller
The polycomb group (PcG) proteins are a large and diverse family that epigenetically repress the transcription of key developmental genes. They form three broad groups of polycomb repressive complexes (PRCs) known as PRC1, PRC2 and Polycomb Repressive DeUBiquitinase, each of which modifies and/or remodels chromatin by distinct mechanisms that are tuned by having variable compositions of core and accessory subunits. Until recently, relatively little was known about how the various PcG proteins assemble to form the PRCs; however, studies by several groups have now allowed us to start piecing together the PcG puzzle...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28202543/nucleosome-like-ssdna-histone-octamer-complexes-and-the-implication-for-dna-double-strand-break-repair
#8
Nicholas L Adkins, Sarah G Swygert, Parminder Kaur, Hengyao Niu, Sergei A Grigoryev, Patrick Sung, Hong Wang, Craig L Peterson
Repair of DNA double strand breaks (DSBs) is key for maintenance of genome integrity. When DSBs are repaired by homologous recombination, DNA ends can undergo extensive processing, producing long stretches of single-stranded DNA (ssDNA). In vivo, DSB processing occurs in the context of chromatin, and studies indicate that histones may remain associated with processed DSBs. Here we demonstrate that histones are not evicted from ssDNA after in vitro chromatin resection. In addition, we reconstitute histone-ssDNA complexes (termed ssNucs) with ssDNA and recombinant histones and analyze these particles by a combination of native gel electrophoresis, sedimentation velocity, electron microscopy, and a recently developed electrostatic force microscopy technique, DREEM (Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy)...
February 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28202515/systematic-in-vivo-inactivation-of-chromatin-regulating-enzymes-identifies-setd2-as-a-potent-tumor-suppressor-in-lung-adenocarcinoma
#9
David M Walter, Olivia S Venancio, Elizabeth L Buza, John W Tobias, Charuhas Deshpande, A Andrea Gudiel, Caroline Kim-Kiselak, Michelle Cicchini, Travis J Yates, David M Feldser
Chromatin modifying genes are frequently mutated in human lung adenocarcinoma, but the functional impact of these mutations on disease initiation and progression is not well understood. Using a CRISPR-based approach, we systematically inactivated three of the most commonly mutated chromatin regulatory genes in two KrasG12D-driven mouse models of lung adenocarcinoma to characterize the impact of their loss. Targeted inactivation of SWI/SNF nucleosome remodeling complex members Smarca4 (Brg1) or Arid1a had complex effects on lung adenocarcinoma initiation and progression...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28199314/whole-genome-landscape-of-pancreatic-neuroendocrine-tumours
#10
Aldo Scarpa, David K Chang, Katia Nones, Vincenzo Corbo, Ann-Marie Patch, Peter Bailey, Rita T Lawlor, Amber L Johns, David K Miller, Andrea Mafficini, Borislav Rusev, Maria Scardoni, Davide Antonello, Stefano Barbi, Katarzyna O Sikora, Sara Cingarlini, Caterina Vicentini, Skye McKay, Michael C J Quinn, Timothy J C Bruxner, Angelika N Christ, Ivon Harliwong, Senel Idrisoglu, Suzanne McLean, Craig Nourse, Ehsan Nourbakhsh, Peter J Wilson, Matthew J Anderson, J Lynn Fink, Felicity Newell, Nick Waddell, Oliver Holmes, Stephen H Kazakoff, Conrad Leonard, Scott Wood, Qinying Xu, Shivashankar Hiriyur Nagaraj, Eliana Amato, Irene Dalai, Samantha Bersani, Ivana Cataldo, Angelo P Dei Tos, Paola Capelli, Maria Vittoria Davì, Luca Landoni, Anna Malpaga, Marco Miotto, Vicki L J Whitehall, Barbara A Leggett, Janelle L Harris, Jonathan Harris, Marc D Jones, Jeremy Humphris, Lorraine A Chantrill, Venessa Chin, Adnan M Nagrial, Marina Pajic, Christopher J Scarlett, Andreia Pinho, Ilse Rooman, Christopher Toon, Jianmin Wu, Mark Pinese, Mark Cowley, Andrew Barbour, Amanda Mawson, Emily S Humphrey, Emily K Colvin, Angela Chou, Jessica A Lovell, Nigel B Jamieson, Fraser Duthie, Marie-Claude Gingras, William E Fisher, Rebecca A Dagg, Loretta M S Lau, Michael Lee, Hilda A Pickett, Roger R Reddel, Jaswinder S Samra, James G Kench, Neil D Merrett, Krishna Epari, Nam Q Nguyen, Nikolajs Zeps, Massimo Falconi, Michele Simbolo, Giovanni Butturini, George Van Buren, Stefano Partelli, Matteo Fassan, Kum Kum Khanna, Anthony J Gill, David A Wheeler, Richard A Gibbs, Elizabeth A Musgrove, Claudio Bassi, Giampaolo Tortora, Paolo Pederzoli, John V Pearson, Nicola Waddell, Andrew V Biankin, Sean M Grimmond
The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2...
February 15, 2017: Nature
https://www.readbyqxmd.com/read/28197914/sumoylation-in-development-and-differentiation
#11
Adeline F Deyrieux, Van G Wilson
Tissue morphogenesis is a fascinating aspect of both developmental biology and regeneration of certain adult organs, and timely control of cellular differentiation is a key to these processes. During development, events interrupting cellular differentiation and leading to organ failure are embryonic lethal; likewise, perturbation of differentiation in regenerating tissues leads to dysfunction and disease. At the molecular level, cellular differentiation is orchestrated by a well-coordinated cascade of transcription factors (TFs) and chromatin remodeling complexes that drive gene expression...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28197905/sumo-and-chromatin-remodeling
#12
David Wotton, Lucy F Pemberton, Jacqueline Merrill-Schools
Many of the known SUMO substrates are nuclear proteins, which regulate gene expression and chromatin dynamics. Sumoylation, in general, appears to correlate with decreased transcriptional activity, and in many cases modulation of the chromatin template is implicated. Sumoylation of the core histones is associated with transcriptional silencing, and transcription factor sumoylation can decrease gene expression by promoting recruitment of chromatin modifying enzymes. Additionally, sumoylation of transcriptional corepressors and chromatin remodeling enzymes can influence interactions with other transcriptional regulators, and alter their enzymatic activity...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28191871/distinct-modes-of-smad2-chromatin-binding-and-remodeling-shape-the-transcriptional-response-to-nodal-activin-signaling
#13
Davide M Coda, Tessa Gaarenstroom, Philip East, Harshil Patel, Daniel S J Miller, Anna Lobley, Nik Matthews, Aengus Stewart, Caroline S Hill
NODAL/Activin signaling orchestrates key processes during embryonic development via SMAD2. How SMAD2 activates programs of gene expression that are modulated over time however, is not known. Here we delineate the sequence of events that occur from SMAD2 binding to transcriptional activation, and the mechanisms underlying them. NODAL/Activin signaling induces dramatic chromatin landscape changes, and a dynamic transcriptional network regulated by SMAD2, acting via multiple mechanisms. Crucially we have discovered two modes of SMAD2 binding...
February 13, 2017: ELife
https://www.readbyqxmd.com/read/28189102/coordinated-events-of-nuclear-assembly
#14
REVIEW
Dollie LaJoie, Katharine S Ullman
Each time a metazoan cell undergoes open mitosis, the nucleus is dismantled in order to partition DNA content to the daughter cells. After chromosomes separate, changes at the chromatin surface usher in reestablishment of nuclear architecture. Proteins destined for the nuclear envelope are attracted to chromatin and concomitantly recruit membrane. As nuclear envelope and protein constituents spread to coat chromatin, distinct regions emerge-some rich in rapid pore formation, others occupied by microtubules that remain attached to kinetochores...
February 8, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28186195/cenp-a-chromatin-disassembly-in-stressed-and-senescent-murine-cells
#15
Sabrine Hédouin, Giacomo Grillo, Ivana Ivkovic, Guillaume Velasco, Claire Francastel
Centromeres are chromosomal domains essential for genomic stability. We report here the remarkable transcriptional and epigenetic perturbations at murine centromeres in genotoxic stress conditions. A strong and selective transcriptional activation of centromeric repeats is detected within hours. This is followed by disorganization of centromeres with striking delocalization of nucleosomal CENP-A, the key determinant of centromere identity and function, in a mechanism requiring active transcription of centromeric repeats, the DNA Damage Response (DDR) effector ATM and chromatin remodelers/histone chaperones...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28184006/the-human-dna-ligase-iii%C3%AE-x-ray-repair-cross-complementing-protein-1-complex-performs-dna-nick-repair-after-transient-unwrapping-of-nucleosomal-dna
#16
Wendy J Cannan, Ishtiaque Rashid, Alan E Tomkinson, Susan S Wallace, David S Pederson
Reactive oxygen species generate potentially cytotoxic and mutagenic lesions in DNA, both between and within the nucleosomes that package DNA in chromatin. The vast majority of these lesions are subject to base excision repair (BER). Enzymes that catalyze the first three steps in BER can act at many sites in nucleosomes without the aid of chromatin-remodeling agents, and without irreversibly disrupting the host nucleosome. Here, we show that the same is true is true for a protein complex comprising DNA ligase IIIα and the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1), which completes the fourth and final step in (short-patch) BER...
February 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28182012/loss-of-brg1-induces-crc-cell-senescence-by-regulating-p53-p21-pathway
#17
Guihua Wang, Yinjia Fu, Fuqing Hu, Jinqing Lan, Feng Xu, Xi Yang, Xuelai Luo, Jing Wang, Junbo Hu
Brahma-related gene-1 (BRG1) is the specific ATPase of switch/sucrose nonfermentable chromatin-remodeling complex that is aberrantly expressed or mutated in various cancers. However, the exact role of BRG1 in oncogenesis remains unknown. In this study, we demonstrate that the knockdown (KD) of BRG1 promotes cellular senescence by influencing the SIRT1/p53/p21 signal axis in colorectal cancer (CRC). In particular, we reveal that the expression level of BRG1 is inversely correlated with p21, one of the classic senescence regulators, and is decreased in senescent CRC cells...
February 9, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28181539/dissecting-the-brown-adipogenic-regulatory-network-using-integrative-genomics
#18
Rachana N Pradhan, Johannes J Bues, Vincent Gardeux, Petra C Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K Raghav, Bart Deplancke
Brown adipocytes regulate energy expenditure via mitochondrial uncoupling, which makes them attractive therapeutic targets to tackle obesity. However, the regulatory mechanisms underlying brown adipogenesis are still poorly understood. To address this, we profiled the transcriptome and chromatin state during mouse brown fat cell differentiation, revealing extensive gene expression changes and chromatin remodeling, especially during the first day post-differentiation. To identify putatively causal regulators, we performed transcription factor binding site overrepresentation analyses in active chromatin regions and prioritized factors based on their expression correlation with the bona-fide brown adipogenic marker Ucp1 across multiple mouse and human datasets...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28181261/the-search-for-potent-small-molecule-hdacis-in-cancer-treatment-a-decade-after-vorinostat
#19
REVIEW
Chiara Zagni, Giuseppe Floresta, Giulia Monciino, Antonio Rescifina
Histone deacetylases (HDACs) play a crucial role in the remodeling of chromatin, and are involved in the epigenetic regulation of gene expression. In the last decade, inhibition of HDACs came out as a target for specific epigenetic changes associated with cancer and other diseases. Until now, more than 20 HDAC inhibitors (HDACIs) have entered clinical studies, and some of them (e.g., vorinostat, romidepsin) have been approved for the treatment of cutaneous T-cell lymphoma. This review provides an overview of current knowledge, progress, and molecular mechanisms of HDACIs, covering a period from 2011 until 2015...
February 9, 2017: Medicinal Research Reviews
https://www.readbyqxmd.com/read/28179136/expression-purification-and-characterization-of-the-human-mta2-rbbp7-complex
#20
Christoffer Brasen, Jerzy Dorosz, Anders Wiuf, Thomas Boesen, Osman Mirza, Michael Gajhede
The repressive Nucleosome Remodeling and histone Deacetylation (NuRD) complex remodels the chromatin structure by coupling ATP-dependent remodeling activity with histone deacetylase function and plays important roles in regulating gene transcription, DNA damage repair and chromatin assembly. The complex is composed of six subunits: Metastasis Associated proteins MTA1/2/3 initially recruit histone chaperones RBBP4/7 followed by the histone deacetylases HDAC1/2 forming a core complex. Further association of the CpG-binding protein MBD2/3, p66α/β and the ATP-dependent helicase CDH3/4 constitutes the NuRD complex...
February 4, 2017: Biochimica et Biophysica Acta
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