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Chromatin modulation

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https://www.readbyqxmd.com/read/29474480/role-of-su-hw-zinc-finger-10-and-interaction-with-cp190-and-mod-mdg4-proteins-in-recruiting-the-su-hw-complex-to-chromatin-sites-in-drosophila
#1
Larisa Melnikova, Margarita Kostyuchenko, Alexander Parshikov, Pavel Georgiev, Anton Golovnin
Su(Hw) belongs to the class of proteins that organize chromosome architecture and boundaries/insulators between regulatory domains. This protein contains a cluster of 12 zinc finger domains most of which are responsible for binding to three different modules in the consensus site. Su(Hw) forms a complex with CP190 and Mod(mdg4)-67.2 proteins that binds to well-known Drosophila insulators. To understand how Su(Hw) performs its activities and binds to specific sites in chromatin, we have examined the previously described su(Hw)f mutation that disrupts the 10th zinc finger (ZF10) responsible for Su(Hw) binding to the upstream module...
2018: PloS One
https://www.readbyqxmd.com/read/29472540/exploiting-genetic-variation-to-uncover-rules-of-transcription-factor-binding-and-chromatin-accessibility
#2
Vivek Behera, Perry Evans, Carolyne J Face, Nicole Hamagami, Laavanya Sankaranarayanan, Cheryl A Keller, Belinda Giardine, Kai Tan, Ross C Hardison, Junwei Shi, Gerd A Blobel
Single-nucleotide variants that underlie phenotypic variation can affect chromatin occupancy of transcription factors (TFs). To delineate determinants of in vivo TF binding and chromatin accessibility, we introduce an approach that compares ChIP-seq and DNase-seq data sets from genetically divergent murine erythroid cell lines. The impact of discriminatory single-nucleotide variants on TF ChIP signal enables definition at single base resolution of in vivo binding characteristics of nuclear factors GATA1, TAL1, and CTCF...
February 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29472317/dynamic-control-of-chromosome-topology-and-gene-expression-by-a-chromatin-modification
#3
Qian Bian, Erika C Anderson, Katjuša Brejc, Barbara J Meyer
The function of chromatin modification in establishing higher-order chromosome structure during gene regulation has been elusive. We dissected the machinery and mechanism underlying the enrichment of histone modification H4K20me1 on hermaphrodite X chromosomes during Caenorhabditis elegans dosage compensation and discovered a key role for H4K20me1 in regulating X-chromosome topology and chromosome-wide gene expression. Structural and functional analysis of the dosage compensation complex (DCC) subunit DPY-21 revealed a novel Jumonji C demethylase subfamily that converts H4K20me2 to H4K20me1 in worms and mammals...
February 22, 2018: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29472234/hypoxia-triggers-senp1-sentrin-specific-protease-1-modulation-of-klf15-kruppel-like-factor-15-and-transcriptional-regulation-of-arg2-arginase-2-in-pulmonary-endothelium
#4
Deepesh Pandey, Yohei Nomura, Max C Rossberg, Daijiro Hori, Anil Bhatta, Gizem Keceli, Thorsten Leucker, Lakshmi Santhanam, Larissa A Shimoda, Dan Berkowitz, Lewis Romer
OBJECTIVE: KLF15 (Kruppel-like factor 15) has recently been shown to suppress activation of proinflammatory processes that contribute to atherogenesis in vascular smooth muscle, however, the role of KLF15 in vascular endothelial function is unknown. Arginase mediates inflammatory vasculopathy and vascular injury in pulmonary hypertension. Here, we tested the hypothesis that KLF15 is a critical regulator of hypoxia-induced Arg2 (arginase 2) transcription in human pulmonary microvascular endothelial cells (HPMEC)...
February 22, 2018: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/29471289/single-nucleotide-polymorphism-facilitated-down-regulation-of-the-cohesin-stromal-antigen-1-implications-for-colorectal-cancer-racial-disparities
#5
Somenath Datta, Richard M Sherva, Mart De La Cruz, Michelle T Long, Priya Roy, Vadim Backman, Sanjib Chowdhury, Hemant K Roy
The biological underpinnings for racial disparities in colorectal cancer (CRC) incidence remain to be elucidated. We have previously reported that the cohesin SA-1 down-regulation is an early event in colon carcinogenesis which is dramatically accentuated in African-Americans. In order to investigate the mechanism, we evaluated single nucleotide polymorphisms (SNPs) for association with SA-1-related outcomes followed by gene editing of candidate SNP. We observed that rs34149860 SNP was significantly associated with a lower colonic mucosal SA-1 expression and evaluation of public databases showed striking racial discordance...
February 19, 2018: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29467493/c-jun-ap-1-overexpression-reprograms-er%C3%AE-signaling-related-to-tamoxifen-response-in-er%C3%AE-positive-breast-cancer
#6
Huan He, Indranil Sinha, Rongrong Fan, Lars-Arne Haldosen, Feifei Yan, Chunyan Zhao, Karin Dahlman-Wright
A critical mechanism that has been proposed for transcription regulation by estrogen receptor α (ER) is the tethering of ER to DNA via other transcription factors, such as AP-1. However, genome-wide assessment of the overlap in chromatin binding repertoires of these two transcription factors has not been reported. Here, we show that the AP-1 transcription factor c-Jun interacts with ER and that c-Jun chromatin binding shows extensive overlap with ER binding at the global level. Further, we show that c-Jun overexpression reprograms ER chromatin binding and modulates ER-mediated gene regulation...
February 22, 2018: Oncogene
https://www.readbyqxmd.com/read/29467311/epstein-barr-virus-nuclear-antigen-leader-protein-co-activates-ep300
#7
Chong Wang, Hufeng Zhou, Yong Xue, Jun Liang, Yohei Narita, Catherine Gerdt, Amy Y Zheng, Runsheng Jiang, Stephen Trudeau, Chih-Wen Peng, Benjamin Gewurz, Bo Zhao
Epstein-Barr virus nuclear antigen (EBNA) leader protein (EBNALP) is one of the first viral genes expressed upon B-cell infection. EBNALP is essential for EBV-mediated B cell immortalization. EBNALP is thought to function primarily by co-activaing EBNA2-mediated transcription. Chromatin immune precipitation followed by deep-sequencing (ChIP-seq) studies highlight that EBNALP frequently co-occupies DNA sites with host cell transcription factors (TFs), in particular EP300, implicating a broader role in transcription regulation...
February 21, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29463645/molecular-architecture-of-the-essential-yeast-histone-acetyltransferase-complex-nua4-redefines-its-multi-modularity
#8
Dheva Setiaputra, Salar Ahmad, Udit Dalwadi, Anne-Lise Steunou, Shan Lu, James D Ross, Meng-Qiu Dong, Jacques Côté, Calvin K Yip
Conserved from yeast to humans, the NuA4 histone acetyltransferase is a large multisubunit complex essential for cell viability through regulation of gene expression, genome maintenance, metabolism, and cell fate during development and stress. How the different NuA4 subunits work in concert with one another to perform these diverse functions remains unclear, and addressing this central question requires a comprehensive understanding of NuA4's molecular architecture and subunit organization. We have determined the structure of fully assembled native yeast NuA4 by single-particle electron microscopy...
February 20, 2018: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/29462149/the-ino80-chromatin-remodeler-sustains-metabolic-stability-by-promoting-tor-signaling-and-regulating-histone-acetylation
#9
Sean L Beckwith, Erin K Schwartz, Pablo E Garcia-Nieto, Devin A King, Graeme J Gowans, Ka Man Wong, Tessa L Eckley, Alexander P Paraschuk, Egan L Peltan, Laura R Lee, Wei Yao, Ashby J Morrison
Chromatin remodeling complexes are essential for gene expression programs that coordinate cell function with metabolic status. However, how these remodelers are integrated in metabolic stability pathways is not well known. Here, we report an expansive genetic screen with chromatin remodelers and metabolic regulators in Saccharomyces cerevisiae. We found that, unlike the SWR1 remodeler, the INO80 chromatin remodeling complex is composed of multiple distinct functional subunit modules. We identified a strikingly divergent genetic signature for the Ies6 subunit module that links the INO80 complex to metabolic homeostasis...
February 20, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29456384/tea-polyphenols-and-prevention-of-epigenetic-aberrations-in-cancer
#10
REVIEW
Arundhati Bag, Niladri Bag
Tea polyphenols are secondary metabolites of tea plants and are well known for beneficial health effects. They can protect from a variety of illnesses including cancers. Tea polyphenols can prevent cancer by modulating epigenetic aberrations taking place in DNA methylation, histone modifications, and micro-RNAs. By altering these epimutations, they regulate chromatin dynamics and expression of genes those induce or suppress cancer formation. However, majority of the studies in existing literature are carried out for green tea polyphenols rather than black tea polyphenols despite the fact that black tea is the most commonly consumed form of tea (78%) followed by green tea (20%) and other forms of tea...
January 2018: Journal of Natural Science, Biology, and Medicine
https://www.readbyqxmd.com/read/29455435/dna-methylation-regulated-micrornas-in-hpv-16-induced-head-and-neck-squamous-cell-carcinoma-hnscc
#11
M K Sannigrahi, Rajni Sharma, Varinder Singh, Naresh K Panda, Vidya Rattan, Madhu Khullar
INTRODUCTION: Epigenetic modifications have been reported to play an important role in regulating gene expression and these modifications become critical when they have a role in controlling another important layer of epigenetic regulation namely microRNAs. In the present study, we have identified the microRNAs that may be regulated by promoter DNA methylation and histone acetylation in Human papilloma virus-positive head and neck squamous cell carcinoma. METHODOLOGY: HPV-negative cell line (UPCI:SCC-116) and HPV-16 +ve cell line (UPCI:SCC-090) were treated with methylation inhibitor (5-aza-2'-deoxycytidine, AZA) and acetylation inhibitor (Trichostatin-A, TSA), followed by micro-array analysis...
February 17, 2018: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29452642/the-yeast-ino80-complex-operates-as-a-tunable-dna-length-sensitive-switch-to-regulate-nucleosome-sliding
#12
Coral Y Zhou, Stephanie L Johnson, Laura J Lee, Adam D Longhurst, Sean L Beckwith, Matthew J Johnson, Ashby J Morrison, Geeta J Narlikar
The yeast INO80 chromatin remodeling complex plays essential roles in regulating DNA damage repair, replication, and promoter architecture. INO80's role in these processes is likely related to its ability to slide nucleosomes, but the underlying mechanism is poorly understood. Here we use ensemble and single-molecule enzymology to study INO80-catalyzed nucleosome sliding. We find that the rate of nucleosome sliding by INO80 increases ∼100-fold when the flanking DNA length is increased from 40 to 60 bp. Furthermore, once sliding is initiated, INO80 moves the nucleosome rapidly at least 20 bp without pausing to re-assess flanking DNA length, and it can change the direction of nucleosome sliding without dissociation...
February 15, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29450107/macrogenomic-engineering-via-modulation-of-the-scaling-of-chromatin-packing-density
#13
Luay M Almassalha, Greta M Bauer, Wenli Wu, Lusik Cherkezyan, Di Zhang, Alexis Kendra, Scott Gladstein, John E Chandler, David VanDerway, Brandon-Luke L Seagle, Andrey Ugolkov, Daniel D Billadeau, Thomas V O'Halloran, Andrew P Mazar, Hemant K Roy, Igal Szleifer, Shohreh Shahabi, Vadim Backman
Many human diseases result from the dysregulation of the complex interactions between tens to thousands of genes. However, approaches for the transcriptional modulation of many genes simultaneously in a predictive manner are lacking. Here, through the combination of simulations, systems modelling and in vitro experiments, we provide a physical regulatory framework based on chromatin packing-density heterogeneity for modulating the genomic information space. Because transcriptional interactions are essentially chemical reactions, they depend largely on the local physical nanoenvironment...
November 2017: Nature Biomedical Engineering
https://www.readbyqxmd.com/read/29449904/expression-profiling-of-chromatin-modifying-enzymes-and-global-dna-methylation-in-cd4-t-cells-from-patients-with-chronic-hiv-infection-at-different-hiv-control-and-progression-states
#14
Roberta Nicoleta Bogoi, Alicia de Pablo, Eulalia Valencia, Luz Martín-Carbonero, Victoria Moreno, Helem Haydee Vilchez-Rueda, Victor Asensi, Rosa Rodriguez, Victor Toledano, Berta Rodés
Background: Integration of human immunodeficiency virus type 1 (HIV-1) into the host genome causes global disruption of the chromatin environment. The abundance level of various chromatin-modifying enzymes produces these alterations and affects both the provirus and cellular gene expression. Here, we investigated potential changes in enzyme expression and global DNA methylation in chronically infected individuals with HIV-1 and compared these changes with non-HIV infected individuals...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29449332/inhibition-of-endothelial-notch1-signaling-attenuates-inflammation-by-reducing-cytokine-mediated-histone-acetylation-at-inflammatory-enhancers
#15
Lars la Cour Poulsen, Reidunn Jetne Edelmann, Stig Krüger, Rodrigo Diéguez-Hurtado, Akshay Shah, Tor Espen Stav-Noraas, Anastasia Renzi, Monika Szymanska, Junbai Wang, Manuel Ehling, Rui Benedito, Monika Kasprzycka, Espen Bækkevold, Olav Sundnes, Kim S Midwood, Helge Scott, Philippe Collas, Christian W Siebel, Ralf H Adams, Guttorm Haraldsen, Eirik Sundlisæter, Johanna Hol
OBJECTIVE: Endothelial upregulation of adhesion molecules serves to recruit leukocytes to inflammatory sites and appears to be promoted by NOTCH1; however, current models based on interactions between active NOTCH1 and NF-κB components cannot explain the transcriptional selectivity exerted by NOTCH1 in this context. APPROACH AND RESULTS: Observing that Cre/Lox-induced conditional mutations of endothelial Notch modulated inflammation in murine contact hypersensitivity, we found that IL (interleukin)-1β stimulation induced rapid recruitment of RELA to genomic sites occupied by NOTCH1-RBPJ and that NOTCH1 knockdown reduced H3K27 acetylation at a subset of NF-κB-directed inflammatory enhancers...
February 15, 2018: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/29449088/temperature-modulates-tissue-specification-program-to-control-fruit-dehiscence-in-brassicaceae
#16
Xin-Ran Li, Joyita Deb, S Vinod Kumar, Lars Østergaard
Plants respond to diurnal and seasonal changes in temperature by reprogramming vital developmental pathways. Understanding the molecular mechanisms that define environmental modulation of plant growth and reproduction is critical in the context of climate change that threatens crop yield worldwide. Here, we report that elevated temperature accelerates fruit dehiscence in members of the Brassicaceae family including the model plant Arabidopsis thaliana and important crop species. Arabidopsis fruit development is controlled by a network of interacting regulatory genes...
February 7, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29447380/sirtuins-in-gamete-biology-and-reproductive-physiology-emerging-roles-and-therapeutic-potential-in-female-and-male-infertility
#17
Carla Tatone, Giovanna Di Emidio, Arcangelo Barbonetti, Gaspare Carta, Alberto M Luciano, Stefano Falone, Fernanda Amicarelli
BACKGROUND: Sirtuins (SIRT1-7) are a family of NAD+-dependent deacetylases that catalyze post-translational modifications of proteins. Together, they respond to metabolic challenges, inflammatory signals or hypoxic/oxidative stress, and are associated with aging and longevity. The role of Sirtuins in the regulation of fertility emerged in 2003 when a defective reproductive phenotype was observed in SIRT1-null mice. Although studies on Sirtuins in reproductive biology have been increasing in the last years, a recent comprehensive update on this issue is still lacking...
February 13, 2018: Human Reproduction Update
https://www.readbyqxmd.com/read/29447134/histone-deacetylase-5-hdac5-regulates-neuropathic-pain-through-sry-related-hmg-box-10-sox10-dependent-mechanism-in-mice
#18
Pan Gu, Zhiqiang Pan, Xiao-Min Wang, Liting Sun, Lydia Wai Tai, Chi Wai Cheung
A strong link between histone deacetylases (HDACs) and nociceptive hypersensitivity has been indicated in different pain models. However, the underlying molecular and cellular mechanisms remain elusive. Here, we discovered that partial sciatic nerve ligation-induced mechanical allodynia and thermal hyperalgesia in mice were associated with increased mRNA and protein expressions of HDAC5 (a member of class IIa HDACs) and SRY-related HMG-box 10 (SOX10) in the ipsilateral lumbar dorsal horn. Gene knockdown of spinal HDAC5 or SOX10 attenuated partial sciatic nerve ligation-induced nociceptive hypersensitivity, companied with decrease of spinal neuronal sensitization markers, namely phosphorylated-Erk, phosphorylated-GluN1 (ser896), and c-Fos...
March 2018: Pain
https://www.readbyqxmd.com/read/29440389/antisense-transcription-dependent-chromatin-signature-modulates-sense-transcript-dynamics
#19
Thomas Brown, Françoise S Howe, Struan C Murray, Meredith Wouters, Philipp Lorenz, Emily Seward, Scott Rata, Andrew Angel, Jane Mellor
Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript degradation...
February 12, 2018: Molecular Systems Biology
https://www.readbyqxmd.com/read/29439026/rev-erb%C3%AE-dynamically-modulates-chromatin-looping-to-control-circadian-gene-transcription
#20
Yong Hoon Kim, Sajid A Marhon, Yuxiang Zhang, David J Steger, Kyoung-Jae Won, Mitchell A Lazar
Mammalian physiology exhibits 24-hour cyclicity due to circadian rhythms of gene expression controlled by transcription factors (TF) that comprise molecular clocks. Core clock TFs bind to the genome at enhancer sequences to regulate circadian gene expression, but not all binding sites are equally functional. Here we demonstrate that circadian gene expression in mouse liver is controlled by rhythmic chromatin interactions between enhancers and promoters. Rev-erbα, a core repressive TF of the clock, opposes functional loop formation between Rev-erbα-regulated enhancers and circadian target gene promoters by recruitment of the NCoR-HDAC3 corepressor complex, histone deacetylation, and eviction of the elongation factor BRD4 and the looping factor MED1...
February 8, 2018: Science
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