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Chromatin-associated RNA

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https://www.readbyqxmd.com/read/28818098/sex-chromosomes-drive-gene-expression-and-regulatory-dimorphisms-in-mouse-embryonic-stem-cells
#1
Rachael J Werner, Bryant M Schultz, Jacklyn M Huhn, Jaroslav Jelinek, Jozef Madzo, Nora Engel
BACKGROUND: Pre-implantation embryos exhibit sexual dimorphisms in both primates and rodents. To determine whether these differences reflected sex-biased expression patterns, we generated transcriptome profiles for six 40,XX, six 40,XY, and two 39,X mouse embryonic stem (ES) cells by RNA sequencing. RESULTS: We found hundreds of coding and non-coding RNAs that were differentially expressed between male and female cells. Surprisingly, the majority of these were autosomal and included RNA encoding transcription and epigenetic and chromatin remodeling factors...
August 17, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/28815539/long-noncoding-rnas-in-plants
#2
Hsiao-Lin V Wang, Julia A Chekanova
The eukaryotic genomes are pervasively transcribed. In addition to protein-coding RNAs, thousands of long noncoding RNAs (lncRNAs) modulate key molecular and biological processes. Most lncRNAs are found in the nucleus and associate with chromatin, but lncRNAs can function in both nuclear and cytoplasmic compartments. Emerging work has found that many lncRNAs regulate gene expression and can affect genome stability and nuclear domain organization both in plant and in the animal kingdom. Here, we describe the major plant lncRNAs and how they act, with a focus on research in Arabidopsis thaliana and our emerging understanding of lncRNA functions in serving as molecular sponges and decoys, functioning in regulation of transcription and silencing, particularly in RNA-directed DNA methylation, and in epigenetic regulation of flowering time...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28810927/stat3-mediated-upregulation-of-lncrna-hoxd-as1-as-a-cerna-facilitates-liver-cancer-metastasis-by-regulating-sox4
#3
Hui Wang, Xisong Huo, Xin-Rong Yang, Jia He, Lijun Cheng, Na Wang, Xuan Deng, Haojie Jin, Ning Wang, Cun Wang, Fangyu Zhao, Jingyuan Fang, Ming Yao, Jia Fan, Wenxin Qin
BACKGROUND: Several of the thousands of human long noncoding RNAs (lncRNAs) have been functionally characterized, yet their potential involvement in hepatocellular carcinoma (HCC) remains poorly understood. METHODS: LncRNA-HOXD-AS1 was identified by microarray and validated by real-time PCR. The clinicopathological significance of HOXD-AS1 was analyzed by Kaplan-Meier method. Chromatin immunoprecipitation was conducted to examine the mechanism of HOXD-AS1 upregulation...
August 14, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28806732/loss-of-the-chromatin-modifier-kdm2aa-causes-brafv600e-independent-spontaneous-melanoma-in-zebrafish
#4
Catherine M Scahill, Zsofia Digby, Ian M Sealy, Sonia Wojciechowska, Richard J White, John E Collins, Derek L Stemple, Till Bartke, Marie E Mathers, E Elizabeth Patton, Elisabeth M Busch-Nentwich
KDM2A is a histone demethylase associated with transcriptional silencing, however very little is known about its in vivo role in development and disease. Here we demonstrate that loss of the orthologue kdm2aa in zebrafish causes widespread transcriptional disruption and leads to spontaneous melanomas at a high frequency. Fish homozygous for two independent premature stop codon alleles show reduced growth and survival, a strong male sex bias, and homozygous females exhibit a progressive oogenesis defect. kdm2aa mutant fish also develop melanomas from early adulthood onwards which are independent from mutations in braf and other common oncogenes and tumour suppressors as revealed by deep whole exome sequencing...
August 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28802249/high-resolution-mapping-of-chromatin-conformation-in-cardiac-myocytes-reveals-structural-remodeling-of-the-epigenome-in-heart-failure
#5
Manuel Rosa-Garrido, Douglas J Chapski, Anthony D Schmitt, Todd H Kimball, Elaheh Karbassi, Emma Monte, Enrique Balderas, Matteo Pellegrini, Tsai-Ting Shih, Elizabeth Soehalim, David A Liem, Peipei Ping, Niels J Galjart, Shuxun Ren, Yibin Wang, Bing Ren, Thomas M Vondriska
Background -Cardiovascular disease is associated with epigenomic changes in the heart, however the endogenous structure of cardiac myocyte chromatin has never been determined. Methods -To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype...
August 11, 2017: Circulation
https://www.readbyqxmd.com/read/28800314/long-noncoding-rna-pvt1-promotes-hepatocellular-carcinoma-progression-through-regulating-mir-214
#6
Xun Gou, Xiyan Zhao, Zhengrong Wang
BACKGROUND: Long noncoding RNAs (lncRNA) have been verified to be involved in hepatocellular carcinoma (HCC) progression. However, the potential biologic function of PVT1 in HCC is not still fully known. METHODS: PVT1 and miR-214 were detected by qRT-PCR assays in HCC tissues and adjacent normal tissues. CCK8, cell colony and transwell invasion assays were performed to evaluate cell proliferation and invasion abilities. Western-blot assay was performed to detect the protein of E-cadherin and Vimentin...
July 31, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28793256/dynamics-of-rna-polymerase-ii-pausing-and-bivalent-histone-h3-methylation-during-neuronal-differentiation-in-brain-development
#7
Jiancheng Liu, Xiwei Wu, Heying Zhang, Gerd P Pfeifer, Qiang Lu
During cellular differentiation, genes important for differentiation are expected to be silent in stem/progenitor cells yet can be readily activated. RNA polymerase II (Pol II) pausing and bivalent chromatin marks are two paradigms suited for establishing such a poised state of gene expression; however, their specific contributions in development are not well understood. Here we characterized Pol II pausing and H3K4me3/H3K27me3 marks in neural progenitor cells (NPCs) and their daughter neurons purified from the developing mouse cortex...
August 8, 2017: Cell Reports
https://www.readbyqxmd.com/read/28783101/analysis-of-argonaute-4-associated-long-non-coding-rna-in-arabidopsis-thaliana-sheds-novel-insights-into-gene-regulation-through-rna-directed-dna-methylation
#8
Phil Chi Khang Au, Elizabeth S Dennis, Ming-Bo Wang
RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28782042/polycomb-repressive-complex-1-modifies-transcription-of-active-genes
#9
Michelle Pherson, Ziva Misulovin, Maria Gause, Kathie Mihindukulasuriya, Amanda Swain, Dale Dorsett
This study examines the role of Polycomb repressive complex 1 (PRC1) at active genes. The PRC1 and PRC2 complexes are crucial for epigenetic silencing during development of an organism. They are recruited to Polycomb response elements (PREs) and establish silenced domains over several kilobases. Recent studies show that PRC1 is also directly recruited to active genes by the cohesin complex. Cohesin participates broadly in control of gene transcription, but it is unknown whether cohesin-recruited PRC1 also plays a role in transcriptional control of active genes...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28780664/unique-sequence-organization-and-small-rna-expression-of-a-selfish-b-chromosome
#10
Yue Li, Xueyuan A Jing, John C Aldrich, C Clifford, Jian Chen, Omar S Akbari, Patrick M Ferree
B chromosomes are found in numerous plants and animals. These nonessential, supernumerary chromosomes are often composed primarily of noncoding DNA repeats similar to those found within transcriptionally "silenced" heterochromatin. In order to persist within their resident genomes, many B chromosomes exhibit exceptional cellular behaviors, including asymmetric segregation into gametes and induction of genome elimination during early development. An important goal in understanding these behaviors is to identify unique B chromosome sequences and characterize their transcriptional contributions...
August 5, 2017: Chromosoma
https://www.readbyqxmd.com/read/28777933/heterozygous-de-novo-ubtf-gain-of-function-variant-is-associated-with-neurodegeneration-in-childhood
#11
Simon Edvardson, Claudia M Nicolae, Pankaj B Agrawal, Cyril Mignot, Katelyn Payne, Asuri Narayan Prasad, Chitra Prasad, Laurie Sadler, Caroline Nava, Thomas E Mullen, Amber Begtrup, Berivan Baskin, Zöe Powis, Avraham Shaag, Boris Keren, George-Lucian Moldovan, Orly Elpeleg
Ribosomal RNA (rRNA) is transcribed from rDNA by RNA polymerase I (Pol I) to produce the 45S precursor of the 28S, 5.8S, and 18S rRNA components of the ribosome. Two transcription factors have been defined for Pol I in mammals, the selectivity factor SL1, and the upstream binding transcription factor (UBF), which interacts with the upstream control element to facilitate the assembly of the transcription initiation complex including SL1 and Pol I. In seven unrelated affected individuals, all suffering from developmental regression starting at 2...
August 3, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28771467/comprehensive-analysis-of-nucleocytoplasmic-dynamics-of-mrna-in-drosophila-cells
#12
Tao Chen, Bas van Steensel
Eukaryotic mRNAs undergo a cycle of transcription, nuclear export, and degradation. A major challenge is to obtain a global, quantitative view of these processes. Here we measured the genome-wide nucleocytoplasmic dynamics of mRNA in Drosophila cells by metabolic labeling in combination with cellular fractionation. By mathematical modeling of these data we determined rates of transcription, export and cytoplasmic decay for 5420 genes. We characterized these kinetic rates and investigated links with mRNA features, RNA-binding proteins (RBPs) and chromatin states...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28768201/human-tfiih-kinase-cdk7-regulates-transcription-associated-chromatin-modifications
#13
Christopher C Ebmeier, Benjamin Erickson, Benjamin L Allen, Mary A Allen, Hyunmin Kim, Nova Fong, Jeremy R Jacobsen, Kaiwei Liang, Ali Shilatifard, Robin D Dowell, William M Old, David L Bentley, Dylan J Taatjes
CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3' ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5' ends and H3K36me3 was displaced toward gene 3' ends in CDK7as cells...
August 1, 2017: Cell Reports
https://www.readbyqxmd.com/read/28767436/rnai-mediated-knockdown-of-parp1-does-not-improve-the-development-of-female-cloned-mouse-embryos
#14
Guang-Yu Bai, Si-Hang Song, Rui-Zhen Sun, Zi-Hui Zhang, Jingyu Li, Zhen-Dong Wang, Zhong-Hua Liu, Lei Lei
Somatic cell nuclear transfer is an important technique for life science research, but its efficiency is still extremely low, and most genes that are important during early development, such as X chromosome-linked genes, are not appropriately expressed during this process. Poly (ADP-ribose) polymerase (PARP) is an enzyme that transfers ADP ribose clusters to target proteins. PARP family members such as PARP1 participate in cellular signalling pathways through poly (ADP-ribosylation) (PARylation), which ultimately promotes changes in chromatin structure, gene expression, and the localization and activity of proteins that mediate signalling responses...
July 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28766296/methods-for-extraction-of-rna-proteins-or-protein-complexes-from-subcellular-compartments-of-eukaryotic-cells
#15
Kyu-Hyeon Yeom, Andrey Damianov
Eukaryotic organelles or subcellular compartments can be selectively isolated based on their physical density and their stability in the presence of nonionic detergents. This chapter describes a protocol for the preparation of cytoplasm, nucleoplasm, and chromatin, in addition to isolation of RNA and proteins from these fractions. Proteins and protein complexes stably associated with chromatin and other high molecular weight nuclear components can be extracted under non-denaturing conditions by enzymatic digestion of RNA and DNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28764817/the-rpmi-1640-vitamin-mixture-promotes-bovine-blastocyst-development-in-vitro-and-downregulates-gene-expression-of-txnip-with-epigenetic-modification-of-associated-histones
#16
S Ikeda, M Sugimoto, S Kume
Diverse environmental conditions surrounding preimplantation embryos, including available nutrients, affect their metabolism and development in both short- and long-term manner. Thioredoxin-interacting protein (TXNIP) is a possible marker for preimplantation stress that is implicated in in vitro fertilization- (IVF) induced long-term DOHaD effects. B vitamins, as participants in one-carbon metabolism, may affect preimplantation embryos by epigenetic alterations of metabolically and developmentally important genes...
August 2, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/28760200/rna-dependent-stabilization-of-suv39h1-at-constitutive-heterochromatin
#17
Whitney L Johnson, William T Yewdell, Jason C Bell, Shannon M McNulty, Zachary Duda, Rachel J O'Neill, Beth A Sullivan, Aaron F Straight
Heterochromatin formed by the SUV39 histone methyltransferases represses transcription from repetitive DNA sequences and ensures genomic stability. How SUV39 enzymes localize to their target genomic loci remains unclear. Here, we demonstrate that chromatin-associated RNA contributes to the stable association of SUV39H1 with constitutive heterochromatin in human cells. We find that RNA associated with mitotic chromosomes is concentrated at pericentric heterochromatin, and is encoded, in part, by repetitive α-satellite sequences, which are retained in cis at their transcription sites...
August 1, 2017: ELife
https://www.readbyqxmd.com/read/28760199/major-satellite-repeat-rna-stabilize-heterochromatin-retention-of-suv39h-enzymes-by-rna-nucleosome-association-and-rna-dna-hybrid-formation
#18
Oscar Velazquez Camacho, Carmen Galan, Kalina Swist-Rosowska, Reagan Ching, Michael Gamalinda, Fethullah Karabiber, Inti De La Rosa-Velazquez, Bettina Engist, Birgit Koschorz, Nicholas Shukeir, Megumi Onishi-Seebacher, Suzanne van de Nobelen, Thomas Jenuwein
The Suv39h1 and Suv39h2 histone lysine methyltransferases are hallmark enzymes at mammalian heterochromatin. We show here that the mouse Suv39h2 enzyme differs from Suv39h1 by containing an N-terminal basic domain that facilitates retention at mitotic chromatin and provides an additional affinity for major satellite repeat RNA. To analyze an RNA-dependent interaction with chromatin, we purified native nucleosomes from mouse ES cells and detect that Suv39h1 and Suv39h2 exclusively associate with poly-nucleosomes...
August 1, 2017: ELife
https://www.readbyqxmd.com/read/28759577/modular-function-of-long-noncoding-rna-coldair-in-the-vernalization-response
#19
Dong-Hwan Kim, Yanpeng Xi, Sibum Sung
The long noncoding RNA COLDAIR is necessary for the repression of a floral repressor FLOWERING LOCUS C (FLC) during vernalization in Arabidopsis thaliana. The repression of FLC is mediated by increased enrichment of Polycomb Repressive Complex 2 (PRC2) and subsequent trimethylation of Histone H3 Lysine 27 (H3K27me3) at FLC chromatin. In this study we found that the association of COLDAIR with chromatin occurs only at the FLC locus and that the central region of the COLDAIR transcript is critical for this interaction...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28754859/ccat-1-promotes-proliferation-and-inhibits-apoptosis-of-cervical-cancer-cells-via-the-wnt-signaling-pathway
#20
Jun Zhang, Yali Gao
Though the long noncoding RNA colon cancer associated transcript-1 (CCAT-1) has been shown to be involved in tumors of other tissues, its involvement in cervical cancer is still unknown. Therefore, the aim of this study was to investigate the molecular mechanism of CCAT-1 in cervical cancer. We quantified the expression of CCAT-1 long noncoding RNA in samples of cervical cancer tissue by real-time PCR. Effects of CCAT-1 expression on the proliferation and apoptosis of HeLa and CaSki cells were assessed by cell-count, colony-formation, and flow cytometry assays...
July 10, 2017: Oncotarget
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