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Chromatin-associated RNA

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https://www.readbyqxmd.com/read/29684168/emerin-modulates-spatial-organization-of-chromosome-territories-in-cells-on-softer-matrices
#1
Roopali Pradhan, Devika Ranade, Kundan Sengupta
Cells perceive and relay external mechanical forces into the nucleus through the nuclear envelope. Here we examined the effect of lowering substrate stiffness as a paradigm to address the impact of altered mechanical forces on nuclear structure-function relationships. RNA sequencing of cells on softer matrices revealed significant transcriptional imbalances, predominantly in chromatin associated processes and transcriptional deregulation of human Chromosome 1. Furthermore, 3-Dimensional fluorescence in situ hybridization (3D-FISH) analyses showed a significant mislocalization of Chromosome 1 and 19 Territories (CT) into the nuclear interior, consistent with their transcriptional deregulation...
April 19, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29678826/rna-binding-protein-hur-regulates-scn5a-expression-through-stabilizing-mef2c-transcription-factor-mrna
#2
Anyu Zhou, Guangbin Shi, Gyeoung-Jin Kang, An Xie, Hong Liu, Ning Jiang, Man Liu, Euy-Myoung Jeong, Samuel C Dudley
BACKGROUND: Although transcription is the initial process of gene expression, posttranscriptional gene expression regulation has also played a critical role for fine-tuning gene expression in a fast, precise, and cost-effective manner. Although the regulation of sodium channel α-subunit ( SCN5A ) mRNA expression has been studied at both transcriptional and pre-mRNA splicing levels, the molecular mechanisms governing SCN5A mRNA expression are far from clear. METHODS AND RESULTS: Herein, we show that, as evidenced by ribonucleoprotein immunoprecipitation assay, RNA binding protein Hu antigen R/ELAV like RNA binding protein 1 (HuR/ELAVL1) and myocyte enhancer factor-2C (MEF2C) transcription factor mRNA are associated...
April 20, 2018: Journal of the American Heart Association
https://www.readbyqxmd.com/read/29676649/asbestos-induces-epigenetic-repression-of-ras-association-domain-containing-protein-1-p16-kinase-4a-inhibitor-and-p14-alternative-reading-frame-in-normal-human-mesothelial-cells
#3
Sichuan Xi, Eden C Payabyab, David M Straughan, Emily S Reardon, Mary Zhang, Julie A Hong, R Taylor Ripley, Chuong D Hoang, David S Schrump
RATIONALE: Whereas asbestos burden has been linked to cytogenetic alterations in malignant pleural mesotheliomas, epigenetic aberrations induced by these fibers have not been fully delineated. OBJECTIVES: The objective of this study was to establish an in vitro model to characterize early epigenetic events potentially contributing to malignant pleural mesothelioma. METHODS: Normal human mesothelial cells (LP9 and LP3) were cultured with or without crocidolite asbestos fibers (1 or 2 μg/cm2 ) for up to 10 days...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29671830/seed-dormancy-involves-a-transcriptional-program-that-supports-early-plastid-functionality-during-imbibition
#4
Alberto Gianinetti, Franca Finocchiaro, Paolo Bagnaresi, Antonella Zechini, Primetta Faccioli, Luigi Cattivelli, Giampiero Valè, Chiara Biselli
Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days)...
April 19, 2018: Plants (Basel, Switzerland)
https://www.readbyqxmd.com/read/29670067/cpg-methylation-changes-g-quadruplex-structures-derived-from-gene-promoters-and-interaction-with-vegf-and-sp1
#5
Kaori Tsukakoshi, Shiori Saito, Wataru Yoshida, Shinichi Goto, Kazunori Ikebukuro
G-quadruplex (G4) is a DNA/RNA conformation that consists of two or more G-tetrads resulting from four-guanine bases connected by Hoogsteen-type hydrogen bonds, which is often found in the telomeres of chromatin, as well as in the promoter regions of genes. The function of G4 in the genomic DNA is being elucidated and some G4-protein interactions have been reported; these are believed to play a role in vital cellular functions. In this study, we focused on CpG methylation, a well-known epigenetic modification of the genomic DNA, especially found in the promoter regions...
April 18, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29669339/upregulation-of-lncdq-is-associated-with-poor-prognosis-and-promotes-tumor-progression-via-epigenetic-regulation-of-the-emt-pathway-in-hcc
#6
Bing Zeng, Zewei Lin, Huilin Ye, Di Cheng, Guangtao Zhang, Jindu Zhou, Zhifeng Huang, Meng Wang, Canfeng Cai, Jun Zeng, Chaoming Tang, Jikui Liu
BACKGROUND/AIMS: Long noncoding RNAs (lncRNAs) are key regulators of cancer initiation and progression. In this study, we investigated the clinical value and functional role of LncRNA DQ786243 (LncDQ) in the pathogenesis of hepatocellular carcinoma (HCC). METHODS: To investigate the expression level of LncDQ in HCC, we performed quantitative real-time PCR using total RNA extracted from HCC tumor tissues and their matched non-neoplastic counterparts, as well as from the serum of HCC patients and healthy volunteers...
April 13, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29665865/integrative-analysis-reveals-functional-and-regulatory-roles-of-h3k79me2-in-mediating-alternative-splicing
#7
Tianbao Li, Qi Liu, Nick Garza, Steven Kornblau, Victor X Jin
BACKGROUND: Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers. METHODS: In this study, we integrated AS events derived from RNA-seq with H3K79me2 ChIP-seq data across 34 different normal and cancer cell types and found the higher enrichment of H3K79me2 in two AS types, skipping exon (SE) and alternative 3' splice site (A3SS)...
April 17, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29662614/transcriptional-orchestration-of-mitochondrial-homeostasis-in-a-cellular-model-of-pgc-1-related-coactivator-dependent-thyroid-tumor
#8
Solenne Dumont, Soazig Le Pennec, Audrey Donnart, Raluca Teusan, Marja Steenman, Catherine Chevalier, Rémi Houlgatte, Frédérique Savagner
The PGC-1 (Peroxisome proliferator-activated receptor Gamma Coactivator-1) family of coactivators (PGC-1α, PGC-1β, and PRC) plays a central role in the transcriptional control of mitochondrial biogenesis and oxidative phosphorylation (OXPHOS) processes. These coactivators integrate mitochondrial energy production into cell metabolism using complementary pathways. The XTC.UC1 cell line is a mitochondria-rich model of thyroid tumors whose biogenesis is almost exclusively dependent on PRC. Here we aim to propose an integrative view of the cellular pathways regulated by PRC through integration of cDNA and miRNA microarray data and chromatin immunoprecipitation results obtained from XTC...
March 23, 2018: Oncotarget
https://www.readbyqxmd.com/read/29661885/the-long-non-coding-rna-paupar-promotes-kap1-dependent-chromatin-changes-and-regulates-olfactory-bulb-neurogenesis
#9
Ioanna Pavlaki, Farah Alammari, Bin Sun, Neil Clark, Tamara Sirey, Sheena Lee, Dan J Woodcock, Chris P Ponting, Francis G Szele, Keith W Vance
Many long non-coding RNAs (lncRNAs) are expressed during central nervous system (CNS) development, yet their in vivo roles and mechanisms of action remain poorly understood. Paupar , a CNS-expressed lncRNA, controls neuroblastoma cell growth by binding and modulating the activity of transcriptional regulatory elements in a genome-wide manner. We show here that the Paupar lncRNA directly binds KAP1, an essential epigenetic regulatory protein, and thereby regulates the expression of shared target genes important for proliferation and neuronal differentiation...
April 16, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29659982/transcription-start-site-analysis-reveals-widespread-divergent-transcription-in-d-melanogaster-and-core-promoter-encoded-enhancer-activities
#10
Sarah Rennie, Maria Dalby, Marta Lloret-Llinares, Stylianos Bakoulis, Christian Dalager Vaagensø, Torben Heick Jensen, Robin Andersson
Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed...
April 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29659108/bel1-like-homeodomain-11-regulates-chloroplast-development-and-chlorophyll-synthesis-in-tomato-fruit
#11
Lanhuan Meng, Zhongqi Fan, Qiang Zhang, Cuicui Wang, Ying Gao, Yikang Deng, Benzhong Zhu, Hongliang Zhu, Chen Jianye, Wei Shan, Xunren Yin, Silin Zhong, Donald Grierson, Cai-Zhong Jiang, Yunbo Luo, Da-Qi Fu
Chloroplast development and chlorophyll(Chl)metabolism in unripe tomato contribute to the growth and quality of the fruit. However, the mechanism is poorly understood. In this work, we initially studied seven homeobox-containing transcription factors (TFs) with specific ripening-associated expression patterns by virus-induced gene silencing (VIGS) technology and found that inhibiting the expression of one of these TFs, BEL1-LIKE HOMEODOMAIN11 (SlBEL11), significantly increased Chl levels in unripe tomato fruit...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29659013/dietary-fat-and-fiber-interact-to-uniquely-modify-global-histone-post-translational-epigenetic-programming-in-a-rat-colon-cancer-progression-model
#12
Karen Triff, Mathew W McLean, Evelyn Callaway, Jennifer Goldsby, Ivan Ivanov, Robert S Chapkin
Dietary fermentable fiber generates short-chain fatty acids (SCFA), e.g., butyrate, in the colonic lumen which serves as a chemoprotective histone deacetylase inhibitor and/or as an acetylation substrate for histone acetylases. In addition, n-3 polyunsaturated fatty acids (n-3 PUFA) in fish oil can affect the chromatin landscape by acting as ligands for tumor suppressive nuclear receptors. In an effort to gain insight into the global dimension of post-translational modification of histones (including H3K4me3 and H3K9ac) and clarify the chemoprotective impact of dietary bioactive compounds on transcriptional control in a preclinical model of colon cancer, we generated high-resolution genome-wide RNA (RNA-Seq) and "chromatin-state" (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed diets containing bioactive (i) fish oil, (ii) fermentable fiber (a rich source of SCFA), (iii) a combination of fish oil plus pectin or (iv) control, devoid of fish oil or pectin...
April 16, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29657305/strengths-and-weaknesses-of-the-current-strategies-to-map-and-characterize-r-loops
#13
REVIEW
Vincent Vanoosthuyse
R-loops are evolutionarily conserved three-stranded structures that result from the formation of stable DNA:RNA hybrids in the genome. R-loops have attracted increasing interest in recent years as potent regulators of gene expression and genome stability. In particular, their strong association with severe replication stress makes them potential oncogenic structures. Despite their importance, the rules that govern their formation and their dynamics are still controversial and an in-depth description of their direct impact on chromatin organization and DNA transactions is still lacking...
March 27, 2018: Non-Coding RNA
https://www.readbyqxmd.com/read/29650150/the-swi-snf-subunit-swi3b-regulates-iamt1-expression-via-chromatin-remodeling-in-arabidopsis-leaf-development
#14
Wenxing Han, Danlu Han, Zhipeng He, Huan Hu, Qian Wu, Juanjuan Zhang, Jieming Jiang, Genji Qin, Yuhai Cui, Jianbin Lai, Chengwei Yang
The SWI/SNF complex is crucial to chromatin remodeling in various biological processes in different species, but the distinct functions of its components in plant development remain unclear. Here we uncovered the role of SWI3B, a subunit of the Arabidopsis thaliana SWI/SNF complex, via RNA interference. Knockdown of SWI3B resulted in an upward-curling leaf phenotype. Further investigation showed that the RNA level of IAA carboxyl methyltransferase 1 (IAMT1), encoding an enzyme involved in auxin metabolism, was dramatically elevated in the knockdown (SWI3B-RNAi) plants...
June 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29648534/chromatin-associated-rna-sequencing-char-seq-maps-genome-wide-rna-to-dna-contacts
#15
Jason C Bell, David Jukam, Nicole A Teran, Viviana I Risca, Owen K Smith, Whitney L Johnson, Jan M Skotheim, William James Greenleaf, Aaron F Straight
RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing...
April 12, 2018: ELife
https://www.readbyqxmd.com/read/29644006/the-long-non-coding-rna-hotair-is-transcriptionally-activated-by-hoxa9-and-is-an-independent-prognostic-marker-in-patients-with-malignant-glioma
#16
Ana Xavier-Magalhães, Céline S Gonçalves, Anne Fogli, Tatiana Lourenço, Marta Pojo, Bruno Pereira, Miguel Rocha, Maria Celeste Lopes, Inês Crespo, Olinda Rebelo, Herminio Tão, João Lima, Ricardo Moreira, Afonso A Pinto, Chris Jones, Rui M Reis, Joseph F Costello, Philippe Arnaud, Nuno Sousa, Bruno M Costa
The lncRNA HOTAIR has been implicated in several human cancers. Here, we evaluated the molecular alterations and upstream regulatory mechanisms of HOTAIR in glioma, the most common primary brain tumors, and its clinical relevance. HOTAIR gene expression, methylation, copy-number and prognostic value were investigated in human gliomas integrating data from online datasets and our cohorts. High levels of HOTAIR were associated with higher grades of glioma, particularly IDH wild-type cases. Mechanistically, HOTAIR was overexpressed in a gene dosage-independent manner, while DNA methylation levels of particular CpGs in HOTAIR locus were associated with HOTAIR expression levels in GBM clinical specimens and cell lines...
March 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29642935/sp1-induced-upregulation-of-lncrna-spry4-it1-exerts-oncogenic-properties-by-scaffolding-ezh2-lsd1-dnmt1-and-sponging-mir-101-3p-in-cholangiocarcinoma
#17
Yi Xu, Yue Yao, Xingming Jiang, Xiangyu Zhong, Zhidong Wang, Chunlong Li, Pengcheng Kang, Kaiming Leng, Daolin Ji, Zhenglong Li, Lining Huang, Wei Qin, Yunfu Cui
BACKGROUND: Accumulating evidence has indicated that long non-coding RNAs (lncRNAs) behave as a novel class of transcription products during multiple cancer processes. However, the mechanisms responsible for their alteration in cholangiocarcinoma (CCA) are not fully understood. METHODS: The expression of SPRY4-IT1 in CCA tissues and cell lines was determined by RT-qPCR, and the association between SPRY4-IT1 transcription and clinicopathologic features was analyzed...
April 11, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29628212/chromatin-higher-order-folding-a-perspective-with-linker-dna-angles
#18
REVIEW
Sergei A Grigoryev
The mechanism by which the "beads-on-a-string" nucleosome chain folds into various higher-order chromatin structures in eukaryotic cell nuclei is still poorly understood. The various models depicting higher-order chromatin as regular helical fibers and the very opposite "polymer melt" theory imply that interactions between nucleosome "beads" make the main contribution to the chromatin compaction. Other models in which the geometry of linker DNA "strings" entering and exiting the nucleosome define the three-dimensional structure predict that small changes in the linker DNA configuration may strongly affect nucleosome chain folding and chromatin higher-order structure...
April 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29626011/centromere-transcription-allows-cenp-a-to-transit-from-chromatin-association-to-stable-incorporation
#19
Georg O M Bobkov, Nick Gilbert, Patrick Heun
Centromeres are essential for chromosome segregation and are specified epigenetically by the presence of the histone H3 variant CENP-A. In flies and humans, replenishment of the centromeric mark is uncoupled from DNA replication and requires the removal of H3 "placeholder" nucleosomes. Although transcription at centromeres has been previously linked to the loading of new CENP-A, the underlying molecular mechanism remains poorly understood. Here, we used Drosophila melanogaster tissue culture cells to show that centromeric presence of actively transcribing RNA polymerase II temporally coincides with de novo deposition of dCENP-A...
April 6, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29625054/a-pan-cancer-analysis-of-enhancer-expression-in-nearly-9000-patient-samples
#20
Han Chen, Chunyan Li, Xinxin Peng, Zhicheng Zhou, John N Weinstein, Han Liang
The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on "chromatin-state" to explain their interplay...
April 5, 2018: Cell
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