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Chromatin-associated RNA

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https://www.readbyqxmd.com/read/29467285/angiogenic-patterning-by-steel-an-endothelial-enriched-long-noncoding-rna
#1
H S Jeffrey Man, Aravin N Sukumar, Gabrielle C Lam, Paul J Turgeon, Matthew S Yan, Kyung Ha Ku, Michelle K Dubinsky, J J David Ho, Jenny Jing Wang, Sunit Das, Nora Mitchell, Peter Oettgen, Michael V Sefton, Philip A Marsden
Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell type-specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for s pliced- t ranscript e ndothelial- e nriched lncRNA (STEEL) in angiogenic potential, macrovascular/microvascular identity, and shear stress responsiveness...
February 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29463953/autosomal-dominant-retinitis-pigmentosa-rhodopsin-mutant-q344x-drives-specific-alterations-in-chromatin-complex-gene-transcription
#2
Katie L Bales, Lara Ianov, Andrew J Kennedy, J David Sweatt, Alecia K Gross
Purpose: Epigenetic and transcriptional mechanisms have been shown to contribute to long-lasting functional changes in adult neurons. The purpose of this study was to identify any such modifications in diseased retinal tissues from a mouse model of rhodopsin mutation-associated autosomal dominant retinitis pigmentosa (ADRP), Q344X, relative to age-matched wild-type (WT) controls. Methods: We performed RNA sequencing (RNA-seq) at poly(A) selected RNA to profile the transcriptional patterns in 3-week-old ADRP mouse model rhodopsin Q344X compared to WT controls...
2018: Molecular Vision
https://www.readbyqxmd.com/read/29458328/dynamics-of-promoter-bivalency-and-rnap-ii-pausing-in-mouse-stem-and-differentiated-cells
#3
Anna Mantsoki, Guillaume Devailly, Anagha Joshi
BACKGROUND: Mammalian embryonic stem cells display a unique epigenetic and transcriptional state to facilitate pluripotency by maintaining lineage-specification genes in a poised state. Two epigenetic and transcription processes involved in maintaining poised state are bivalent chromatin, characterized by the simultaneous presence of activating and repressive histone methylation marks, and RNA polymerase II (RNAPII) promoter proximal pausing. However, the dynamics of histone modifications and RNAPII at promoters in diverse cellular contexts remains underexplored...
February 20, 2018: BMC Developmental Biology
https://www.readbyqxmd.com/read/29458327/histone-modification-profiling-in-breast-cancer-cell-lines-highlights-commonalities-and-differences-among-subtypes
#4
Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L Allton, Dana Richardson, Jing Li, Hector L Franco, Anusha Nagari, Venkat S Malladi, Luis Della Coletta, Melissa S Simper, Khandan Keyomarsi, Jianjun Shen, Mark T Bedford, Xiaobing Shi, Michelle C Barton, W Lee Kraus, Wei Li, Sharon Y R Dent
BACKGROUND: Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy. RESULTS: To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells...
February 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29456084/rescue-of-fragile-x-syndrome-neurons-by-dna-methylation-editing-of-the-fmr1-gene
#5
X Shawn Liu, Hao Wu, Marine Krzisch, Xuebing Wu, John Graef, Julien Muffat, Denes Hnisz, Charles H Li, Bingbing Yuan, Chuanyun Xu, Yun Li, Dan Vershkov, Angela Cacace, Richard A Young, Rudolf Jaenisch
Fragile X syndrome (FXS), the most common genetic form of intellectual disability in males, is caused by silencing of the FMR1 gene associated with hypermethylation of the CGG expansion mutation in the 5' UTR of FMR1 in FXS patients. Here, we applied recently developed DNA methylation editing tools to reverse this hypermethylation event. Targeted demethylation of the CGG expansion by dCas9-Tet1/single guide RNA (sgRNA) switched the heterochromatin status of the upstream FMR1 promoter to an active chromatin state, restoring a persistent expression of FMR1 in FXS iPSCs...
February 8, 2018: Cell
https://www.readbyqxmd.com/read/29447171/brca2-pds5-and-wapl-differentially-control-cohesin-chromosome-association-and-function
#6
Ziva Misulovin, Michelle Pherson, Maria Gause, Dale Dorsett
The cohesin complex topologically encircles chromosomes and mediates sister chromatid cohesion to ensure accurate chromosome segregation upon cell division. Cohesin also participates in DNA repair and gene transcription. The Nipped-B-Mau2 protein complex loads cohesin onto chromosomes and the Pds5-Wapl complex removes cohesin. Pds5 is also essential for sister chromatid cohesion, indicating that it has functions beyond cohesin removal. The Brca2 DNA repair protein interacts with Pds5, but the roles of this complex beyond DNA repair are unknown...
February 15, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29442331/role-of-zic-family-proteins-in-transcriptional-regulation-and-chromatin-remodeling
#7
Minoru Hatayama, Jun Aruga
Proper functions of Zic proteins are essential for animals in health and disease. Here, we summarize our current understanding of the molecular properties and functions of the Zic family across animal species and paralog subtypes. Zics are basic proteins with some posttranslational modifications and can move to the cell nucleus via importin- and CRM1-based nucleocytoplasmic shuttling mechanisms. Degradation is mediated by the ubiquitin proteasome system. Many Zic proteins are capable of binding to two types of target DNA sequences (CTGCTG-core-type and GC-stretch-type)...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29438720/selenite-and-methylseleninic-acid-epigenetically-affects-distinct-gene-sets-in-myeloid-leukemia-a-genome-wide-epigenetic-analysis
#8
Prajakta Khalkar, Hani Abdulkadir Ali, Paula Codó, Nuria Díaz Argelich, Anni Martikainen, Mohsen Karimi Arzenani, Sören Lehmann, Julian Walfridsson, Johanna Ungerstedt, Aristi P Fernandes
Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq)...
February 10, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29432179/parp-1-dependent-recruitment-of-cold-inducible-rna-binding-protein-promotes-double-strand-break-repair-and-genome-stability
#9
Jung-Kuei Chen, Wen-Ling Lin, Zhang Chen, Hung-Wen Liu
Maintenance of genome integrity is critical for both faithful propagation of genetic information and prevention of mutagenesis induced by various DNA damage events. Here we report cold-inducible RNA-binding protein (CIRBP) as a newly identified key regulator in DNA double-strand break (DSB) repair. On DNA damage, CIRBP temporarily accumulates at the damaged regions and is poly(ADP ribosyl)ated by poly(ADP ribose) polymerase-1 (PARP-1). Its dissociation from the sites of damage may depend on its phosphorylation status as mediated by phosphatidylinositol 3-kinase-related kinases...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29429127/tissue-and-strain-specific-effects-of-a-genotoxic-carcinogen-1-3-butadiene-on-chromatin-and-transcription
#10
Jennifer W Israel, Grace A Chappell, Jeremy M Simon, Sebastian Pott, Alexias Safi, Lauren Lewis, Paul Cotney, Hala S Boulos, Wanda Bodnar, Jason D Lieb, Gregory E Crawford, Terrence S Furey, Ivan Rusyn
Epigenetic effects of environmental chemicals are under intense investigation to fill existing knowledge gaps between environmental/occupational exposures and adverse health outcomes. Chromatin accessibility is one prominent mechanism of epigenetic control of transcription, and understanding of the chemical effects on both could inform the causal role of epigenetic alterations in disease mechanisms. In this study, we hypothesized that baseline variability in chromatin organization and transcription profiles among various tissues and mouse strains influence the outcome of exposure to the DNA damaging chemical 1,3-butadiene...
February 10, 2018: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29428901/fragile-x-mental-retardation-protein-participates-in-non-coding-rna-pathways
#11
En-Hui Li, Xin Zhao, Ce Zhang, Wei Liu
Fragile X syndrome is one of the most common forms of inherited intellectual disability. It is caused by mutations of the Fragile X mental retardation 1(FMR1) gene, resulting in either the loss or abnormal expression of the Fragile X mental retardation protein (FMRP). Recent research showed that FMRP participates in non-coding RNA pathways and plays various important roles in physiology, thereby extending our knowledge of the pathogenesis of the Fragile X syndrome. Initial studies showed that the Drosophila FMRP participates in siRNA and miRNA pathways by interacting with Dicer, Ago1 and Ago2, involved in neural activity and the fate determination of the germline stem cells...
February 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29428674/genes-and-pathways-regulated-by-androgens-in-human-neural-cells-potential-candidates-for-the-male-excess-in-autism-spectrum-disorder
#12
Angélique Quartier, Laure Chatrousse, Claire Redin, Céline Keime, Nicolas Haumesser, Anne Maglott-Roth, Laurent Brino, Stéphanie Le Gras, Alexandra Benchoua, Jean-Louis Mandel, Amélie Piton
BACKGROUND: Prenatal exposure to androgens during brain development in male individuals may participate to increase their susceptibility to develop neurodevelopmental disorders such as autism spectrum disorder (ASD) and intellectual disability. However, little is known about the action of androgens in human neural cells. METHODS: We used human neural stem cells differentiated from embryonic stem cells to investigate targets of androgens. RESULTS: RNA sequencing revealed that treatment with dihydrotestosterone (DHT) leads to subtle but significant changes in the expression of about 200 genes, encoding proteins of extracellular matrix or involved in signal transduction of growth factors (e...
January 9, 2018: Biological Psychiatry
https://www.readbyqxmd.com/read/29425494/crosstalk-between-the-rna-methylation-and-histone-binding-activities-of-mepce-regulates-p-tefb-activation-on-chromatin
#13
Samantha B Shelton, Nakul M Shah, Nathan S Abell, Sravan K Devanathan, Marvin Mercado, Blerta Xhemalçe
RNAP II switching from the paused to the productive transcription elongation state is a pivotal regulatory step that requires specific phosphorylations catalyzed by the P-TEFb kinase. Nucleosolic P-TEFb activity is inhibited by its interaction with the ribonuclear protein complex built around the 7SK small nuclear RNA (7SK snRNP). MePCE is the RNA methyltransferase that methylates and stabilizes 7SK in the nucleosol. Here, we report that MePCE also binds chromatin through the histone H4 tail to serve as a P-TEFb activator at specific genes important for cellular identity...
February 6, 2018: Cell Reports
https://www.readbyqxmd.com/read/29414823/serine-threonine-kinase-35-a-target-gene-of-stat3-regulates-the-proliferation-and-apoptosis-of-osteosarcoma-cells
#14
Zhong Wu, Jie Liu, Siyuan Hu, Yuchang Zhu, Shaohua Li
BACKGROUND/AIMS: Serine/threonine kinase 35 (STK35) may be associated with Parkinson disease and human colorectal cancer, but there have been no reports on the expression levels or roles of STK35 in osteosarcoma. METHODS: STK35 mRNA expression was determined in osteosarcoma and bone cyst tissues by real-time PCR. Cell proliferation and apoptosis were assessed by Cell Counting Kit-8 (CCK-8) assay and flow cytometry analysis, respectively. RESULTS: STK35 was up-regulated in osteosarcoma tissues as indicated by analyzing publicly available expression data (GEO dataset E-MEXP-3628) and real-time PCR analysis on our own cohort...
January 31, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29414698/fret-image-correlation-spectroscopy-reveals-rnapii-independent-p-tefb-recruitment-on-chromatin
#15
Gabriel Bidaux, Corentin Le Nézet, Mariano Gonzalez Pisfil, Mélanie Henry, Alessandro Furlan, Oliver Bensaude, Bernard Vandenbunder, Laurent Héliot
Biochemical studies have revealed that the RNA Polymerase II (RNAPII) pause release is triggered by phosphorylation of the transcription machinery by the positive transcription elongation factor b (P-TEFb). However, there are no direct report that P-TEFb and RNA polymerase II interact in single living cells and the biophysical mechanisms mediating this association are still unclear. Förster resonance energy transfer (FRET) detects molecular interactions at the subcellular level. Time domain fluorescence lifetime imaging provides an accurate quantification of FRET efficiency, EFRET, because it is fluorochrome concentration-independent and insensitive to fluorescence bleed-through...
February 6, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29411384/a-novel-antisense-long-noncoding-rna-twisted-leaf-maintains-leaf-blade-flattening-by-regulating-its-associated-sense-r2r3-myb-gene-in-rice
#16
Xue Liu, Dayong Li, Donglei Zhang, Dedong Yin, Yi Zhao, Chengjun Ji, Xianfeng Zhao, Xiaobing Li, Qun He, Runsheng Chen, Songnian Hu, Lihuang Zhu
Natural antisense long noncoding RNAs (lncRNAs) are widespread in many organisms. However, their biological functions remain largely unknown, particularly in plants. We report the identification and characterization of an endogenous lncRNA, TWISTED LEAF (TL), which is transcribed from the opposite strand of the R2R3 MYB transcription factor gene locus, OsMYB60, in rice (Oryza sativa). TL and OsMYB60 were found to be coexpressed in many different tissues, and the expression level of TL was higher than that of OsMYB60...
February 7, 2018: New Phytologist
https://www.readbyqxmd.com/read/29408647/whole-exome-mutational-and-transcriptional-landscapes-of-combined-hepatocellular-cholangiocarcinoma-and-intrahepatic-cholangiocarcinoma-reveal-molecular-diversity
#17
Zhen-Hao Liu, Bao-Feng Lian, Qiong-Zhu Dong, Han Sun, Jin-Wang Wei, Yuan-Yuan Sheng, Wei Li, Yixue Li, Lu Xie, Lei Liu, Lun-Xiu Qin
BACKGROUND: Primary liver cancer (PLC) is the third largest contributor to cancer mortality in the world. PLC is a heterogeneous disease that encompasses several biologically distinct subtypes including hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). CHC is a distinct, albeit rare, subtype of PLC and is comprised of cells with histopathological features of both HCC and ICC. Several studies have focused on the mutation and expression landscapes of HCC and ICC...
January 31, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29408237/chromatin-modification-and-global-transcriptional-silencing-in-the-oocyte-mediated-by-the-mrna-decay-activator-zfp36l2
#18
Jennifer N Dumdie, Kyucheol Cho, Madhuvanthi Ramaiah, David Skarbrevik, Sergio Mora-Castilla, Deborah J Stumpo, Jens Lykke-Andersen, Louise C Laurent, Perry J Blackshear, Miles F Wilkinson, Heidi Cook-Andersen
Global transcriptional silencing is a highly conserved mechanism central to the oocyte-to-embryo transition. We report the unexpected discovery that global transcriptional silencing in oocytes depends on an mRNA decay activator. Oocyte-specific loss of ZFP36L2 an RNA-binding protein that promotes AU-rich element-dependent mRNA decay prevents global transcriptional silencing and causes oocyte maturation and fertilization defects, as well as complete female infertility in the mouse. Single-cell RNA sequencing revealed that ZFP36L2 downregulates mRNAs encoding transcription and chromatin modification regulators, including a large group of mRNAs for histone demethylases targeting H3K4 and H3K9, which we show are bound and degraded by ZFP36L2...
February 5, 2018: Developmental Cell
https://www.readbyqxmd.com/read/29402885/transcriptional-decomposition-reveals-active-chromatin-architectures-and-cell-specific-regulatory-interactions
#19
Sarah Rennie, Maria Dalby, Lucas van Duin, Robin Andersson
Transcriptional regulation is tightly coupled with chromosomal positioning and three-dimensional chromatin architecture. However, it is unclear what proportion of transcriptional activity is reflecting such organisation, how much can be informed by RNA expression alone and how this impacts disease. Here, we develop a computational transcriptional decomposition approach separating the proportion of expression associated with genome organisation from independent effects not directly related to genomic positioning...
February 5, 2018: Nature Communications
https://www.readbyqxmd.com/read/29399063/expression-profile-and-promoter-analysis-of-hepis
#20
Fen Hu, Yunfeng Zhang
Human embryo lung cellular protein interacting with severe acute respiratory syndrome-coronavirus nonstructural protein-10 (HEPIS) is a novel transcriptional repressor, the expression profile and promoter activity of which have not been well studied. In the present study, in situ hybridization of RNA was used to study differential HEPIS expression levels in different types of cancer and normal tissues. A total of six truncated lengths of the HEPIS promoter regulatory sequences were cloned into the pGL3-basic vector, and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and dual luciferase reporter assays were performed...
January 2018: Experimental and Therapeutic Medicine
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