keyword
MENU ▼
Read by QxMD icon Read
search

Chromatin-associated RNA

keyword
https://www.readbyqxmd.com/read/28531944/upregulation-of-ccat2-promotes-cell-proliferation-by-repressing-the-p15-in-breast-cancer
#1
Xin Deng, Yi Zhao, Xin Wu, Guoqing Song
BACKGROUND: Long non-coding RNAs (lncRNAs) are demonstrated to function as modulators of both transcriptional and post-transcriptional regulation in various types of tumors progression. The objective of the study is to investigate the clinical significance and underlying mechanism of Colon cancer associated transcript 2 (CCAT2) involved in breast cancer. METHODS: QT-PCR was performed to examine the relative expression levels of CCAT2 in breast cancer tissues and adjacent normal tissues...
May 17, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28526340/unfolding-the-pathogenesis-of-scleroderma-through-genomics-and-epigenomics
#2
REVIEW
Pei-Suen Tsou, Amr H Sawalha
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated...
May 16, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28525378/irf5-is-elevated-in-childhood-onset-sle-and-regulated-by-histone-acetyltransferase-and-histone-deacetylase-inhibitors
#3
Jin Shu, Ling Li, Lan-Bo Zhou, Jun Qian, Zhi-Dan Fan, Li-Li Zhuang, Lu-Lu Wang, Rui Jin, Hai-Guo Yu, Guo-Ping Zhou
Interferon regulatory factor 5 (IRF5) plays a critical role in the induction of type I interferon, proinflammatory cytokines and chemokines, and participates in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE). However, the relationship between IRF5 and childhood-onset SLE remains elusive. In the present study, we demonstrated that levels of mRNA expression of IRF5, IFN-α, and Sp1 were significantly increased in childhood-onset SLE, as seen on quantitative real-time PCR, and the expression of Sp1 and IFN-α was positively correlated with IRF5...
May 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28515787/a-computational-approach-for-the-functional-classification-of-the-epigenome
#4
Francesco Gandolfi, Anna Tramontano
BACKGROUND: In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, we propose a novel approach to explore functional interactions between different epigenetic modifications and extract combinatorial profiles that can be used to annotate the chromatin in a finite number of functional classes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28507061/rnf8-mediates-histone-h3-ubiquitylation-and-promotes-glycolysis-and-tumorigenesis
#5
Yan Xia, Weiwei Yang, Ming Fa, Xinjian Li, Yugang Wang, Yuhui Jiang, Yanhua Zheng, Jong-Ho Lee, Jing Li, Zhimin Lu
Disassembly of nucleosomes in which genomic DNA is packaged with histone regulates gene expression. However, the mechanisms underlying nucleosome disassembly for gene expression remain elusive. We show here that epidermal growth factor receptor activation results in the binding of the RNF8 forkhead-associated domain to pyruvate kinase M2-phosphorylated histone H3-T11, leading to K48-linked polyubiquitylation of histone H3 at K4 and subsequent proteasome-dependent protein degradation. In addition, H3 polyubiquitylation induces histone dissociation from chromatin, nucleosome disassembly, and binding of RNA polymerase II to MYC and CCND1 promoter regions for transcription...
May 15, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28506839/evolutionary-relationships-among-protein-lysine-deacetylases-of-parasites-causing-neglected-diseases
#6
Larissa L S Scholte, Marina M Mourão, Fabiano Sviatopolk-Mirsky Pais, Jelena Melesina, Dina Robaa, Angela C Volpini, Wolfgang Sippl, Raymond J Pierce, Guilherme Oliveira, Laila A Nahum
The availability of the genomic data of diverse parasites provides an opportunity to identify new drug candidates against neglected tropical diseases affecting people worldwide. Histone modifying enzymes (HMEs) are potential candidates since they play key roles in the regulation of chromatin modifications, thus globally regulating gene expression. Furthermore, aberrant epigenetic states are often associated with human diseases, leading to great interest in HMEs as therapeutic targets. Our work focused on two families of protein lysine deacetylases (HDACs and sirtuins)...
May 13, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28506463/rna-pol-ii-dynamics-modulate-co-transcriptional-chromatin-modification-ctd-phosphorylation-and-transcriptional-direction
#7
Nova Fong, Tassa Saldi, Ryan M Sheridan, Michael A Cortazar, David L Bentley
Eukaryotic genes are marked by conserved post-translational modifications on the RNA pol II C-terminal domain (CTD) and the chromatin template. How the 5'-3' profiles of these marks are established is poorly understood. Using pol II mutants in human cells, we found that slow transcription repositioned specific co-transcriptionally deposited chromatin modifications; histone H3 lysine 36 trimethyl (H3K36me3) shifted within genes toward 5' ends, and histone H3 lysine 4 dimethyl (H3K4me2) extended farther upstream of start sites...
May 18, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28504305/intranuclear-and-higher-order-chromatin-organization-of-the-major-histone-gene-cluster-in-breast-cancer
#8
Andrew J Fritz, Prachi N Ghule, Joseph R Boyd, Coralee E Tye, Natalie A Page, Deli Hong, Adam S Weinheimer, A Rasim Barutcu, Diana L Gerrard, Seth Frietze, Sayyed K Zaidi, Anthony Imbalzano, Jane B Lian, Janet L Stein, Gary S Stein
Alterations in nuclear morphology are common in cancer progression. However, the degree to which gross morphological abnormalities translate into compromised higher-order chromatin organization is poorly understood. To explore the functional links between gene expression and chromatin structure in breast cancer, we performed RNA-seq gene expression analysis on the basal breast cancer progression model based on human MCF10A cells. Positional gene enrichment identified the major histone gene cluster at chromosome 6p22 as one of the most significantly upregulated (and not amplified) clusters of genes from the normal-like MCF10A to premalignant MCF10AT1 and metastatic MCF10CA1a cells...
May 15, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28502041/glucose-can-epigenetically-alter-the-gene-expression-of-neurotrophic-factors-in-the-murine-brain-cells
#9
Md Shamim Hossain, Yutaka Oomura, Toshihiko Katafuchi
Glucose is believed to improve the memory in both human and mice, but the detailed insights were mostly elusive. In this study, we focused on two major neurotrophic factors, brain-derived neurotrophic factor (BDNF) and fibroblast growth factor 1 (FGF1), which are believed to be associated with the memory enhancement and assessed their expressional regulation among the murine neuronal and glial cells. Our findings showed that the glucose administration increased phosphorylated Akt, phosphorylated CREB, exon 1- and exon 4-specific BDNF transcripts, and FGF1 transcripts that are associated with the epigenetic changes expected to open the chromatin and a reduction in histone deacetylase 2 (HDAC2) in neurons and astrocytes of the murine hippocampus...
May 13, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28499864/role-of-hepatitis-b-core-protein-in-hbv-transcription-and-recruitment-of-histone-acetyltransferases-to-cccdna-minichromosome
#10
Chun Kong Chong, Ching Yan Serene Cheng, Sin Yi Jasmine Tsoi, Fung-Yu Huang, Fen Liu, Wai-Kay Seto, Ching-Lung Lai, Man-Fung Yuen, Danny Ka-Ho Wong
The hepatitis B core protein (HBc) has been suggested to interact with covalently closed circular DNA (cccDNA) and regulate hepatitis B virus (HBV) transcription. However, direct evidence is lacking. We aimed to identify the specific HBc region(s) responsible for transcription regulation and its interaction with cccDNA. Seventeen mutants with mutations at the four arginine-rich clusters of the HBc carboxyl-terminal domain (CTD) were created. The effect of HBc mutations on the levels of HBV DNA, RNA, and hepatitis B surface antigen (HBsAg) were measured...
May 10, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28496150/long-non-coding-rna-particle-bridges-histone-and-dna-methylation
#11
Valerie Bríd O'Leary, Sarah Hain, Doris Maugg, Jan Smida, Omid Azimzadeh, Soile Tapio, Saak Victor Ovsepian, Michael John Atkinson
PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) expression is transiently elevated following low dose irradiation typically encountered in the workplace and from natural sources. This long non-coding RNA recruits epigenetic silencers for cis-acting repression of its neighbouring Methionine adenosyltransferase 2A gene. It now emerges that PARTICLE operates as a trans-acting mediator of DNA and histone lysine methylation. Chromatin immunoprecipitation sequencing (ChIP-seq) and immunological evidence established elevated PARTICLE expression linked to increased histone 3 lysine 27 trimethylation...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28488757/stimulation-of-pol-iii-dependent-5s-rrna-and-u6-snrna-gene-expression-by-ap-1-transcription-factors
#12
Richa Ahuja, Vijay Kumar
RNA polymerase III transcribes structurally diverse group of essential non-coding RNAs including 5S rRNA and U6 snRNA. These non-coding RNAs are involved in RNA processing and ribosome biogenesis, thus, coupling Pol III activity to the rate of protein synthesis, cell growth and proliferation. Even though a few Pol II-associated transcription factors have been reported to participate in Pol III-dependent transcription, its activation by AP-1 factors c-Fos and c-Jun has remained unexplored. Here, we show that c-Fos and c-Jun bind to specific sites in the regulatory regions of 5S rRNA (type I) and U6 snRNA (type III) gene promoters and stimulate their transcription...
May 10, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28487942/cyclic-amp-responsive-element-binding-protein-induces-metastatic-renal-cell-carcinoma-by-mediating-the-expression-of-matrix-metallopeptidase-2-9-and-proteins-associated-with-epithelial-mesenchymal-transition
#13
Xue Wang, Hui Cui, Zhongguan Lou, Shuaishuai Huang, Yu Ren, Ping Wang, Guobin Weng
Renal cell carcinoma (RCC) is the most frequently occurring malignancy of the kidney worldwide. Anti-angiogenic targeted therapies inhibit the progression of RCC, however, limited effects on the invasion or metastasis of tumor cells have been observed. Cyclic AMP responsive element‑binding protein (CREB) is a serine/threonine kinase that has been implicated in the regulation of cell proliferation, apoptosis, cycle progression and metastasis, amongst others. Our previous research demonstrated that phosphorylated CREB (pCREB) was upregulated in human renal cancer cell lines and tissues, and decreased pCREB at the Ser133 site inhibited the growth and metastatic activity of OS‑RC‑2 cells...
June 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28487353/the-chromatin-remodelling-factor-atrx-suppresses-r-loops-in-transcribed-telomeric-repeats
#14
Diu Tt Nguyen, Hsiao Phin J Voon, Barbara Xella, Caroline Scott, David Clynes, Christian Babbs, Helena Ayyub, Jon Kerry, Jacqueline A Sharpe, Jackie A Sloane-Stanley, Sue Butler, Chris A Fisher, Nicki E Gray, Thomas Jenuwein, Douglas R Higgs, Richard J Gibbons
ATRX is a chromatin remodelling factor found at a wide range of tandemly repeated sequences including telomeres (TTAGGG)n ATRX mutations are found in nearly all tumours that maintain their telomeres via the alternative lengthening of telomere (ALT) pathway, and ATRX is known to suppress this pathway. Here, we show that recruitment of ATRX to telomeric repeats depends on repeat number, orientation and, critically, on repeat transcription. Importantly, the transcribed telomeric repeats form RNA-DNA hybrids (R-loops) whose abundance correlates with the recruitment of ATRX Here, we show loss of ATRX is also associated with increased R-loop formation...
May 9, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28483910/rna-binding-by-the-histone-methyltransferases-set1-and-set2
#15
Camille Sayou, Gonzalo Millán-Zambrano, Helena Santos-Rosa, Elisabeth Petfalski, Samuel Robson, Jonathan Houseley, Tony Kouzarides, David Tollervey
Histone methylation at H3K4 and H3K36 is commonly associated with genes actively transcribed by RNA polymerase II (RNAPII) and is catalyzed by yeast Set1 and Set2, respectively. Here we report that both methyltransferases can be UV-crosslinked to RNA in vivo. High-throughput sequencing of the bound RNAs revealed strong Set1 enrichment near the transcription start site, whereas Set2 was distributed along pre-mRNAs. A subset of transcripts showed notably high enrichment for Set1 or Set2 binding relative to RNAPII, suggesting functional post-transcriptional interactions...
May 8, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28475896/the-rna-exosome-syncs-iav-rnapii-transcription-to-promote-viral-ribogenesis-and-infectivity
#16
Alexander Rialdi, Judd Hultquist, David Jimenez-Morales, Zuleyma Peralta, Laura Campisi, Romain Fenouil, Natasha Moshkina, Zhen Zhen Wang, Brice Laffleur, Robyn M Kaake, Michael J McGregor, Kelsey Haas, Evangelos Pefanis, Randy A Albrecht, Lars Pache, Sumit Chanda, Joanna Jen, Jordi Ochando, Minji Byun, Uttiya Basu, Adolfo García-Sastre, Nevan Krogan, Harm van Bakel, Ivan Marazzi
The nuclear RNA exosome is an essential multi-subunit complex that controls RNA homeostasis. Congenital mutations in RNA exosome genes are associated with neurodegenerative diseases. Little is known about the role of the RNA exosome in the cellular response to pathogens. Here, using NGS and human and mouse genetics, we show that influenza A virus (IAV) ribogenesis and growth are suppressed by impaired RNA exosome activity. Mechanistically, the nuclear RNA exosome coordinates the initial steps of viral transcription with RNAPII at host promoters...
May 4, 2017: Cell
https://www.readbyqxmd.com/read/28475736/chd1-regulates-cell-fate-determination-by-activation-of-differentiation-induced-genes
#17
Simon J Baumgart, Zeynab Najafova, Tareq Hossan, Wanhua Xie, Sankari Nagarajan, Vijayalakshmi Kari, Nicholas Ditzel, Moustapha Kassem, Steven A Johnsen
The coordinated temporal and spatial activation of gene expression is essential for proper stem cell differentiation. The Chromodomain Helicase DNA-binding protein 1 (CHD1) is a chromatin remodeler closely associated with transcription and nucleosome turnover downstream of the transcriptional start site (TSS). In this study, we show that CHD1 is required for the induction of osteoblast-specific gene expression, extracellular-matrix mineralization and ectopic bone formation in vivo. Genome-wide occupancy analyses revealed increased CHD1 occupancy around the TSS of differentiation-activated genes...
May 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28474362/identification-of-physical-interactions-between-genomic-regions-by-enchip-seq
#18
Toshitsugu Fujita, Miyuki Yuno, Yutaka Suzuki, Sumio Sugano, Hodaka Fujii
Physical interactions between genomic regions play critical roles in the regulation of genome functions, including gene expression. Here, we show the feasibility of using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) in combination with next-generation sequencing (NGS) (enChIP-Seq) to detect such interactions. In enChIP-Seq, the target genomic region is captured by an engineered DNA-binding complex, such as a clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a catalytically inactive form of Cas9 and a single guide RNA...
May 5, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28473805/reactivation-and-lytic-replication-of-kaposi-s-sarcoma-associated-herpesvirus-an-update
#19
REVIEW
Kawalpreet K Aneja, Yan Yuan
The life cycle of Kaposi's sarcoma-associated herpesvirus (KSHV) consists of two phases, latent and lytic. The virus establishes latency as a strategy for avoiding host immune surveillance and fusing symbiotically with the host for lifetime persistent infection. However, latency can be disrupted and KSHV is reactivated for entry into the lytic replication. Viral lytic replication is crucial for efficient dissemination from its long-term reservoir to the sites of disease and for the spread of the virus to new hosts...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28473753/mechanical-strain-promotes-oligodendrocyte-differentiation-by-global-changes-of-gene-expression
#20
Anna Jagielska, Alexis L Lowe, Ekta Makhija, Liliana Wroblewska, Jochen Guck, Robin J M Franklin, G V Shivashankar, Krystyn J Van Vliet
Differentiation of oligodendrocyte progenitor cells (OPC) to oligodendrocytes and subsequent axon myelination are critical steps in vertebrate central nervous system (CNS) development and regeneration. Growing evidence supports the significance of mechanical factors in oligodendrocyte biology. Here, we explore the effect of mechanical strains within physiological range on OPC proliferation and differentiation, and strain-associated changes in chromatin structure, epigenetics, and gene expression. Sustained tensile strain of 10-15% inhibited OPC proliferation and promoted differentiation into oligodendrocytes...
2017: Frontiers in Cellular Neuroscience
keyword
keyword
116436
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"