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https://www.readbyqxmd.com/read/27924033/chipbase-v2-0-decoding-transcriptional-regulatory-networks-of-non-coding-rnas-and-protein-coding-genes-from-chip-seq-data
#1
Ke-Ren Zhou, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive. In this study, we developed ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) to explore the transcriptional regulatory networks of ncRNAs and PCGs. ChIPBase v2.0 has been expanded with ∼10 200 curated ChIP-seq datasets, which represent about 20 times expansion when comparing to the previous released version...
October 23, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923386/divan-accurate-identification-of-non-coding-disease-specific-risk-variants-using-multi-omics-profiles
#2
Li Chen, Peng Jin, Zhaohui S Qin
Understanding the link between non-coding sequence variants, identified in genome-wide association studies, and the pathophysiology of complex diseases remains challenging due to a lack of annotations in non-coding regions. To overcome this, we developed DIVAN, a novel feature selection and ensemble learning framework, which identifies disease-specific risk variants by leveraging a comprehensive collection of genome-wide epigenomic profiles across cell types and factors, along with other static genomic features...
December 6, 2016: Genome Biology
https://www.readbyqxmd.com/read/27922002/targeting-the-notch-regulated-non-coding-rna-tug1-for-glioma-treatment
#3
Keisuke Katsushima, Atsushi Natsume, Fumiharu Ohka, Keiko Shinjo, Akira Hatanaka, Norihisa Ichimura, Shinya Sato, Satoru Takahashi, Hiroshi Kimura, Yasushi Totoki, Tatsuhiro Shibata, Mitsuru Naito, Hyun Jin Kim, Kanjiro Miyata, Kazunori Kataoka, Yutaka Kondo
Targeting self-renewal is an important goal in cancer therapy and recent studies have focused on Notch signalling in the maintenance of stemness of glioma stem cells (GSCs). Understanding cancer-specific Notch regulation would improve specificity of targeting this pathway. In this study, we find that Notch1 activation in GSCs specifically induces expression of the lncRNA, TUG1. TUG1 coordinately promotes self-renewal by sponging miR-145 in the cytoplasm and recruiting polycomb to repress differentiation genes by locus-specific methylation of histone H3K27 via YY1-binding activity in the nucleus...
December 6, 2016: Nature Communications
https://www.readbyqxmd.com/read/27921370/not-just-for-coding-a-new-role-for-histone-tails-in-replication-enzyme-activation
#4
Anja-Katrin Bielinsky, Wendy Leung
The processing of Okazaki fragments when they are assembled into nucleosomes has received little attention. In this issue of The FEBS Journal, Seo and colleagues show that binding to histone tails stimulates the enzymatic activity of flap endonuclease 1 (Rad27). Histone tails are structurally similar to the C terminus of Rad27 and can thus mimic its autostimulatory function. This study highlights an active regulatory role for nucleosomes on DNA metabolism.
December 2016: FEBS Journal
https://www.readbyqxmd.com/read/27900472/tissue-specific-expression-of-telomerase-reverse-transcriptase-gene-variants-in-nicotiana-tabacum
#5
Jana Fišerová Jurečková, Eva Sýkorová, Said Hafidh, David Honys, Jiří Fajkus, Miloslava Fojtová
In tobacco, three sequence variants of the TERT gene have been described. We revealed unbalanced levels of TERT variant transcripts in vegetative tobacco tissues and enhanced TERT transcription and telomerase activity in reproductive tissues. Telomerase is a ribonucleoprotein complex responsible for the maintenance of telomeres, structures delimiting ends of linear eukaryotic chromosomes. In the Nicotiana tabacum (tobacco) allotetraploid plant, three sequence variants (paralogs) of the gene coding for the telomerase reverse transcriptase subunit (TERT) have been described, two of them derived from the maternal N...
November 29, 2016: Planta
https://www.readbyqxmd.com/read/27897123/the-epigenetic-regulation-in-tooth-development-and-regeneration
#6
Yao Lin, Liwei Zheng, Li Fan, Wei Kuang, Rui Guo, Jiong Lin, Jiahua Wu, Jiali Tan
Teeth are formed through sequential and reciprocal interactions between epithelial and mesenchymal tissues and they are essential to physical and psychological health. In-depth knowledge of tooth development, from histology to the underlying mechanisms, is necessary for the regeneration of lost teeth. Therefore, the review firstly introduced tooth development, and summarized the use of tooth-derived stem cells. To date, epigenetic regulation has been shown to have roles in numerous activities, including odontogenesis...
November 29, 2016: Current Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/27895308/epigenetic-inhibition-of-mir-663b-by-long-non-coding-rna-hotair-promotes-pancreatic-cancer-cell-proliferation-via-up-regulation-of-insulin-like-growth-factor-2
#7
Huihua Cai, Yong An, Xuemin Chen, Donglin Sun, Tongbing Chen, Yan Peng, Feng Zhu, Yong Jiang, Xiaozhou He
Pancreatic cancer is one of the most deadly cancers with a poor prognosis. Although microRNAs are involving in the carcinogenesis and development of pancreatic cancer, little information is known regarding the role of miR-663b in pancreatic cancer. In this study, the expression of miR-663b in pancreatic cancer cells was down-regulated by hypermethylation in its putative promoter region, and overexpression of miR-663b repressed cell proliferation, invasion and migration, and induced apoptosis in pancreatic cancer cells...
November 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/27892767/epigenetic-modifications-in-multiple-myeloma-recent-advances-on-the-role-of-dna-and-histone-methylation
#8
Nicola Amodio, Patrizia D'Aquila, Giuseppe Passarino, Pierfrancesco Tassone, Dina Bellizzi
Multiple Myeloma (MM) is a clonal late B-cell disorder accounting for about 13% of hematological cancers and 1% of all neoplastic diseases. Recent studies on the molecular pathogenesis and biology of MM have highlighted a complex epigenomic landscape contributing to MM onset, prognosis and high individual variability. Areas covered: We describe here the current knowledge on epigenetic events characterizing MM initiation and progression, focusing on the role of DNA and histone methylation and on the most promising epi-therapeutic approaches targeting the methylation pathway...
November 28, 2016: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/27892455/selective-suppression-of-antisense-transcription-by-set2-mediated-h3k36-methylation
#9
Swaminathan Venkatesh, Hua Li, Madelaine M Gogol, Jerry L Workman
Maintenance of a regular chromatin structure over the coding regions of genes occurs co-transcriptionally via the 'chromatin resetting' pathway. One of the central players in this pathway is the histone methyltransferase Set2. Here we show that the loss of Set2 in yeast, Saccharomyces cerevisiae, results in transcription initiation of antisense RNAs embedded within body of protein-coding genes. These RNAs are distinct from the previously identified non-coding RNAs and cover 11% of the yeast genome. These RNA species have been named Set2-repressed antisense transcripts (SRATs) since the co-transcriptional addition of the H3K36 methyl mark by Set2 over their start sites results in their suppression...
November 28, 2016: Nature Communications
https://www.readbyqxmd.com/read/27891322/epigenetics-in-schistosomes-what-we-know-and-what-we-need-know
#10
REVIEW
Weiwei Liu
Schistosomes are metazoan parasites and can cause schistosomiasis. Epigenetic modifications include DNA methylation, histone modifications and non-coding RNAs. Some enzymes involved in epigenetic modification and microRNA processes have been developed as drugs to treat the disease. Compared with humans and vertebrates, an in-depth understanding of epigenetic modifications in schistosomes is starting to be realized. DNA methylation, histone modifications and non-coding RNAs play important roles in the development and reproduction of schistosomes and in interactions between the host and schistosomes...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27880868/origin-and-evolution-of-the-metazoan-non-coding-regulatory-genome
#11
REVIEW
Federico Gaiti, Andrew D Calcino, Miloš Tanurdžić, Bernard M Degnan
Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa...
November 20, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27876555/one-carbon-metabolism-and-epigenetics
#12
REVIEW
Simonetta Friso, Silvia Udali, Domenica De Santis, Sang-Woon Choi
The function of one-carbon metabolism is that of regulating the provision of methyl groups for biological methylation reactions including that of DNA and histone proteins. Methylation at specific sites into the DNA sequence and at histone tails are among the major epigenetic feature of mammalian genome for the regulation of gene expression. The enzymes within one-carbon metabolism are dependent from a number of vitamins or nutrients that serve either as co-factors or methyl acceptors or donors among which folate, vitamin B12, vitamin B6, betaine, choline and methionine have a major role...
November 19, 2016: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/27870837/ubiquitin-utilizes-an-acidic-surface-patch-to-alter-chromatin-structure
#13
Galia T Debelouchina, Karola Gerecht, Tom W Muir
Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen-deuterium exchange strategy coupled with NMR spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic 'wedge' that prevents the intimate association of neighboring nucleosomes...
November 21, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27865480/biofluids-cell-mechanics-and-epigenetics-flow-induced-epigenetic-mechanisms-of-endothelial-gene-expression
#14
Peter F Davies, Elisabetta Manduchi, Juan M Jiménez, Yi-Zhou Jiang
Epigenetics is the regulation of gene expression (transcription) in response to changes in the cell environment through genomic modifications that largely involve the non-coding fraction of the human genome and that cannot be attributed to modification of the primary DNA sequence. Epigenetics is dominant in establishing cell fate and positioning during programmed embryonic development. However the same pathways are used by mature postnatal and adult mammalian cells during normal physiology and are implicated in disease mechanisms...
November 11, 2016: Journal of Biomechanics
https://www.readbyqxmd.com/read/27862226/histone-h4-methyltransferase-suv420h2-maintains-fidelity-of-osteoblast-differentiation
#15
Khani Farzaneh, Roman Thaler, Christopher R Paradise, David R Deyle, Marianne Kruijthof-de Julio, Mario Galindo, Jonathan A Gordon, Gary S Stein, Amel Dudakovic, Andre J van Wijnen
Osteogenic lineage commitment and progression is controlled by multiple signaling pathways (e.g., WNT, BMP, FGF) that converge on bone-related transcription factors. Access of osteogenic transcription factors to chromatin is controlled by epigenetic regulators that generate post-translational modifications of histones ("histone code"), as well as read, edit and/or erase these modifications. Our understanding of the biological role of epigenetic regulators in osteoblast differentiation remains limited. Therefore, we performed next-generation RNA sequencing (RNA-seq) and established which chromatin-related proteins are robustly expressed in mouse bone tissues (e...
November 9, 2016: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/27860235/a-functional-pseudogene-nmral2p-is-regulated-by-nrf2-and-serves-as-a-co-activator-of-nqo1-in-sulforaphane-treated-colon-cancer-cells
#16
Gavin S Johnson, Jia Li, Laura M Beaver, W Mohaiza Dashwood, Deqiang Sun, Praveen Rajendran, David E Williams, Emily Ho, Roderick H Dashwood
SCOPE: The anticancer agent sulforaphane (SFN) acts via multiple mechanisms to modulate gene expression, including the induction of nuclear factor (erythroid-derived 2)-like 2 (Nrf2)-dependent signaling and the inhibition of histone deacetylase activity. Transcriptomics studies were performed in SFN-treated human colon cancer cells and in non-transformed colonic epithelial cells in order to pursue new mechanistic leads. METHODS AND RESULTS: RNA-sequencing corroborated the expected changes in cancer-related pathways after SFN treatment...
November 18, 2016: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/27858503/high-throughput-sequencing-of-two-populations-of-extracellular-vesicles-provides-an-mrna-signature-that-can-be-detected-in-the-circulation-of-breast-cancer-patients
#17
Andrew Conley, Valentina R Minciacchi, Dhong Hyun Lee, Beatrice S Knudsen, Beth Y Karlan, Luigi Citrigno, Giuseppe Viglietto, Muneesh Tewari, Michael R Freeman, Francesca Demichelis, Dolores Di Vizio
Extracellular vesicles (EVs) contain a wide range of RNA types with a reported prevalence of non-coding RNA. To date a comprehensive characterization of the protein coding transcripts in EVs is still lacking. We performed RNA-Sequencing (RNA-Seq) of two EV populations and identified a small fraction of transcripts that were expressed at significantly different levels in large oncosomes and exosomes, suggesting they may mediate specialized functions. However, these two EV populations exhibited a common mRNA signature that, in comparison to their donor cells, was significantly enriched in mRNAs encoding E2F transcriptional targets and histone proteins...
November 18, 2016: RNA Biology
https://www.readbyqxmd.com/read/27855160/transcription-factors-encoded-on-core-and-accessory-chromosomes-of-fusarium-oxysporum-induce-expression-of-effector-genes
#18
H Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M Schmidt, Léon Langereis, Joanna M Lukasiewicz, Timothy R Hughes, Martijn Rep
Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27851915/epigenomic-profiling-of-human-cd4-t-cells-supports-a-linear-differentiation-model-and-highlights-molecular-regulators-of-memory-development
#19
Pawel Durek, Karl Nordström, Gilles Gasparoni, Abdulrahman Salhab, Christopher Kressler, Melanie de Almeida, Kevin Bassler, Thomas Ulas, Florian Schmidt, Jieyi Xiong, Petar Glažar, Filippos Klironomos, Anupam Sinha, Sarah Kinkley, Xinyi Yang, Laura Arrigoni, Azim Dehghani Amirabad, Fatemeh Behjati Ardakani, Lars Feuerbach, Oliver Gorka, Peter Ebert, Fabian Müller, Na Li, Stefan Frischbutter, Stephan Schlickeiser, Carla Cendon, Sebastian Fröhler, Bärbel Felder, Nina Gasparoni, Charles D Imbusch, Barbara Hutter, Gideon Zipprich, Yvonne Tauchmann, Simon Reinke, Georgi Wassilew, Ute Hoffmann, Andreas S Richter, Lina Sieverling, Hyun-Dong Chang, Uta Syrbe, Ulrich Kalus, Jürgen Eils, Benedikt Brors, Thomas Manke, Jürgen Ruland, Thomas Lengauer, Nikolaus Rajewsky, Wei Chen, Jun Dong, Birgit Sawitzki, Ho-Ryun Chung, Philip Rosenstiel, Marcel H Schulz, Joachim L Schultze, Andreas Radbruch, Jörn Walter, Alf Hamann, Julia K Polansky
The impact of epigenetics on the differentiation of memory T (Tmem) cells is poorly defined. We generated deep epigenomes comprising genome-wide profiles of DNA methylation, histone modifications, DNA accessibility, and coding and non-coding RNA expression in naive, central-, effector-, and terminally differentiated CD45RA(+) CD4(+) Tmem cells from blood and CD69(+) Tmem cells from bone marrow (BM-Tmem). We observed a progressive and proliferation-associated global loss of DNA methylation in heterochromatic parts of the genome during Tmem cell differentiation...
November 15, 2016: Immunity
https://www.readbyqxmd.com/read/27845892/lncrna-h19-confers-chemoresistance-in-er%C3%AE-positive-breast-cancer-through-epigenetic-silencing-of-the-pro-apoptotic-gene-bik
#20
Xinxin Si, Ruochen Zang, Erbao Zhang, Yue Liu, Xiao Shi, Ershao Zhang, Lipei Shao, Andi Li, Nan Yang, Xiao Han, Beijing Pan, Zhihong Zhang, Luan Sun, Yujie Sun
Breast cancer is a common malignancy in women. Acquisition of drug resistance is one of the main obstacles encountered in breast cancer therapy. Long non-coding RNA (lncRNA) has been demonstrated to play vital roles in both development and tumorigenesis. However, the relationship between lncRNAs and the development of chemoresistance is not well established. In the present study, the high expression of lncRNA H19 was identified as a powerful factor associated with paclitaxel (PTX) resistance in ERα-positive breast cancer cells, but not in ERα-negative breast cancer cells...
November 10, 2016: Oncotarget
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