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https://www.readbyqxmd.com/read/28334833/chip-seq-analysis-of-the-luxr-type-regulator-vjbr-reveals-novel-insights-into-the-brucella-virulence-gene-expression-network
#1
Claudia L Kleinman, Gabriela Sycz, Hernán R Bonomi, Romina M Rodríguez, Angeles Zorreguieta, Rodrigo Sieira
LuxR-type transcription factors control diverse physiological functions necessary for bacterial adaptation to environmental changes. In the intracellular pathogen Brucella, the LuxR homolog VjbR has been shown to regulate the expression of virulence factors acting at early stages of the intracellular infection and, directly or indirectly, hundreds of additional genes. However, the precise determination of VjbR direct targets has so far proved elusive. Here, we performed chromatin immunoprecipitation of VjbR followed by next-generation sequencing (ChIP-seq)...
March 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28329686/demethylated-hsatii-dna-and-hsatii-rna-foci-sequester-prc1-and-mecp2-into-cancer-specific-nuclear-bodies
#2
Lisa L Hall, Meg Byron, Dawn M Carone, Troy W Whitfield, Gayle P Pouliot, Andrew Fischer, Peter Jones, Jeanne B Lawrence
This study reveals that high-copy satellite II (HSATII) sequences in the human genome can bind and impact distribution of chromatin regulatory proteins and that this goes awry in cancer. In many cancers, master regulatory proteins form two types of cancer-specific nuclear bodies, caused by locus-specific deregulation of HSATII. DNA demethylation at the 1q12 mega-satellite, common in cancer, causes PRC1 aggregation into prominent Cancer-Associated Polycomb (CAP) bodies. These loci remain silent, whereas HSATII loci with reduced PRC1 become derepressed, reflecting imbalanced distribution of UbH2A on these and other PcG-regulated loci...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28325872/small-rna-mediated-repair-of-uv-induced-dna-lesions-by-the-dna-damage-binding-protein-2-and-argonaute-1
#3
Catherine Schalk, Valérie Cognat, Stéfanie Graindorge, Timothée Vincent, Olivier Voinnet, Jean Molinier
As photosynthetic organisms, plants need to prevent irreversible UV-induced DNA lesions. Through an unbiased, genome-wide approach, we have uncovered a previously unrecognized interplay between Global Genome Repair and small interfering RNAs (siRNAs) in the recognition of DNA photoproducts, prevalently in intergenic regions. Genetic and biochemical approaches indicate that, upon UV irradiation, the DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and ARGONAUTE 1 (AGO1) of Arabidopsis thaliana form a chromatin-bound complex together with 21-nt siRNAs, which likely facilitates recognition of DNA damages in an RNA/DNA complementary strand-specific manner...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28323953/activation-of-male-liver-chromatin-accessibility-and-stat5-dependent-gene-transcription-by-plasma-growth-hormone-pulses
#4
Jeannette Connerney, Dana Lau-Corona, Andy Rampersaud, David J Waxman
Sex-differences in pituitary growth hormone (GH) secretion (pulsatile in males vs near continuous/persistent in females) impart sex-dependent expression to hundreds of genes in adult mouse liver. STAT5, a GH-activated transcription factor that is essential for liver sexual dimorphism, is dynamically activated in direct response to each male plasma GH pulse. However, the impact of GH-induced STAT5 pulses on liver chromatin accessibility and downstream transcriptional events is unknown. Here, we investigate the impact of a single pulse of GH given to hypophysectomized mice on local liver chromatin accessibility [DNase hypersensitive site analysis], transcription rates [hnRNA analysis], and gene expression [quantitative PCR and RNA-Seq] determined 30, 90 or 240 min later...
February 17, 2017: Endocrinology
https://www.readbyqxmd.com/read/28323041/quantitative-analyses-of-the-3d-nuclear-landscape-recorded-with-super-resolved-fluorescence-microscopy
#5
Volker J Schmid, Marion Cremer, Thomas Cremer
Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction...
March 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28321119/notch1-mutated-chronic-lymphocytic-leukemia-cells-are-characterized-by-a-myc-related-overexpression-of-nucleophosmin-1-and-ribosome-associated-components
#6
F Pozzo, T Bittolo, E Vendramini, R Bomben, P Bulian, F M Rossi, A Zucchetto, E Tissino, M Degan, G D'Arena, F Di Raimondo, F Zaja, G Pozzato, D Rossi, G Gaidano, G Del Poeta, V Gattei, M Dal Bo
In chronic lymphocytic leukemia (CLL), the mechanisms controlling cell growth and proliferation in presence of NOTCH1 mutations remain largely unexplored. By performing a gene expression profile of NOTCH1 mutated (NOTCH1-mut) versus NOTCH1 wild type CLL, we identified a gene signature of NOTCH1-mut CLL characterized by upregulation of genes related to ribosome biogenesis, such as nucleophosmin1 (NPM1) and ribosomal proteins (RNPs). Activation of NOTCH1 signaling by EDTA or by co-culture with JAGGED1-expressing stromal cells increased NPM1 expression, and inhibition of NOTCH1 signaling by either NOTCH1-specific small interfering RNA (siRNA) or γ-secretase inhibitor reduced NPM1 expression...
March 21, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28315775/assessment-of-histone-tail-modifications-and-transcriptional-profiling-during-colon-cancer-progression-reveals-a-global-decrease-in-h3k4me3-activity
#7
Karen Triff, Mathew W McLean, Kranti Konganti, Jiahui Pang, Evelyn Callaway, Beiyan Zhou, Ivan Ivanov, Robert S Chapkin
During colon cancer, epigenetic alterations contribute to the dysregulation of major cellular functions and signaling pathways. Modifications in chromatin signatures such as H3K4me3 and H3K9ac, which are associated with transcriptionally active genes, can lead to genomic instability and perturb the expression of gene sets associated with oncogenic processes. In order to further elucidate early pre-tumorigenic epigenetic molecular events driving CRC, we integrated diverse, genome-wide, epigenetic inputs (by high throughput sequencing of RNA, H3K4me3, and H3K9ac) and compared differentially expressed transcripts (DE) and enriched regions (DER) in an in-vivo rat colon cancer progression model...
March 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28297679/integrative-genomic-analysis-of-cholangiocarcinoma-identifies-distinct-idh-mutant-molecular-profiles
#8
Farshad Farshidfar, Siyuan Zheng, Marie-Claude Gingras, Yulia Newton, Juliann Shih, A Gordon Robertson, Toshinori Hinoue, Katherine A Hoadley, Ewan A Gibb, Jason Roszik, Kyle R Covington, Chia-Chin Wu, Eve Shinbrot, Nicolas Stransky, Apurva Hegde, Ju Dong Yang, Ed Reznik, Sara Sadeghi, Chandra Sekhar Pedamallu, Akinyemi I Ojesina, Julian M Hess, J Todd Auman, Suhn K Rhie, Reanne Bowlby, Mitesh J Borad, Andrew X Zhu, Josh M Stuart, Chris Sander, Rehan Akbani, Andrew D Cherniack, Vikram Deshpande, Taofic Mounajjed, Wai Chin Foo, Michael S Torbenson, David E Kleiner, Peter W Laird, David A Wheeler, Autumn J McRee, Oliver F Bathe, Jesper B Andersen, Nabeel Bardeesy, Lewis R Roberts, Lawrence N Kwong
Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28293300/silencing-markers-are-retained-on-pericentric-heterochromatin-during-murine-primordial-germ-cell-development
#9
Aristea Magaraki, Godfried van der Heijden, Esther Sleddens-Linkels, Leonidas Magarakis, Wiggert A van Cappellen, Antoine H F M Peters, Joost Gribnau, Willy M Baarends, Maureen Eijpe
BACKGROUND: In the nuclei of most mammalian cells, pericentric heterochromatin is characterized by DNA methylation, histone modifications such as H3K9me3 and H4K20me3, and specific binding proteins like heterochromatin-binding protein 1 isoforms (HP1 isoforms). Maintenance of this specialized chromatin structure is of great importance for genome integrity and for the controlled repression of the repetitive elements within the pericentric DNA sequence. Here we have studied histone modifications at pericentric heterochromatin during primordial germ cell (PGC) development using different fixation conditions and fluorescent immunohistochemical and immunocytochemical protocols...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28291796/the-effect-of-acetaminophen-on-ubiquitin-homeostasis-in-saccharomyces-cerevisiae
#10
Angelina Huseinovic, Jolanda S van Leeuwen, Tibor van Welsem, Iris Stulemeijer, Fred van Leeuwen, Nico P E Vermeulen, Jan M Kooter, J Chris Vos
Acetaminophen (APAP), although considered a safe drug, is one of the major causes of acute liver failure by overdose, and therapeutic chronic use can cause serious health problems. Although the reactive APAP metabolite N-acetyl-p-benzoquinoneimine (NAPQI) is clearly linked to liver toxicity, toxicity of APAP is also found without drug metabolism of APAP to NAPQI. To get more insight into mechanisms of APAP toxicity, a genome-wide screen in Saccharomyces cerevisiae for APAP-resistant deletion strains was performed...
2017: PloS One
https://www.readbyqxmd.com/read/28291707/epigenetics-of-atherosclerosis-emerging-mechanisms-and-methods
#11
REVIEW
Nadiya Khyzha, Azad Alizada, Michael D Wilson, Jason E Fish
Atherosclerosis is a vascular pathology characterized by inflammation and plaque build-up within arterial vessel walls. Vessel occlusion, often occurring after plaque rupture, can result in myocardial and cerebral infarction. Epigenetic changes are increasingly being associated with atherosclerosis and are of interest from both therapeutic and biomarker perspectives. Emerging genomic approaches that profile DNA methylation, chromatin accessibility, post-translational histone modifications, transcription factor binding, and RNA expression in low or single cell populations are poised to enhance our spatiotemporal understanding of atherogenesis...
March 10, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28288683/chromatin-landscapes-and-genetic-risk-for-juvenile-idiopathic-arthritis
#12
Lisha Zhu, Kaiyu Jiang, Karstin Webber, Laiping Wong, Tao Liu, Yanmin Chen, James N Jarvis
BACKGROUND: The transcriptomes of peripheral blood cells in children with juvenile idiopathic arthritis (JIA) have distinct transcriptional aberrations that suggest impairment of transcriptional regulation. To gain a better understanding of this phenomenon, we studied known JIA genetic risk loci, the majority of which are located in non-coding regions, where transcription is regulated and coordinated on a genome-wide basis. We examined human neutrophils and CD4 primary T cells to identify genes and functional elements located within those risk loci...
March 14, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28282036/heterarchy-of-transcription-factors-driving-basal-and-luminal-cell-phenotypes-in-human-urothelium
#13
Carl Fishwick, Janet Higgins, Lawrence Percival-Alwyn, Arianna Hustler, Joanna Pearson, Sarah Bastkowski, Simon Moxon, David Swarbreck, Chris D Greenman, Jennifer Southgate
Cell differentiation is affected by complex networks of transcription factors that co-ordinate re-organisation of the chromatin landscape. The hierarchies of these relationships can be difficult to dissect. During in vitro differentiation of normal human uro-epithelial cells, formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) and RNA-seq was used to identify alterations in chromatin accessibility and gene expression changes following activation of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) as a differentiation-initiating event...
March 10, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28273165/transcriptome-profiling-of-influenza-a-virus-infected-lung-epithelial-a549-cells-with-lariciresinol-4-%C3%AE-d-glucopyranoside-treatment
#14
Beixian Zhou, Jing Li, Xiaoli Liang, Zifeng Yang, Zhihong Jiang
The influenza A virus is an acute contagious pathogen that affects the human respiratory system and can cause severe lung disease and even death. Lariciresinol-4-β-D-glucopyranoside is a lignan that is extracted from Isatis indigotica, which is a medicinal herb plant that was commonly applied to treat infections, the common cold, fever and inflammatory diseases. Our previous study demonstrated that lariciresinol-4-β-D-glucopyranoside possesses anti-viral and anti-inflammatory properties. However, the comprehensive and detailed mechanisms that underlie the effect of lariciresinol-4-β-D-glucopyranoside interventions against influenza virus infection remain to be elucidated...
2017: PloS One
https://www.readbyqxmd.com/read/28273073/src-2-mediated-coactivation-of-anti-tumorigenic-target-genes-suppresses-myc-induced-liver-cancer
#15
Shruthy Suresh, Deniz Durakoglugil, Xiaorong Zhou, Bokai Zhu, Sarah A Comerford, Chao Xing, Xian-Jin Xie, Brian York, Kathryn A O'Donnell
Hepatocellular carcinoma (HCC) is the fifth most common solid tumor in the world and the third leading cause of cancer-associated deaths. A Sleeping Beauty-mediated transposon mutagenesis screen previously identified mutations that cooperate with MYC to accelerate liver tumorigenesis. This revealed a tumor suppressor role for Steroid Receptor Coactivator 2/Nuclear Receptor Coactivator 2 (Src-2/Ncoa2) in liver cancer. In contrast, SRC-2 promotes survival and metastasis in prostate cancer cells, suggesting a tissue-specific and context-dependent role for SRC-2 in tumorigenesis...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28270561/a-saga-of-cancer-epigenetics-linking-epigenetics-to-alternative-splicing
#16
REVIEW
Sathiya Pandi Narayanan, Smriti Singh, Sanjeev Shukla
The discovery of an increasing number of alternative splicing events in the human genome highlighted that ∼94% of genes generate alternatively spliced transcripts that may produce different protein isoforms with diverse functions. It is now well known that several diseases are a direct and indirect consequence of aberrant splicing events in humans. In addition to the conventional mode of alternative splicing regulation by 'cis' RNA-binding sites and 'trans' RNA-binding proteins, recent literature provides enormous evidence for epigenetic regulation of alternative splicing...
March 7, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28263841/the-formation-and-modification-of-chromatin-like-structure-of-human-parvovirus-b19-regulate-viral-genome-replication-and-rna-processing
#17
Huanzhou Xu, Sujuan Hao, Junmei Zhang, Zhen Chen, Hanzhong Wang, Wuxiang Guan
B19 virus (B19V) is a single stranded virus in the genus of Erythroparvovirus in the family of Parvoviridae. One of the limiting steps of B19V infection is the replication of viral genome which affected the alternative processing of its RNA. Minute virus of mice (MVM) and adeno-associated virus (AAV) has been reported to form chromatin-like structure within hours after infection of cells. However, the role of chromatin-like structure is unclear. In the present study, we found that B19V formed chromatin-like structure after 12h when B19V infectious clone was co-transfected with pHelper plasmid to HEK293T cells...
March 2, 2017: Virus Research
https://www.readbyqxmd.com/read/28262505/distinct-roles-of-brd2-and-brd4-in-potentiating-the-transcriptional-program-for-th17-cell-differentiation
#18
Ka Lung Cheung, Fan Zhang, Anbalagan Jaganathan, Rajal Sharma, Qiang Zhang, Tsuyoshi Konuma, Tong Shen, June-Yong Lee, Chunyan Ren, Chih-Hung Chen, Geming Lu, Matthew R Olson, Weijia Zhang, Mark H Kaplan, Dan R Littman, Martin J Walsh, Huabao Xiong, Lei Zeng, Ming-Ming Zhou
The BET proteins are major transcriptional regulators and have emerged as new drug targets, but their functional distinction has remained elusive. In this study, we report that the BET family members Brd2 and Brd4 exert distinct genomic functions at genes whose transcription they co-regulate during mouse T helper 17 (Th17) cell differentiation. Brd2 is associated with the chromatin insulator CTCF and the cohesin complex to support cis-regulatory enhancer assembly for gene transcriptional activation. In this context, Brd2 binds the transcription factor Stat3 in an acetylation-sensitive manner and facilitates Stat3 recruitment to active enhancers occupied with transcription factors Irf4 and Batf...
March 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28259922/signal-transduction-involved-in-lipoxin-a4%C3%A2-induced-protection-of-tubular-epithelial-cells-against-hypoxia-reoxygenation-injury
#19
Sheng-Hua Wu, Ming-Jie Wang, Jing Lü, Xiao-Qing Chen
Previous studies have reported that lipoxin A4 (LXA4) may exert a renoprotective effect on ischemia/reperfusion injury in various animal models. The underlying mechanism of LXA4‑induced renoprotection during ischemia/reperfusion injury remains to be elucidated. The present study investigated LXA4‑induced protection on renal tubular cells subjected to hypoxia/reoxygenation (H/R) injury, and determined the effects of peroxisome proliferator‑activated receptor‑γ (PPARγ) and heme oxygenase‑1 (HO‑1) on LXA4 treatment...
February 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28258189/selective-expression-of-tspan2-in-vascular-smooth-muscle-is-independently-regulated-by-tgf-%C3%AE-1-smad-and-myocardin-serum-response-factor
#20
Jinjing Zhao, Wen Wu, Wei Zhang, Yao Wei Lu, Emiley Tou, Jiemei Ye, Ping Gao, David Jourd'heuil, Harold A Singer, Mingfu Wu, Xiaochun Long
Tetraspanins (TSPANs) comprise a large family of 4-transmembrane domain proteins. The importance of TSPANs in vascular smooth muscle cells (VSMCs) is unexplored. Given that TGF-β1 and myocardin (MYOCD) are potent activators for VSMC differentiation, we screened for TGF-β1 and MYOCD/serum response factor (SRF)-regulated TSPANs in VSMC by using RNA-seq analyses and RNA-arrays. TSPAN2 was found to be the only TSPAN family gene induced by TGF-β1 and MYOCD, and reduced by SRF deficiency in VSMCs. We also found that TSPAN2 is highly expressed in smooth muscle-enriched tissues and down-regulated in in vitro models of VSMC phenotypic modulation...
March 3, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
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