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ChIP-Seq

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https://www.readbyqxmd.com/read/29773832/distinct-epigenetic-landscapes-underlie-the-pathobiology-of-pancreatic-cancer-subtypes
#1
Gwen Lomberk, Yuna Blum, Rémy Nicolle, Asha Nair, Krutika Satish Gaonkar, Laetitia Marisa, Angela Mathison, Zhifu Sun, Huihuang Yan, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Tamas Ordog, Jeong-Heon Lee, Gavin Oliver, Eric Klee, Vincent Moutardier, Odile Gayet, Benjamin Bian, Pauline Duconseil, Marine Gilabert, Martin Bigonnet, Stephane Garcia, Olivier Turrini, Jean-Robert Delpero, Marc Giovannini, Philippe Grandval, Mohamed Gasmi, Veronique Secq, Aurélien De Reyniès, Nelson Dusetti, Juan Iovanna, Raul Urrutia
Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29772439/long-noncoding-rna-meg3-inhibits-proliferation-of-chronic-myeloid-leukemia-cells-by-sponging-microrna21
#2
Ziye Li, Lin Yang, Xiaojun Liu, Ziyuan Nie, Jianmin Luo
The long noncoding RNA (lnc) maternally expressed 3 (MEG3) is downregulated in many types of cancers. However, the relationship between lncRNA MEG3, microRNA-21 (miR-21) and chronic myeloid leukemia (CML) blast crisis is unknown. This study examined bone marrow samples from 40 CML patients and 10 healthy donors. Proliferation and apoptosis assays, real-time polymerase chain reaction (PCR), bisulfite sequencing PCR, Western blotting, luciferase assay, RNA pull-down, RNA immunoprecipitation (RIP), co-immunoprecipitation (CoIP) and Chromatin immunoprecipitation (ChIP) were performed...
May 14, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29767371/analysis-of-chip-seq-and-rna-seq-data-with-biowardrobe
#3
Sushmitha Vallabh, Andrey V Kartashov, Artem Barski
The massive amount of information produced by ChIP-Seq, RNA-Seq, and other next-generation sequencing-based methods requires computational data analysis. However, biologists performing these experiments often lack training in bioinformatics. BioWardrobe aims to bridge this gap by providing a convenient user interface and by automating routine data-processing steps. This protocol details the use of BioWardrobe for identifying and visualizing ChIP-Seq peaks, calculating RPKMs, performing differential binding or gene expression analysis, and creating plots and heat maps...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29763523/role-of-basic-pentacysteiene-transcription-factors-in-a-sub-set-of-cytokinin-signaling-responses
#4
Carly M Shanks, Andreas Hecker, Chia-Yi Cheng, Luise Brand, Silvio Collani, Markus Schmid, G Eric Schaller, Dierk Wanke, Klaus Harter, Joseph J Kieber
Cytokinin plays diverse roles in plant growth and development, generally acting by modulating gene transcription in target tissues. The type-B ARR transcription factors have emerged as primary targets of cytokinin signaling and are required for essentially all cytokinin-mediated changes in gene expression. The diversity of cytokinin function is likely imparted by the activity of various transcription factors working with the type-B ARRs to alter specific sets of target genes. One potential set of co-regulators modulating the cytokinin response are the BARLEY B-RECOMBINANT/BASIC PENTACYSTEINE (BBR/BPC) family of plant-specific transcription factors...
May 15, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29760686/the-transcriptional-regulator-tfb-rf1-activates-transcription-of-a-putative-abc-transporter-in-pyrococcus-furiosus
#5
Robert Reichelt, Katharina M A Ruperti, Martina Kreuzer, Stefan Dexl, Michael Thomm, Winfried Hausner
Transcription factor B recruiting factor 1 (TFB-RF1; PF1088) is a transcription regulator which activates transcription on archaeal promoters containing weak TFB recognition elements (BRE) by recruiting TFB to the promoter. The mechanism of activation is described in detail, but nothing is known about the biological function of this protein in Pyrococcus furiosus . The protein is located in an operon structure together with the hypothetical gene pf1089 and western blot as well as end-point RT-PCR experiments revealed an extremely low expression rate of both proteins...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29760208/rpon-dependent-direct-regulation-of-quorum-sensing-and-the-type-vi-secretion-system-in-pseudomonas-aeruginosa-pao1
#6
Xiaolong Shao, Xiaoning Zhang, Yingchao Zhang, Miao Zhu, Pan Yang, Jian Yuan, Yingpeng Xie, Tianhong Zhou, Wei Wang, Sheng Chen, Haihua Liang, Xin Deng
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen of humans, particularly those with cystic fibrosis. As a global regulator, RpoN controls a group of virulence-related factors and quorum sensing (QS) genes in P. aeruginosa To further gain insights into the direct targets of RpoN in vivo , the present study focused on identifying the direct targets of RpoN regulation in QS and the type VI secretion system (T6SS). We performed a chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq) assay that identified 1,068 binding sites of RpoN, mostly including metabolic genes, a group of genes in QS ( lasI , rhlI and pqsR ) and the T6SS ( hcpA and hcpB )...
May 14, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29760157/methyl-cpg-binding-protein-2-mediates-antifibrotic-effects-in-scleroderma-fibroblasts
#7
Ye He, Pei-Suen Tsou, Dinesh Khanna, Amr H Sawalha
OBJECTIVE: Emerging evidence supports a role for epigenetic regulation in the pathogenesis of scleroderma (SSc). We aimed to assess the role of methyl-CpG-binding protein 2 (MeCP2), a key epigenetic regulator, in fibroblast activation and fibrosis in SSc. METHODS: Dermal fibroblasts were isolated from patients with diffuse cutaneous SSc (dcSSc) and from healthy controls. MeCP2 expression was measured by qPCR and western blot. Myofibroblast differentiation was evaluated by gel contraction assay in vitro...
May 14, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29757349/base-pair-resolution-detection-of-transcription-factor-binding-site-by-deep-deconvolutional-network
#8
Sirajul Salekin, Jianqiu Michelle Zhang, Yufei Huang
Motivation: Transcription factor (TF) binds to the promoter region of a gene to control gene expression. Identifying precise transcription factor binding sites (TFBS) is essential for understanding the detailed mechanisms of TF mediated gene regulation. However, there is a shortage of computational approach that can deliver single base pair (bp) resolution prediction of TFBS. Results: In this paper, we propose DeepSNR, a Deep Learning algorithm for predicting transcription factor binding location at Single Nucleotide Resolution de novo from DNA sequence...
May 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29753018/ets-transcription-factor-etsrp-etv2-is-required-for-lymphangiogenesis-and-directly-regulates-vegfr3-flt4-expression
#9
Jennifer A Davis, Andrew L Koenig, Allison Lubert, Brendan Chestnut, Fang Liu, Sharina Palencia Desai, Tamara Winkler, Karolina Pociute, Kyunghee Choi, Saulius Sumanas
The molecular mechanisms initiating the formation of the lymphatic system, lymphangiogenesis, are still poorly understood. Here we have identified a novel role in lymphangiogenesis for an ETS transcription factor, Etv2/Etsrp, a known regulator of embryonic vascular development. Through the use of fully validated photoactivatable morpholinos we show that inducible Etv2 inhibition in zebrafish embryos at 1day post-fertilization (dpf) results in significant inhibition of lymphangiogenesis, while development of blood vessels is unaffected...
May 9, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29752288/comparison-of-hepatic-nrf2-and-ahr-binding-in-2-3-7-8-tetrachlorodibenzo-p-dioxin-tcdd-treated-mice-demonstrates-nrf2-independent-pkm2-induction
#10
Rance Nault, Claire M Doskey, Kelly A Fader, Cheryl E Rockwell, Timothy R Zacharewski
2,3,7,8-Tetrachlorodibenzo- p -dioxin (TCDD) induces hepatic oxidative stress following activation of the aryl hydrocarbon receptor (AhR). Our recent studies showed TCDD induced pyruvate kinase muscle isoform 2 ( Pkm2 ) as a novel antioxidant response in normal differentiated hepatocytes. To investigate cooperative regulation between nuclear factor, erythroid derived 2, like 2 ( Nrf2 ) and the AhR in the induction of Pkm2 , hepatic ChIP-seq analyses were integrated with RNA-seq time course data from mice treated with TCDD for 2 - 168h...
May 11, 2018: Molecular Pharmacology
https://www.readbyqxmd.com/read/29748061/massive-ggaas-in-genomic-repetitive-sequences-serve-as-a-nuclear-reservoir-of-nf-%C3%AE%C2%BAb
#11
Jian Wu, Qiao Wang, Wei Dai, Wei Wang, Ming Yue, Jinke Wang
Nuclear factor κB (NF-κB) is a DNA-binding transcription factor. Characterizing its genomic binding sites is crucial for understanding its gene regulatory function and mechanism in cells. This study characterized the binding sites of NF-κB RelA/p65 in the tumor neurosis factor-α (TNFα) stimulated HeLa cells by a precise chromatin immunoprecipitation-sequencing (ChIP-seq). The results revealed that NF-κB binds nontraditional motifs (nt-motifs) containing conserved GGAA quadruplet. Moreover, nt-motifs mainly distribute in the peaks nearby centromeres that contain a larger number of repetitive elements such as satellite, simple repeats and short interspersed nuclear elements (SINEs)...
April 13, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/29743723/dysregulation-of-ezh2-mir-138-axis-contributes-to-drug-resistance-in-multiple-myeloma-by-downregulating-rbpms
#12
Nasrin Rastgoo, Maryam Pourabdollah, Jahangir Abdi, Donna Reece, Hong Chang
EZH2 is highly expressed in multiple myeloma (MM). However, the molecular mechanisms underlying EZH2 overexpression and its role in drug resistance of MM remain undefined. Here we show that EZH2 is upregulated in drug-resistant MM cells and its aberrant overexpression is associated with poor prognosis of MM patients. Overexpression of EZH2 in parental MM cells renders them resistant to anti-myeloma drugs and suppression of EZH2 displays the opposite effects. Using miRNA target scan algorithms, we identify miR-138 as a regulator of EZH2, which is conversely repressed by EZH2-induced H3K27 trimethylation in MM-resistant cell lines and primary tumor cells...
April 24, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/29738563/development-of-an-efficient-chromatin-immunoprecipitation-method-to-investigate-protein-dna-interaction-in-oleaginous-castor-bean-seeds
#13
Mohammad Enamul Haque, Bing Han, Bin Wang, Yue Wang, Aizhong Liu
Chromatin immunoprecipitation (ChIP) is usually a reliable technique to find the binding sites of a transcription factor. In the current study, we developed a suitable ChIP method using developing castor bean seeds. A castor bean seed with large and persistent endosperm contains high amounts of storage lipids (ca. 50-60%) and is often considered as a model material to studying seed biology. In oleaginous seeds, due to the rich oils which could seriously affect immunoprecipitation and DNA isolation, it is often difficult to carry out a successful ChIP experiment...
2018: PloS One
https://www.readbyqxmd.com/read/29738468/-cawrky40b-in-pepper-acts-as-a-negative-regulator-in-response-to-ralstonia-solanacearum-by-directly-modulating-defense-genes-including-cawrky40
#14
Muhammad Ifnan Khan, Yangwen Zhang, Zhiqin Liu, Jiong Hu, Cailing Liu, Sheng Yang, Ansar Hussain, Muhammad Furqan Ashraf, Ali Noman, Lei Shen, Xiaoqin Xia, Feng Yang, Deyi Guan, Shuilin He
WRKY transcription factors (TFs) have been implicated in plant growth, development, and in response to environmental cues; however, the function of the majority of pepper WRKY TFs remains unclear. In the present study, we functionally characterized CaWRKY40b , a homolog of AtWRKY40 , in pepper immunity. Ralstonia solanacearum inoculation (RSI) in pepper plants resulted in downregulation of CaWRKY40b transcript, and green fluorescent protein (GFP)-tagged CaWRKY40b was localized to the nuclei when transiently overexpressed in the leaves of Nicotiana benthamiana ...
May 8, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29735545/nuclear-igf-1r-interacts-with-regulatory-regions-of-chromatin-to-promote-rna-polymerase-ii-recruitment-and-gene-expression-associated-with-advanced-tumor-stage
#15
Tamara Aleksic, Nicki E Gray, Xiaoning Wu, Guillaume Rieunier, Eliot Osher, Jack Mills, Clare Verrill, Richard J Bryant, Cheng Han, Kathryn Hutchinson, Adam Lambert, Rajeev Kumar, Freddie C Hamdy, Ulrike Weyer-Czernilofsky, Michael Sanderson, Thomas Bogenrieder, Stephen Taylor, Valentine M Macaulay
Internalization of ligand-activated type 1 IGF receptor (IGF-1R) is followed by recycling to the plasma membrane, degradation or nuclear translocation. Nuclear IGF-1R reportedly associates with clinical response to IGF-1R inhibitory drugs, yet its role in the nucleus is poorly characterized. Here we investigated the significance of nuclear IGF-1R in clinical cancers and cell line models. In prostate cancers, IGF-1R was predominantly membrane-localized in benign glands, while malignant epithelium contained prominent internalized (nuclear/cytoplasmic) IGF-1R, and nuclear IGF-1R associated significantly with advanced tumor stage...
May 7, 2018: Cancer Research
https://www.readbyqxmd.com/read/29735531/smad4-deficiency-impairs-chondrocyte-hypertrophy-via-the-runx2-transcription-factor-in-mouse-skeletal-development
#16
Jianyun Yan, Jun Li, Jun Hu, Lu Zhang, Chengguo Wei, Nishat Sultana, Xiaoqiang Cai, Weijia Zhang, Chen-Leng Cai
Chondrocyte hypertrophy is the terminal step in chondrocyte differentiation and is crucial for endochondral bone formation. How signaling pathways regulate chondrocyte hypertrophic differentiation remains incompletely understood. In this study, using a Tbx18:Cre (Tbx18Cre/+) gene-deletion approach, we selectively deleted the gene for the signaling protein SMAD family member 4 (Smad4f/f) in the limbs of mice. We found that the Smad4-deficient mice develop a prominent shortened limb, with decreased expression of chondrocyte differentiation markers, including Col2a1 and Acan, in the humerus at mid-to-late gestation...
May 7, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29733872/experimental-and-integrative-analyses-identify-an-ets1-network-downstream-bcr-abl-in-chronic-myeloid-leukemia-cml
#17
Christophe Desterke, Maud Voldoire, Marie-Laure Bonnet, Nathalie Sorel, Sarah Pagliaro, Hind Rahban, Annelise Bennaceur Griscelli, Emilie Cayssials, Jean-Claude Chomel, Ali G Turhan
The BCR-ABL oncogene, hallmark of chronic myeloid leukemia (CML), has been shown to activate several signaling pathways in leukemic cells. The natural history of this disease has been radically modified by tyrosine kinase inhibitors (TKIs). However, resistance to several lines of TKI therapies and progression to blast crisis (BC) remain significant concerns. In order to identify novel signaling pathways induced by BCR-ABL, we performed a transcriptome analysis in BCR-ABL-expressing UT-7 cell line. More than 2000 genes differentially expressed between BCR-ABL-expressing and parental UT-7 cells were identified, and ETS1 was found to be the most up-regulated...
May 4, 2018: Experimental Hematology
https://www.readbyqxmd.com/read/29733395/towards-a-map-of-cis-regulatory-sequences-in-the-human-genome
#18
Meng Niu, Ehsan Tabari, Pengyu Ni, Zhengchang Su
Accumulating evidence indicates that transcription factor (TF) binding sites, or cis-regulatory elements (CREs), and their clusters termed cis-regulatory modules (CRMs) play a more important role than do gene-coding sequences in specifying complex traits in humans, including the susceptibility to common complex diseases. To fully characterize their roles in deriving the complex traits/diseases, it is necessary to annotate all CREs and CRMs encoded in the human genome. However, the current annotations of CREs and CRMs in the human genome are still very limited and mostly coarse-grained, as they often lack the detailed information of CREs in CRMs...
May 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29733394/sin3a-tet1-interaction-activates-gene-transcription-and-is-required-for-embryonic-stem-cell-pluripotency
#19
Fugui Zhu, Qianshu Zhu, Dan Ye, Qingquan Zhang, Yiwei Yang, Xudong Guo, Zhenping Liu, Zeyidan Jiapaer, Xiaoping Wan, Guiying Wang, Wen Chen, Songcheng Zhu, Cizhong Jiang, Weiyang Shi, Jiuhong Kang
Sin3a is a core component of histone-deacetylation-activity-associated transcriptional repressor complex, playing important roles in early embryo development. Here, we reported that down-regulation of Sin3a led to the loss of embryonic stem cell (ESC) self-renewal and skewed differentiation into mesendoderm lineage. We found that Sin3a functioned as a transcriptional coactivator of the critical Nodal antagonist Lefty1 through interacting with Tet1 to de-methylate the Lefty1 promoter. Further studies showed that two amino acid residues (Phe147, Phe182) in the PAH1 domain of Sin3a are essential for Sin3a-Tet1 interaction and its activity in regulating pluripotency...
May 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29729076/genome-wide-binding-of-transcription-factor-snail1-in-triple-negative-breast-cancer-cells
#20
Varun Maturi, Anita Morén, Stefan Enroth, Carl-Henrik Heldin, Aristidis Moustakas
Transcriptional regulation mediated by the zinc finger protein Snail1 controls early embryogenesis. By binding to the epithelial tumor suppressor CDH1 gene, Snail1 initiates the epithelial-mesenchymal transition (EMT). The EMT generates stem-like cells and promotes invasiveness during cancer progression. Accordingly, Snail1 mRNA and protein is abundantly expressed in triple-negative breast cancers with enhanced metastatic potential and phenotypic signs of the EMT. Such high endogenous Snail1 protein levels permit quantitative chromatin immunoprecipitation-sequencing (ChIP-seq) analysis...
May 4, 2018: Molecular Oncology
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