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David W Scoville Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA

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Kristin Lichti-Kaiser Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA

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Sara A Grimm Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA

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Anton M Jetten Cell Biology Group, Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA

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study was to obtain a better understanding of GLIS3-mediated regulation of gene transcription in pancreatic islets; we therefore performed gene expression analysis on islets from these mice, as well as GLIS3 ChIP-seq analysis. In addition, we compared

Article Type:
Research Article
DOI:
https://doi.org/10.1530/JOE-19-0182
Volume/Issue:
Volume 243: Issue 1
Restricted access
Celia Siu Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
Department of Sciences, University of British Columbia, Vancouver, Canada

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Sam Wiseman Department of Surgery, St. Paul’s Hospital & University of British Columbia, Vancouver, Canada

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Sitanshu Gakkhar Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada

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Alireza Heravi-Moussavi Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada

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Misha Bilenky Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada

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Annaick Carles Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

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Thomas Sierocinski Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

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Angela Tam Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada

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Eric Zhao Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada

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Katayoon Kasaian Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada

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Richard A Moore Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada

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Andrew J Mungall Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada

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Blair Walker Department of Pathology and Laboratory Medicine, St. Paul’s Hospital & University of British Columbia, Vancouver, Canada

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Thomas Thomson Department of Pathology and Laboratory Medicine, BC Cancer Agency & University of British Columbia, Vancouver, Canada

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Marco A Marra Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
Department of Medical Genetics, University of British Columbia, Vancouver, Canada

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Martin Hirst Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

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Steven J M Jones Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
Department of Medical Genetics, University of British Columbia, Vancouver, Canada
Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, Canada

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3, H3K9me3, H3K27me3) profiled with ChIP-seq, a methylome, a transcriptome and a normal and disease-matched genomic sequence. We partitioned the epigenomes into various chromatin states and developed a novel quantitative metric for model selection

Article Type:
Research Article
DOI:
https://doi.org/10.1530/JOE-17-0145
Volume/Issue:
Volume 235: Issue 2
Free access
Koen D Flach Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands

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Wilbert Zwart Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands

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-wide scale ( Carroll et al. 2005 ). With the development of massive parallel high-throughput sequencing techniques, a full genome coverage of ERα became possible (and importantly affordable) through ChIP sequencing (ChIP-seq) ( Welboren et al. 2009 ). Now

Article Type:
Review Article
DOI:
https://doi.org/10.1530/JOE-16-0003
Volume/Issue:
Volume 229: Issue 2
Free access
Brad G Hoffman
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Steven J M Jones Department of Cancer Endocrinology, Micheal Smith Genome Sciences Centre, BC Cancer Research Center, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3

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extremely well with the analysis of DNA fragments enriched by chromatin immunoprecipitation (ChIP-seq; Johnson et al . 2007 , Mardis 2007 ). ChIP is now standard practice in the identification of histone modification locations and transcription factor

Article Type:
Research Article
DOI:
https://doi.org/10.1677/JOE-08-0526
Volume/Issue:
Volume 201: Issue 1
Free access
Jinke Wang The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People's Republic of China

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Jie Lu The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People's Republic of China

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Guangming Gu The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People's Republic of China

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Yingxun Liu The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People's Republic of China

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microarray chip) ( Ren et al . 2000 ) and ChIP-seq (ChIP coupled with parallel DNA sequencing) ( Robertson et al . 2007 ), have generated in vivo DBPs for many TFs, however, because ChIP-based methods identify TFBSs in a particular cell at the time point

Article Type:
Research Article
DOI:
https://doi.org/10.1530/JOE-11-0010
Volume/Issue:
Volume 210: Issue 1
Free access
Ichiro Kaneko Department of Basic Medical Sciences, School of Mathematical and Natural Sciences, University of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USA
Department of Basic Medical Sciences, School of Mathematical and Natural Sciences, University of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USA

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Rimpi K Saini Department of Basic Medical Sciences, School of Mathematical and Natural Sciences, University of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USA

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Kristin P Griffin Department of Basic Medical Sciences, School of Mathematical and Natural Sciences, University of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USA

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G Kerr Whitfield Department of Basic Medical Sciences, School of Mathematical and Natural Sciences, University of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USA

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Mark R Haussler Department of Basic Medical Sciences, School of Mathematical and Natural Sciences, University of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USA

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Peter W Jurutka Department of Basic Medical Sciences, School of Mathematical and Natural Sciences, University of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USA
Department of Basic Medical Sciences, School of Mathematical and Natural Sciences, University of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USA

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detectable 1,25D-dependent VDR/RXR binding sites when ChIP-Seq analysis is carried out ( St John et al . 2014 ). Therefore, the in vivo relevance of VDREs residing in the mouse FGF23 gene remains to be confirmed. Recently, functional VDREs have been

Article Type:
Research Article
DOI:
https://doi.org/10.1530/JOE-15-0225
Volume/Issue:
Volume 226: Issue 3
Free access
Aijun Zhang Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Douglas H Sieglaff Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Jean Philippe York Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Ji Ho Suh Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Stephen D Ayers Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Glenn E Winnier Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Alexei Kharitonenkov Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Christopher Pin Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA
Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Pumin Zhang Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Paul Webb Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Xuefeng Xia Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA
Houston Methodist Research Institute, College of Arts and Sciences, Departments of Paediatrics, Children's Health Research Institute, Department of Molecular Physiology and Biophysics, The Third Affiliated Hospital of Guangzhou Medical University, Genomic Medicine Program, 6670 Bertner Ave, Houston, Texas 77030, USA

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Fgf21 locus independently of PPARα, we consulted a published ChIP-chip dataset and our own preliminary ChIP-Seq results. Results of recent studies have indicated the presence of an intronic TRβ-binding peak within the Fgf21 locus in mouse cerebellum

Article Type:
Research Article
DOI:
https://doi.org/10.1530/JOE-14-0440
Volume/Issue:
Volume 224: Issue 3
Free access
Elliott P Brooks Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA

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Lori Sussel Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA

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specificity ( Fig. 4C ). PAX6 chromatin immunoprecipitation sequencing (ChIP-seq) in αTC cells depleted of Paupar revealed more than 2000 differentially bound sites, many of which overlapped with regulatory regions of α enriched genes. Importantly

Article Type:
Review Article
Collections:
100 years of glucagon: Anniversary collection
DOI:
https://doi.org/10.1530/JOE-22-0297
Volume/Issue:
Volume 258: Issue 2
Free access
Carolina Gaudenzi Neuro-Epigenetics Research Group, Dorothy Hodgkin Building, University of Bristol, Bristol, United Kingdom

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Karen R Mifsud Neuro-Epigenetics Research Group, Dorothy Hodgkin Building, University of Bristol, Bristol, United Kingdom

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Johannes M H M Reul Neuro-Epigenetics Research Group, Dorothy Hodgkin Building, University of Bristol, Bristol, United Kingdom

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conditions ( Gesing et al. 2001 ), binding of the MR to GREs was muted. These observations clearly clashed with the concept of MR-mediated tonic effects on brain function. Recent ChIP-sequencing (ChIP-seq) analysis of MR interaction with the entire rat

Article Type:
Review Article
DOI:
https://doi.org/10.1530/JOE-22-0293
Volume/Issue:
Volume 258: Issue 2
Open access
Marian Joëls Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center, Utrecht, The Netherlands
University of Groningen, University Medical Center, Groningen, The Netherlands

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E Ronald de Kloet Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands

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(ChIP-seq) identified 2470 specific binding sites of which 39% were localised within in genes ( Fig. 2 ) ( Polman et al . 2013 ). Of these binding sites in total 918 and 1470 were exclusive for MR and GR, respectively, whereas 475 sites were overlapping

Article Type:
Review Article
DOI:
https://doi.org/10.1530/JOE-16-0660
Volume/Issue:
Volume 234: Issue 1
Free access