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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
Yaxiong Huang Department of Reproductive Medicine center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, PR China
Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan Hubei Province, PR China
Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan Hubei Province, PR China
Department of Gynaecology and Obstetrics, Sinopharm Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei Province, PR China

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Zihan Wang Department of Reproductive Medicine center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, PR China
Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan Hubei Province, PR China
Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan Hubei Province, PR China

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Bin Li Department of Gynaecology and Obstetrics, Sinopharm Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei Province, PR China

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Lina Ke Department of Gynaecology and Obstetrics, Sinopharm Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei Province, PR China

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Yao Xiong Department of Reproductive Medicine center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, PR China
Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan Hubei Province, PR China
Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan Hubei Province, PR China

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Yuanzhen Zhang Department of Reproductive Medicine center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, PR China
Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan Hubei Province, PR China
Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan Hubei Province, PR China

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-associated infertility. Further experiments revealed that knockdown of KLF15 reversed the expression of EMT markers in Ishikawa cells. Through RNA-seq and ChIP-qPCR assays, we discovered that KLF15 directly binds to TWIST2 promoter regions and may act as a transcription

Article Type:
Research Article
DOI:
https://doi.org/10.1530/JOE-23-0319
Volume/Issue:
Volume 261: Issue 2
Open 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
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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. Many of the initial genetic studies in mice were performed before the availability of advanced RNA-, ChIP- and ATAC-seq techniques that can be applied to small numbers of cells. Thus, we have sparse knowledge of the molecular mechanisms of factors such

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
Joyce Emons
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Bas E Dutilh Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Eva Decker Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Heide Pirzer Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Carsten Sticht Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Norbert Gretz Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Gudrun Rappold Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Ewan R Cameron Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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James C Neil Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Gary S Stein Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Andre J van Wijnen Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Jan Maarten Wit
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Janine N Post Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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Marcel Karperien Department of Paediatrics, Centre for Molecular and Biomolecular Informatics, Department of Human Molecular Genetics, Medical Research Center, Molecular Oncology Laboratory, Department of Cell Biology, Department of Tissue Regeneration, Leiden University Medical Center, 2300 ZA Leiden, The Netherlands

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. PNAS 98 6871 – 6876 doi:10.1073/pnas.121180498 . Welboren WJ van Driel MA Janssen-Megens EM van Heeringen SJ Sweep FC Span PN Stunnenberg HG 2009 ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to

Article Type:
Research Article
DOI:
https://doi.org/10.1530/JOE-10-0219
Volume/Issue:
Volume 209: Issue 2
Free access
Jinyu Ma Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University,Nantong, China

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Yuejun Wang Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University,Nantong, China

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Jie Ding Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University,Nantong, China

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Shouping Zhang Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University,Nantong, China

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Yinuo Yang Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University,Nantong, China

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Cheng Sun Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education; NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University,Nantong, China
Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, Institute of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China

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-PCR. ChIP assay ChIP assay was performed by using an Acetyl-Histone H3 ChIP kit (EPIGENTEK; P2012) according to the manufacturer’s instructions. Briefly, cells were treated with cross-linking buffer for 20 min on a rocking device, and then cells were

Article Type:
Research Article
DOI:
https://doi.org/10.1530/JOE-20-0472
Volume/Issue:
Volume 249: Issue 3
Restricted access