ArticleCell reports2019
Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function.
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Article in Cell reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44citing papers in PubMed
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44 citing papers in PubMed, 82 citations in OpenAlex.
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- Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets.Scientific reports · 2024Article
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- LncRNA ARGI Contributes to Virus-Induced Pancreatic β Cell Inflammation Through Transcriptional Activation of IFN-Stimulated Genes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
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- Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes.Genomics, proteomics & bioinformatics · 2023Article
- Glucocorticoid-mediated induction of ZBTB16 affects insulin secretion in human islets and EndoC-βH1 β-cells.iScience · 2023Article
- Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers.BMC genomics · 2023Article
- Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones.PLoS genetics · 2023Article
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Authors and funding
28 authors at 8 institutions in 1 country.
Nathan LawlorThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Eladio J MárquezThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Peter OrchardDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
Narisu NarisuNational Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Muhammad Saad ShamimCenter for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA; Department of Bioengineering, Rice University, Houston, TX 77030, USA.
Asa ThibodeauThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Arushi VarshneyDepartment of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
Romy KursaweThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Michael R ErdosNational Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Matt KankeDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
Huiya GuCenter for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Evgenia PakNational Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Amalia DutraNational Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Sheikh RussellCenter for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
Xingwang LiThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Emaly PiecuchThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA.
Oscar LuoThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Peter S ChinesNational Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Christian FuchbsergerDepartment of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA.
NIH Intramural Sequencing Center
Praveen SethupathyDepartment of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
Aviva Presser AidenCenter for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
Yijun RuanThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Erez Lieberman AidenCenter for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computer Science, Department of Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Francis S CollinsNational Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
Duygu UcarThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.
Stephen C J ParkerDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
Michael L StitzelThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA. Electronic address: michael.stitzel@jax.org.
Jackson Laboratory · USNational Human Genome Research Institute · USUniversity of Michigan–Ann Arbor · USBaylor College of Medicine · USCornell University · USRice University · USMassachusetts Institute of Technology · USUniversity of Connecticut · US
Funding
Inter- and Intra-Species Comparative SequencingZIBHG000196 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI THOMAS, JAMES · 2009 to 2025
$177.6MGenetic analysis of type II diabetes in Finnish populationZIAHG000024 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI ERDOS, MICHAEL · 2009 to 2025
$38.2MNHGRI/DIR Cytogenetics and Microscopy CoreZICHG200348 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI WINCOVITCH, STEPHEN · 2010 to 2025
$20.3MUniversity of Michigan Training Program in Genomic ScienceT32HG000040 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Sebastian Zoellner · 1995 to 2026
$16.4MGENETIC ANALYSIS OF TYPE II DIABETES IN FINNISH POPULATIONZ01HG000024 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI COLLINS, FRANCIS S. · 1995 to 2008
$6.2MGENOME WIDE MAPPING OF LOOPS USING IN SITU HI-CUM1HG009375 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI LIEBERMAN-AIDEN, EREZ · 2017 to 2021
$4.7MExploring how the genome folds through proximity ligation and sequencingDP2OD008540 · OD · BROAD INSTITUTE, INC. · PI LIEBERMAN-AIDEN, EREZ · 2011 to 2016
$3.0MContext-specific and combinatorial genetic regulatory grammars in diabetesR01DK117960 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Stephen CJ Parker · 2018 to 2026
$2.8MSupplement - Beyond pairwise DNA contacts: exploring higher-order genome structure using proximity ligationU01HL130010 · NHLBI · BAYLOR COLLEGE OF MEDICINE · PI LIEBERMAN-AIDEN, EREZ · 2015 to 2019
$2.3MInvestigation of noncoding variation in human pancreatic islets and their developR00DK092251 · NIDDK · JACKSON LABORATORY · PI STITZEL, MICHAEL LEE · 2014 to 2016
$794kSynthesizing genome, epigenome, and transcriptome datasets in type 2 diabetes.R00DK099240 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI PARKER, STEPHEN CJ · 2015 to 2017
$726kIntramural NIH HHS Z01 HG000024Intramural NIH HHS ZIA HG000024NHGRI NIH HHS T32 HG000040NHGRI NIH HHS UM1 HG009375NHLBI NIH HHS U01 HL130010NIDDK NIH HHS R00 DK092251NIDDK NIH HHS R00 DK099240NIDDK NIH HHS R01 DK117960NIH HHS DP2 OD008540
Abstract
EndoC-βH1 is emerging as a critical human β cell model to study the genetic and environmental etiologies of β cell (dys)function and diabetes. Comprehensive knowledge of its molecular landscape is lacking, yet required, for effective use of this model. Here, we report chromosomal (spectral karyotyping), genetic (genotyping), epigenomic (ChIP-seq and ATAC-seq), chromatin interaction (Hi-C and Pol2 ChIA-PET), and transcriptomic (RNA-seq and miRNA-seq) maps of EndoC-βH1. Analyses of these maps define known (e.g., PDX1 and ISL1) and putative (e.g., PCSK1 and mir-375) β cell-specific transcriptional cis-regulatory networks and identify allelic effects on cis-regulatory element use. Importantly, comparison with maps generated in primary human islets and/or β cells indicates preservation of chromatin looping but also highlights chromosomal aberrations and fetal genomic signatures in EndoC-βH1. Together, these maps, and a web application we created for their exploration, provide important tools for the design of experiments to probe and manipulate the genetic programs governing β cell identity and (dys)function in diabetes.
Indexed as
Cell LineGene Regulatory NetworksHumansInsulin-Secreting CellsEndoC-βH1(epi)genomegeneticsHi-Chuman pancreatic isletskaryotypePol2 ChIA-PETtranscriptometype 2 diabetesβ cell
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