An encyclopedia of enhancer-gene regulatory interactions in the human genome.

Journal

bioRxiv : the preprint server for biology
Titre abrégé: bioRxiv
Pays: United States
ID NLM: 101680187

Informations de publication

Date de publication:
13 Nov 2023
Historique:
pubmed: 28 11 2023
medline: 28 11 2023
entrez: 28 11 2023
Statut: epublish

Résumé

Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease

Identifiants

DOI: 10.1101/2023.11.09.563812 PMID: 38014075 PMC: PMC10680627
pubmed: 38014075
doi: 10.1101/2023.11.09.563812
pmc: PMC10680627
pii:
doi:

Types de publication

Preprint

Langues

eng

Subventions

Organisme : NHGRI NIH HHS
ID : U24 HG009397
Pays : United States
Organisme : NHGRI NIH HHS
ID : R00 HG012203
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009431
Pays : United States
Organisme : NHGRI NIH HHS
ID : R35 HG011324
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG012103
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG011972
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG012069
Pays : United States
Organisme : NHGRI NIH HHS
ID : K99 HG009917
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009380
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG009395
Pays : United States
Organisme : NHGRI NIH HHS
ID : R00 HG009917
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG012009
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG012367
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG006992
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG009436
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG009446
Pays : United States

Déclaration de conflit d'intérêts

Conflict of Interest Statement Z.A. is employed by Google DeepMind. J.C.U. is an employee of Illumina, Inc. D.R.K. is employed by Calico Life Sciences LLC. Z.W. co-founded Rgenta Therapeutics, and she serves as a scientific advisor for the company and is a member of its board. W.J.G. is an inventor on IP licensed by 10x Genomics. A.Kundaje is on the scientific advisory board of PatchBio, SerImmune and OpenTargets, was a consultant with Illumina, and owns shares in DeepGenomics, ImmunAI and Freenome. J.M.E. is a consultant and equity holder in Martingale Labs, Inc. and has received materials from 10x Genomics unrelated to this study.

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Auteurs

Andreas R Gschwind (AR)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Basic Sciences and Engineering Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA.
ORCID: 0000-0002-0769-6907

Kristy S Mualim (KS)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Department of Plant Biology, Carnegie Institute of Science, Stanford, CA, USA.

Alireza Karbalayghareh (A)

Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Maya U Sheth (MU)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Basic Sciences and Engineering Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA.
Department of Bioengineering, Stanford University, Stanford, CA, USA.

Kushal K Dey (KK)

Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

Evelyn Jagoda (E)

The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Ramil N Nurtdinov (RN)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.

Wang Xi (W)

Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Anthony S Tan (AS)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Basic Sciences and Engineering Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA.

Hank Jones (H)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Basic Sciences and Engineering Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA.
ORCID: 0009-0007-3220-3098

X Rosa Ma (XR)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Basic Sciences and Engineering Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA.

David Yao (D)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0002-2232-524X

Joseph Nasser (J)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Present Address: Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0001-5941-5751

Žiga Avsec (Ž)

Google DeepMind, London, UK.
ORCID: 0000-0002-7790-8936

Benjamin T James (BT)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
ORCID: 0000-0002-6228-055X

Muhammad S Shamim (MS)

The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
Department of Bioengineering, Rice University, Houston, TX, USA.
Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, USA.
ORCID: 0000-0002-2600-5147

Neva C Durand (NC)

Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
Department of Computer Science, Rice University, Houston, TX, USA.
ORCID: 0009-0006-5647-2623

Suhas S P Rao (SSP)

The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
Department of Structural Biology, Stanford University, Stanford, CA, USA.

Ragini Mahajan (R)

The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
Department of Biosciences, Rice University, Houston, TX, USA.

Benjamin R Doughty (BR)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0003-0447-4468

Kalina Andreeva (K)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0002-5206-532X

Jacob C Ulirsch (JC)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Present Address: Artificial Intelligence Laboratory, Illumina, Inc., San Diego, CA, USA.

Kaili Fan (K)

Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Present Address: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
ORCID: 0000-0002-8723-7902

Elizabeth M Perez (EM)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Tri C Nguyen (TC)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Basic Sciences and Engineering Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA.
ORCID: 0000-0002-5141-5228

David R Kelley (DR)

Calico Life Sciences, South San Francisco, CA, USA.
ORCID: 0000-0001-7782-3548

Hilary K Finucane (HK)

Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Jill E Moore (JE)

Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.

Zhiping Weng (Z)

Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
ORCID: 0000-0002-3032-7966

Manolis Kellis (M)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
ORCID: 0000-0001-7113-9630

Michael C Bassik (MC)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

Alkes L Price (AL)

Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

Michael A Beer (MA)

Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
ORCID: 0000-0001-9955-3809

Roderic Guigó (R)

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
ORCID: 0000-0002-5738-4477

John A Stamatoyannopoulos (JA)

Altius Institute for Biomedical Sciences, Seattle, WA, USA.
Clinical Research Division, Fred Hutch Cancer Center, Seattle, WA, USA.

Erez Lieberman Aiden (E)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
Department of Computer Science, Rice University, Houston, TX, USA.

William J Greenleaf (WJ)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Department of Applied Physics, Stanford University, Stanford, CA, USA.
ORCID: 0000-0003-1409-3095

Christina S Leslie (CS)

Memorial Sloan Kettering Cancer Center, New York, NY, USA.
ORCID: 0000-0002-4571-5910

Lars M Steinmetz (LM)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Stanford Genome Technology Center, Palo Alto, CA, USA.
European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
ORCID: 0000-0002-3962-2865

Anshul Kundaje (A)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Department of Computer Science, Stanford University, Stanford, CA, USA.
ORCID: 0000-0003-3084-2287

Jesse M Engreitz (JM)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Basic Sciences and Engineering Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA.
The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
ORCID: 0000-0002-5754-1719

Classifications MeSH