Expanded encyclopaedias of DNA elements in the human and mouse genomes

, Jill E Moore ¹, Michael J Purcaro ¹

¹University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.
²The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
³Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA.
⁴Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA.
⁵Altius Institute for Biomedical Sciences, Seattle, WA, USA.
⁶Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
⁷Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
⁸Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁹Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
¹⁰Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
¹¹Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
¹²Genomics Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
¹³HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
¹⁴Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
¹⁵Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA.
¹⁶Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
¹⁷Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁸Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
¹⁹Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec, Canada.
²⁰Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
²¹Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Quebec, Canada.
²²Department of Biological Science, Florida State University, Tallahassee, FL, USA.
²³Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA.
²⁴Yale University, New Haven, CT, USA.
²⁵Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA.
²⁶Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA.
²⁷Department of Human Genetics, Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
²⁸Tempus Labs, Chicago, IL, USA.
²⁹US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³⁰School of Natural Sciences, University of California, Merced, Merced, CA, USA.
³¹Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
³²HHMI and Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.
³³University of Colorado Boulder, Boulder, CO, USA.
³⁴Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
³⁵Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
³⁶Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
³⁷Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
³⁸Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain.
³⁹Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
⁴⁰Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA. cherry@stanford.edu.
⁴¹HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA. rmyers@hudsonalpha.org.
⁴²Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. biren@ucsd.edu.
⁴³Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA. biren@ucsd.edu.
⁴⁴Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA. graveley@uchc.edu.
⁴⁵Yale University, New Haven, CT, USA. mark@gersteinlab.org.
⁴⁶Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. lapennacchio@lbl.gov.
⁴⁷US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. lapennacchio@lbl.gov.
⁴⁸Comparative Biochemistry Program, University of California, Berkeley, CA, USA. lapennacchio@lbl.gov.
⁴⁹Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA. mpsnyder@stanford.edu.
⁵⁰Cardiovascular Institute, Stanford School of Medicine, Stanford, CA, USA. mpsnyder@stanford.edu.
⁵¹Broad Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Bernstein.Bradley@mgh.harvard.edu.
⁵²Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. woldb@caltech.edu.
⁵³Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA. rch8@psu.edu.
⁵⁴Cold Spring Harbor Laboratory, Functional Genomics, Cold Spring Harbor, NY, USA. gingeras@cshl.edu.
⁵⁵Altius Institute for Biomedical Sciences, Seattle, WA, USA. jstam@altius.org.
⁵⁶Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA. jstam@altius.org.
⁵⁷Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. jstam@altius.org.
⁵⁸University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA. zhiping.weng@umassmed.edu.
⁵⁹Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, Shanghai, China. zhiping.weng@umassmed.edu.
⁶⁰Bioinformatics Program, Boston University, Boston, MA, USA. zhiping.weng@umassmed.edu.

⁰University of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, USA.

The Encyclopedia of DNA Elements (ENCODE) Project mapped human and mouse genomes, identifying millions of regulatory elements. This resource enhances understanding of genome organization and function.

Area Of Science

Genomics
Epigenetics
Molecular Biology

Background

The human and mouse genomes encode RNA and protein, regulating their production.
Understanding genome regulation is crucial for deciphering biological processes.

Purpose Of The Study

To expand the Encyclopedia of DNA Elements (ENCODE) Project's analysis of genomic features.
To create a comprehensive registry of cis-regulatory elements in human and mouse genomes.

Main Methods

Collected 5,992 new experimental datasets on RNA transcription, chromatin structure, DNA methylation, and protein occupancy.
Integrated selected data types to identify candidate cis-regulatory elements.
Developed the SCREEN web server for user-defined access to genomic data.

Main Results

Identified 926,535 human and 339,815 mouse candidate cis-regulatory elements.
These elements cover 7.9% (human) and 3.4% (mouse) of their respective genomes.
Generated systematic data across mouse fetal development.

Conclusions

The ENCODE data portal and SCREEN resource provide extensive genomic information.
This resource aids the scientific community in understanding genome organization and function.
Facilitates deeper insights into gene regulation in humans and mice.

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Summary

Area Of Science

Background

Purpose Of The Study

Main Methods

Main Results

Conclusions

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Expanded encyclopaedias of DNA elements in the human and mouse genomes

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Summary

Area Of Science

Background

Purpose Of The Study

Main Methods

Main Results

Conclusions

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