Expanded encyclopaedias of DNA elements in the human and mouse genomes
- Federico Abascal
- Reyes Acosta
- Nicholas J. Addleman
- Jessika Adrian
- Veena Afzal
- Rizi Ai
- Bronwen L. Aken
- Jennifer A. Akiyama
- Omar Al Jammal
- Henry Amrhein
- Stacie M. Anderson
- Gregory R. Andrews
- Igor A. Antoshechkin
- Kristin Ardlie
- Joel C. Armstrong
- Matthew Astley
- Budhaditya Banerjee
- Amira A. Barkal
- If H. A. Barnes
- Iros Barozzi
- Daniel G. Barrell
- Gemma Barson
- Daniel J. Bates
- Ulugbek K. Baymuradov
- Cassandra Bazile
- M Beer
- Samantha P. Beik
- Michael A. Bender
- Ruth Bennett
- Louis Philip Benoit Bouvrette
- B Bernstein
- Andrew E. Berry
- Anand Bhaskar
- Alexandra Bignell
- Steven M. Blue
- David M. Bodine
- Carles A. Boix
- Nathan Boley
- Tyler M. Borrman
- Beatrice Borsari
- Alan P. Boyle
- Laurel A. Brandsmeier
- Alessandra Breschi
- Emery H. Bresnick
- Jason A. Brooks
- Michael J Buckley
- Christopher B. Burge
- Rachel Byron
- Eileen Cahill
- Lingling Cai
- Lulu Cao
- Mark Carty
- Rosa Castanon
- Andres Castillo
- Hassan Chaı̈b
- Esther T. Chan
- Daniel R. Chee
- Sora Chee
- Hao Chen
- Huaming Chen
- Jiayu Chen
- Songjie Chen
- J. Michael Cherry
- Surya B. Chhetri
- Jyoti Sharma Choudhary
- Jacqueline Chrast
- Dongjun Chung
- Declan Clarke
- Neal A. L. Cody
- Candice J. Coppola
- Julie C. Coursen
- Anthony M. D’Ippolito
- Stephen L. Dalton
- Cassidy Danyko
- Claire Davidson
- José Dávila-Velderrain
- Carrie Davis
- Job Dekker
- Alden Deran
- Gilberto DeSalvo
- Gloria Despacio-Reyes
- Colin N. Dewey
- Diane E. Dickel
- Morgan Diegel
- Mark E. Diekhans
- Vishnu Dileep
- Bo Ding
- Sarah Djebali
- Alexander Yu. Dobin
- Daniel Domı́nguez
- Sarah M. Donaldson
- Jörg Drenkow
- Timothy R. Dreszer
- Yotam Drier
- Michael O. Duff
- Douglas Dunn
- Catharine Eastman
- Joseph R. Ecker
- Matthew D. Edwards
- Nicole C. El-Ali
- MKM Kellis
Nature · 2020 · Nature Portfolio
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Abstract
Abstract The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal ( https://www.encodeproject.org ), including phase II ENCODE 1 and Roadmap Epigenomics 2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis -regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org ) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.