Expanded encyclopaedias of DNA elements in the human and mouse genomes.
null nullJill E MooreMichael J PurcaroHenry E PrattCharles B EpsteinNoam ShoreshJessika AdrianTrupti KawliCarrie A DavisAlexander DobinRajinder KaulJessica HalowEric L Van NostrandPeter FreeseDavid U GorkinYin ShenYupeng HeMark MackiewiczFlorencia Pauli-BehnBrian A WilliamsAli MortazaviCheryl A KellerXiao-Ou ZhangShaimae I ElhajjajyJack HueyDiane E DickelValentina SnetkovaXintao WeiXiaofeng WangJuan Carlos Rivera-MuliaJoel RozowskyJing ZhangSurya B ChhetriJialing ZhangAlec VictorsenKevin P WhiteAxel ViselGene W YeoChristopher B BurgeEric LécuyerDavid M GilbertJob DekkerJohn L RinnEric M MendenhallJoseph R EckerManolis KellisRobert J KleinWilliam S NobleAnshul KundajeRoderic GuigóPeggy J FarnhamJ Michael CherryRichard M MyersBing RenBrenton R GraveleyMark B GersteinLen A PennacchioMichael Paul SnyderBradley E BernsteinBarbara WoldRoss Cameron HardisonThomas R GingerasJohn A StamatoyannopoulosNishigandha PhalkePublished in: Nature (2020)
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 ENCODE1 and Roadmap Epigenomics2 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.
Keyphrases
- endothelial cells
- transcription factor
- phase ii
- phase iii
- clinical trial
- dna methylation
- electronic health record
- induced pluripotent stem cells
- gene expression
- big data
- pluripotent stem cells
- healthcare
- genome wide
- dna damage
- mental health
- high throughput
- single molecule
- cell free
- machine learning
- circulating tumor
- single cell
- wastewater treatment
- randomized controlled trial
- data analysis
- copy number
- artificial intelligence