Expanded encyclopaedias of DNA elements in the human and mouse genomes

By Jill E. Moore, M. Purcaro, H. Pratt, C. Epstein, N. Shoresh, Jessika Adrian, Trupti Kawli, Carrie A. Davis, Alexander Dobin, R. Kaul and 53 more. Nature, 2020

1,946 citations recorded by the source corpus.

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. The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/133080c5d892e843f2ce3fb5c97906cf2b39f22b

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Citations in the corpus

Haplotype-resolved diverse human genomes and integrated analysis of structural variation (2021, neutral): “2B) ( 22 ).”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “Second, the tool will report whether the variant occurs within an enhancer region (as annotated by ENCODE, 52 FANTOM, 53 or VISTA 54 ), and then uses the enhancer-gene links from the PEREGRINE Project to link the variant to the gene whose expression it might impact.”
WILDS: A Benchmark of in-the-Wild Distribution Shifts (2020, neutral): “…platforms have enabled systematic mapping of biochemical activity of genomes across diverse cellular contexts, populations, and species (Consortium et al., 2012; Ho et al., 2014; Kundaje et al., 2015; Aviv et al., 2017; Consortium et al., 2019; Moore et al., 2020; Consortium et al., 2020).”
CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions (2024, methodology): “The ENCODE project and others initiated data portals with versioned and uniform data processing pipelines as well as explored imputation of molecular assays resulting from such data ( 3 ,82 ).”
HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution (2023, background): “Understanding and learning from DNA sequences has long been a goal of biologists and deep learning researchers, as its “language” encodes instructions essential for all living things [16].”