A Comparative Encyclopedia of DNA Elements in the Mouse Genome

By Feng Yue, A. Breschi, J. Vierstra, Weisheng Wu, T. Ryba, R. Sandstrom, Zhihai Ma, Carrie A. Davis, Benjamin D. Pope, Yin Shen and 123 more. Nature, 2014

1,618 citations recorded by the source corpus.

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/277cdb73652a231fc914f6588be1c89921bccff0

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Citations in the corpus

Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM) (2017, positive): “We applied GAM to mouse embryonic stem cells (mESCs) where abundant data is available relating to chromatin contacts and chromatin occupancy at enhancers and promoters5,26,32– 35. mESCs were fixed in optimal conditions, and cryosectioned at a thickness of ~0.22 μm 30,31,36,37.”
Gene co-expression analysis for functional classification and gene–disease predictions (2017, methodology): “Binding sites can be further prioritized by investigating tissue-specific ChIP-seq peaks from ENCODE [15].”
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. (2018, methodology): “We defined a site as distal if it was located > 5 kb upstream and > 1 kb downstream of any transcription start site (TSS) reported in GENCODEmm9, releaseM1.”
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data (2015, background): “Chromatin features are obtained from the mouse ENCODE project [62].”