TY - JOUR
T1 - Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research
AU - Kern, Colin
AU - Wang, Ying
AU - Xu, Xiaoqin
AU - Pan, Zhangyuan
AU - Halstead, Michelle
AU - Chanthavixay, Ganrea
AU - Saelao, Perot
AU - Waters, Susan
AU - Xiang, Ruidong
AU - Chamberlain, Amanda
AU - Korf, Ian
AU - Delany, Mary E.
AU - Cheng, Hans H.
AU - Medrano, Juan F.
AU - Van Eenennaam, Alison L.
AU - Tuggle, Chris K.
AU - Ernst, Catherine
AU - Flicek, Paul
AU - Quon, Gerald
AU - Ross, Pablo
AU - Zhou, Huaijun
N1 - Funding Information:
This study was funded by Agriculture and Food Research Initiative Competitive Grant nos. 2015-67015-22940 and 2018-67012-28026 from the USDA National Institute of Food and Agriculture. Additional support was provided by Pork Checkoff, Aviagen, and Multistate Research Project NRSP8 Cattle, Poultry and Swine Coordination and NC1170 (H.Z.), and the California Agricultural Experimental Station (H.Z.).
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.
AB - Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.
UR - http://www.scopus.com/inward/record.url?scp=85103214970&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85103214970&partnerID=8YFLogxK
U2 - 10.1038/s41467-021-22100-8
DO - 10.1038/s41467-021-22100-8
M3 - Article
C2 - 33758196
AN - SCOPUS:85103214970
VL - 12
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
M1 - 1821
ER -