Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.
Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.
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DOI：
10.1038/s41467-021-22100-8
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发表时间：
2021-03-23
影响因子：
16.6
通讯作者：
Zhou H
中科院分区：
文献类型：
--
作者：
Kern C;Wang Y;Xu X;Pan Z;Halstead M;Chanthavixay G;Saelao P;Waters S;Xiang R;Chamberlain A;Korf I;Delany ME;Cheng HH;Medrano JF;Van Eenennaam AL;Tuggle CK;Ernst C;Flicek P;Quon G;Ross P;Zhou H
基因调控元件是表型变异的中心驱动力，因此对于理解复杂性状的遗传至关重要。动物基因组功能注释联盟的成立是为了合作注释动物基因组中的功能元件，从驯养动物开始。在这里，我们提出了一个广泛的收集数据集从八个不同的组织在三个重要的农业物种：鸡（原鸡），猪（猪），牛（牛）。这些数据集和人类和小鼠的DNA元件百科全书项目的比较分析表明，一组核心的调控元件在功能上是保守的，独立于物种之间的分歧，并且组织特异性转录因子在调控元件及其预测的靶基因上的占有率也是保守的。这些数据集为新兴的比较表观基因组学领域以及农业研究界提供了独特的机会，包括作为全球重要粮食资源的物种。为了解释非编码变异，基因组中调控元件的信息是必不可少的。在这里，作者注释了鸡，猪和牛的调控元件，并描述了物种之间这些元件的保守性。
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. In order to interpret non-coding variants, information about regulatory elements in the genome is essential. Here, the authors annotate regulatory elements in chicken, pig and cattle, and characterize conservation of these elements between species.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
30.8
作者：
He, Qiye;Bardet, Anais F.;Zeitlinger, Julia
通讯作者：
Zeitlinger, Julia
影响因子：
12.3
作者：
Andersson L;Archibald AL;Bottema CD;Brauning R;Burgess SC;Burt DW;Casas E;Cheng HH;Clarke L;Couldrey C;Dalrymple BP;Elsik CG;Foissac S;Giuffra E;Groenen MA;Hayes BJ;Huang LS;Khatib H;Kijas JW;Kim H;Lunney JK;McCarthy FM;McEwan JC;Moore S;Nanduri B;Notredame C;Palti Y;Plastow GS;Reecy JM;Rohrer GA;Sarropoulou E;Schmidt CJ;Silverstein J;Tellam RL;Tixier-Boichard M;Tosser-Klopp G;Tuggle CK;Vilkki J;White SN;Zhao S;Zhou H;FAANG Consortium
通讯作者：
FAANG Consortium