CNEReg Interprets Ruminant-Specific Conserved Non-Coding Elements by Developmental Gene Regulatory Network

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	CNEReg Interprets Ruminant-Specific Conserved Non-Coding Elements by Developmental Gene Regulatory Network
	Pan, XY; Ma, ZX; Sun, XQ; Li, H; Zhang, TT; Zhao, C; Wang, NN; Heller, R; Wong, WH; Wang, W; Jiang, Y; Wang, Y
	2023
发表期刊	GENOMICS PROTEOMICS & BIOINFORMATICS
ISSN	1672-0229
卷号	21 期号:3 页码:632-648
摘要	The genetic information coded in DNA leads to trait innovation via a gene regulatory network (GRN) in development. Here, we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network (CNEReg) to investigate the ruminant multi-chambered stomach innovation. We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep, and revealed 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs). To interpret the function of these active-RSCNEs, we defined toolkit transcription factors (TTFs) and modeled their regulation on rumen-specific genes via batteries of active-RSCNEs during development. Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules. Notably, 6 TTFs (OTX1, SOX21, HOXC8, SOX2, TP63, and PPARG), as well as 16 active-RSCNEs, functionally distinguished the rumen from the esophagus. Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14369
专题	昆明动物研究所
推荐引用方式 GB/T 7714	Pan, XY,Ma, ZX,Sun, XQ,et al. CNEReg Interprets Ruminant-Specific Conserved Non-Coding Elements by Developmental Gene Regulatory Network[J]. GENOMICS PROTEOMICS & BIOINFORMATICS,2023,21(3):632-648.
APA	Pan, XY.,Ma, ZX.,Sun, XQ.,Li, H.,Zhang, TT.,...&Wang, Y.(2023).CNEReg Interprets Ruminant-Specific Conserved Non-Coding Elements by Developmental Gene Regulatory Network.GENOMICS PROTEOMICS & BIOINFORMATICS,21(3),632-648.
MLA	Pan, XY,et al."CNEReg Interprets Ruminant-Specific Conserved Non-Coding Elements by Developmental Gene Regulatory Network".GENOMICS PROTEOMICS & BIOINFORMATICS 21.3(2023):632-648.

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20240531105.pdf（3543KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文