Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs
文献类型： 外文期刊
作者： Wang C.;Chen C.;Lei B.;Qin S.;Zhang Y.;Li K.;Zhang S.;Liu Y.
作者机构：
关键词： （1-1-1）
期刊名称： Genetics Selection Evolution
ISSN： 0999-193X
年卷期： 2024 年 56 卷 1 期
页码：
收录情况： SCIE（2024版）
摘要： Background: Enhancer RNAs (eRNAs) play a crucial role in transcriptional regulation. While significant progress has been made in understanding epigenetic regulation mediated by eRNAs, research on the construction of eRNA-mediated gene regulatory networks (eGRN) and the identification of critical network components that influence complex traits is lacking. Results: Here, employing the pig as a model, we conducted a comprehensive study using H3K27ac histone ChIP-seq and RNA-seq data to construct eRNA expression profiles from multiple tissues of two distinct pig breeds, namely Enshi Black (ES) and Duroc. In addition to revealing the regulatory landscape of eRNAs at the tissue level, we developed an innovative network construction and refinement method by integrating RNA-seq, ChIP-seq, genome-wide association study (GWAS) signals and enhancer-modulating effects of single nucleotide polymorphisms (SNPs) measured by self-transcribing active regulatory region sequencing (STARR-seq) experiments. Using this approach, we unraveled eGRN that significantly influence the growth and development of muscle and fat tissues, and identified several novel genes that affect adipocyte differentiation in a cell line model. Conclusions: Our work not only provides novel insights into the genetic basis of economic pig traits, but also offers a generalizable approach to elucidate the eRNA-mediated transcriptional regulation underlying a wide spectrum of complex traits for diverse organisms. © The Author(s) 2024.
分类号：
- 相关文献
作者其他论文 更多>>
-
Discrimination between the Triglyceride Form and the Ethyl Ester Form of Fish Oil Using Chromatography–Mass Spectrometry
作者：Liu M.;Liu Y.;Wang X.
关键词：chromatography;discrimination;ethyl ester;fish oil;mass spectrometry (MS);triglyceride
-
Application of CRISPR/Cas9 for Rapid Genome Editing of Pseudorabies Virus and Bovine Herpesvirus-1
作者：Yu W.;Liu J.;Liu Y.;Forlenza M.;Chen H.
关键词：CRISPR/Cas9;gene editing;herpesvirus;recombination
-
AwSclB regulates a network for Aspergillus westerdijkiae asexual sporulation and secondary metabolism independent of the fungal light control
作者：Wang G.;Liu Y.;Hu Y.;Pan J.;Wei Z.;Tai B.;Yang B.;Li E.;Xing F.
关键词：Asexual sporulation;Aspergillus westerdijkiae;Light control;Ochratoxin A;Secondary metabolism
-
Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution
作者：Fang Y.;Xiao X.;Lin J.;Lin Q.;Wang J.;Liu K.;Li Z.;Xing J.;Liu Z.;Wang B.;Qi Y.;Long X.;Zeng X.;Hu Y.;Qi J.;Qin Y.;Yang J.;Zhang Y.;Zhang S.;Ye D.;Zhang J.;Liu J.;Tang C.
关键词：
-
GhLCYε-3 characterized as a lycopene cyclase gene responding to drought stress in cotton
作者：Ni K.;Lu X.;Li S.;Li F.;Zhang Y.;Cui R.;Fan Y.;Huang H.;Chen X.;Wang J.;Wang S.;Guo L.;Zhao L.;He Y.;Ye W.
关键词：Carotenoids;Cotton;Functional verification;Lutein;Lycopene cyclase;Reactive oxygen species (ROS)
-
Effect of pre-slaughter fasting time on carcass yield, blood parameters and meat quality in broilers
作者：Wu X.;Zhou Y.;Lu Z.;Zhang Y.;Zhang T.
关键词：Broilers;Carcass Yield;Fasting;Glucose Metabolism;Meat Quality
-
Synergistic dual-mechanism raised structure and vertically aligned porous 3D hydrogel fabric for ultra-high salt-resistant water desalination
作者：Zhang Z.;Wang X.;Li G.;Zhao K.;Liu G.;Wang Y.;Li Z.;Huang J.;Xu Z.;Lai Y.;Qian X.;Zhang S.
关键词：PVA hydrogel;Raised fabric;Seawater desalination;Solar evaporator