Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family.

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Accounts of Chemical Research Pub Date : 2021-08-26 eCollection Date: 2021-01-01 DOI:10.1177/11769343211041382

Chaoxin Zhang, Tao Wang, Tongyan Cui, Shengwei Liu, Bing Zhang, Xue Li, Jian Tang, Peng Wang, Yuanyuan Guo, Zhipeng Wang

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Abstract

The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ, and C/EBPζ. Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

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猪C/EBP基因家族的全基因组系统发育分析、表达模式和转录调控网络。

CCAAT/增强子结合蛋白（C/EBP）转录因子（TF）调节许多重要的生物学过程，如能量代谢、炎症、细胞增殖等。全基因组基因鉴定显示，猪和19个真核生物基因组中共存在99个C/EBP基因。系统发育分析表明，所有C/EBP TF可分为6个亚群，分别命名为C/EBPα、C/EBPβ、C/EBP-δ、C/EBP-ε、C/EBP/γ和C/EBPζ。基因表达分析表明，C/EBPα、C/EBPβ、C/EBP-δ、C/EBP-γ和C/EBP-ζ基因在各种猪组织中普遍表达，表达模式不一致。此外，构建了猪C/EBP调控网络，包括C/EBP基因、转录因子和miRNA。在猪C/EBP调控网络中总共检测到27个前馈环（FFL）基序。基于RNA-seq数据，分析了27个成年猪组织中与FFL亚网络相关的基因表达模式。某些FFL基序可能是组织特异性的。功能富集分析表明C/EBP及其靶基因参与了许多重要的生物学途径。这些结果提供了有价值的信息，阐明了C/EBP家族的进化关系，并有助于理解C/EBP基因的生物学功能。

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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.

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