In silico analysis of promoter region and regulatory elements of sheep keratin-associated protein genes using bioinformatics tools

Q4 Biochemistry, Genetics and Molecular Biology

Animal Gene Pub Date : 2022-06-01 DOI:10.1016/j.angen.2022.200126

Gobena Wagari , Donghee Cho , Bosenu Abera

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引用次数: 1

Abstract

Keratin-associated proteins (KAPs) are constituents of wool and play an important role in determining the characteristics of wool. Variation in many ovine KAP genes are associated with wool traits and are useful as markers for improving wool traits in sheep. The identification of promoters in a gene is an important part of the recognition of a gene's complete structure. In silico study was done with aim of analyzing the promoter regions and transcription factors with the aid of transcription start site (TSSs), regulatory elements and motifs of sheep KAP genes. Most of predicted TSSs (64%) found below -500 bp away from the start codon of the gene being expressed, and the rest were found from −515 to −1502 upstream of start codon. MKAP3 was identified as the most common motif for sheep KAP genes, which serves as binding sites for Zinc finger transcription factor to regulate the expression of the genes. Poor CpG Islands observed might suggest that their gene expression regulation pattern is tissue specific. In general, in silico analysis of KAP genes of sheep could be helpful to add knowledge about gene regulatory elements in the promoter regions. Furthermore, this finding will help for wool traits improvement of sheep.

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利用生物信息学工具分析绵羊角蛋白相关蛋白基因的启动子区域和调控元件

角蛋白相关蛋白(KAPs)是羊毛的组成成分，在决定羊毛的特性方面起着重要作用。许多绵羊KAP基因的变异与羊毛性状有关，是改善绵羊羊毛性状的有用标记。基因启动子的识别是基因完整结构识别的重要组成部分。利用转录起始位点(tss)、调控元件和基序分析了绵羊KAP基因的启动子区和转录因子。大部分预测的tss(64%)出现在距离表达基因起始密码子-500 bp以下，其余的tss出现在起始密码子上游- 515 ~ - 1502处。MKAP3是绵羊KAP基因中最常见的基序，作为锌指转录因子的结合位点，调控基因的表达。观察到的低CpG岛可能提示其基因表达调控模式具有组织特异性。总的来说，对绵羊KAP基因的硅分析有助于增加对启动子区域基因调控元件的认识。此外，这一发现将有助于改善绵羊的羊毛性状。

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Animal Gene Agricultural and Biological Sciences-Insect Science

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期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.