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靶向测序方法的应用揭示了猪基因组中 microRNA 基因的单核苷酸多态性 (SNP) 谱。

Application of the targeted sequencing approach reveals the single nucleotide polymorphism (SNP) repertoire in microRNA genes in the pig genome.

机构信息

Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, Balice, 32-083, Kraków, Poland.

Center for Experimental and Innovative Medicine, The University of Agriculture in Kraków, Rędzina 1c, 30-248, Kraków, Poland.

出版信息

Sci Rep. 2021 May 10;11(1):9848. doi: 10.1038/s41598-021-89363-5.

DOI:10.1038/s41598-021-89363-5
PMID:33972633
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8110958/
Abstract

MicroRNAs (miRNAs) are recognized as gene expression regulators, indirectly orchestrating a plethora of biological processes. Single nucleotide polymorphism (SNP), one of the most common genetic variations in the genome, is established to affect miRNA functioning and influence complex traits and diseases. SNPs in miRNAs have also been associated with important production traits in livestock. Thus, the aim of our study was to reveal the SNP variability of miRNA genes in the genome of the pig, which is a significant farm animal and large-mammal human model. To this end, we applied the targeted sequencing approach, enabling deep sequencing of specified genomic regions. As a result, 73 SNPs localized in 50 distinct pre-miRNAs were identified. In silico analysis revealed that many of the identified SNPs influenced the structure and energy of the hairpin precursors. Moreover, SNPs localized in the seed regions were shown to alter targeted genes and, as a result, enrich different biological pathways. The obtained results corroborate a significant impact of SNPs on the miRNA processing and broaden the state of knowledge in the field of animal genomics. We also report the targeted sequencing approach to be a promising alternative for the whole genome sequencing in miRNA genes focused studies.

摘要

微小 RNA（miRNA）被认为是基因表达的调控因子，间接调控着大量的生物学过程。单核苷酸多态性（SNP）是基因组中最常见的遗传变异之一，被认为会影响 miRNA 的功能，并影响复杂的特征和疾病。miRNA 中的 SNPs 也与家畜的重要生产特征有关。因此，我们的研究旨在揭示猪基因组中 miRNA 基因的 SNP 变异性，猪是一种重要的农场动物和大型哺乳动物模型。为此，我们应用了靶向测序方法，能够对特定的基因组区域进行深度测序。结果，在 50 个不同的前体 miRNA 中发现了 73 个 SNP。计算机分析表明，许多鉴定出的 SNP 影响了发夹前体的结构和能量。此外，位于种子区域的 SNPs 被证明可以改变靶基因，并因此丰富不同的生物学途径。所得结果证实了 SNPs 对 miRNA 加工的显著影响，并拓宽了动物基因组学领域的知识状态。我们还报告了靶向测序方法是 miRNA 基因聚焦研究中全基因组测序的一种有前途的替代方法。

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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a1b/8110958/df3cb23046dd/41598_2021_89363_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a1b/8110958/db7c864eb88c/41598_2021_89363_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a1b/8110958/3043574c2414/41598_2021_89363_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a1b/8110958/46d199a7a1d7/41598_2021_89363_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a1b/8110958/1690e9da0c8f/41598_2021_89363_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a1b/8110958/826c832a2740/41598_2021_89363_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a1b/8110958/bab7b8e0340b/41598_2021_89363_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9a1b/8110958/df3cb23046dd/41598_2021_89363_Fig9_HTML.jpg

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