在天祝白牦牛毛囊周期中进行全基因组 RNA 编辑事件的检测。

Genome-wide detection of RNA editing events during the hair follicles cycle of Tianzhu white yak.

机构信息

Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, 730050, Lanzhou, P.R. China.

Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, 730050, Lanzhou, P.R. China.

出版信息

BMC Genomics. 2022 Oct 31;23(1):737. doi: 10.1186/s12864-022-08951-5.

DOI:10.1186/s12864-022-08951-5

PMID:36316632

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9624038/

Abstract

BACKGROUND

The hair coat is available for the yak to live in the harsh environment of the plateau. Besides, improving the hair production of yak is necessary for its textile industry development. Hair grows from hair follicles (HFs). The HFs undergo periodic growth after birth and are regulated by the complex gene regulatory network. However, the molecular mechanism of HFs regeneration in the Tianzhu white yak remains unclear. RNA editing is a post-transcriptional mechanism that regulates gene expression and produces new transcripts. Hence, we investigated the influence of the A-to-I RNA editing events on the HFs cycle of the Tianzhu white yak.

RESULTS

We finally identified 54,707 adenosine-to-inosine (A-to-I) RNA editing sites (RESs) from RNA sequencing data of the HFs cycle in the Tianzhu white yak. Annotation results showed RESs caused missense amino acid changes in 7 known genes. And 202 A-to-I editing sites altered 23 target genes of 140 microRNAs. A total of 1,722 differential RESs were identified during the HFs cycle of Tianzhu white yak. GO and KEGG enrichment analysis revealed several signaling pathways and GO terms involved skin development, hair growth, and HFs cycle. Such as genes with differential RNA editing levels were significantly enriched in the peroxisome, metabolic pathways, Notch signaling pathway, and PPAR signaling pathway. Besides, the editing sites in HFs development-related genes FAS, APCDD1, WWOX, MPZL3, RUNX1, KANK2, DCN, DSC2, LEPR, HEPHL1, and PTK2B were suggested as the potential RESs involving HFs development.

CONCLUSION

This study investigated the global A-to-I RNA editing events during the HFs cycle of yak skin tissue and expanded the knowledge of A-to-I RNA editing on the HFs cycle. Furthermore, this study revealed that RNA editing-influenced genes may regulate the HFs cycle by participating in the HFs development-related pathways. The findings might provide new insight into the regulation of RNA editing in hair growth.

摘要

背景

毛发是牦牛适应高原恶劣环境的一种表现。此外，提高牦牛的产毛量对其纺织业的发展至关重要。毛发由毛囊（HFs）生长而来。HFs 在出生后经历周期性生长，受复杂的基因调控网络调控。然而，天祝白牦牛 HFs 再生的分子机制尚不清楚。RNA 编辑是一种转录后调控基因表达并产生新转录本的机制。因此，我们研究了 A-to-I RNA 编辑事件对天祝白牦牛 HFs 周期的影响。

结果

我们从天祝白牦牛 HFs 周期的 RNA 测序数据中最终鉴定出 54707 个腺苷到肌苷（A-to-I）RNA 编辑位点（RES）。注释结果表明，RES 导致 7 个已知基因的错义氨基酸变化。202 个 A-to-I 编辑位点改变了 140 个 microRNAs 的 23 个靶基因。总共鉴定出 1722 个差异 RES 在天祝白牦牛 HFs 周期中。GO 和 KEGG 富集分析显示，几个信号通路和 GO 术语参与了皮肤发育、毛发生长和 HFs 周期。例如，具有差异 RNA 编辑水平的基因在过氧化物酶体、代谢途径、Notch 信号通路和 PPAR 信号通路中显著富集。此外，在 HFs 发育相关基因 FAS、APCDD1、WWOX、MPZL3、RUNX1、KANK2、DCN、DSC2、LEPR、HEPHL1 和 PTK2B 中的编辑位点被认为是与 HFs 发育相关的潜在 RES。

结论

本研究调查了牦牛皮肤组织 HFs 周期中全局的 A-to-I RNA 编辑事件，扩展了 A-to-I RNA 编辑对 HFs 周期的认识。此外，本研究表明，受 RNA 编辑影响的基因可能通过参与 HFs 发育相关途径来调节 HFs 周期。这些发现可能为毛发生长过程中 RNA 编辑的调控提供新的见解。