Developmental stage-specific A-to-I editing pattern in the postnatal pineal gland of pigs (Sus scrofa)

Rong Zhou; Wenye Yao; Chundi Xie; Leixia Zhang; Yangli Pei; Hua Li; Zheng Feng; Yalan Yang; Kui Li

doi:10.1186/s40104-020-00495-6

Developmental stage-specific A-to-I editing pattern in the postnatal pineal gland of pigs (Sus scrofa)

J Anim Sci Biotechnol. 2020 Sep 7:11:90. doi: 10.1186/s40104-020-00495-6. eCollection 2020.

Authors

Rong Zhou^{1

2}, Wenye Yao², Chundi Xie², Leixia Zhang¹, Yangli Pei¹, Hua Li¹, Zheng Feng¹, Yalan Yang¹, Kui Li^{1

2}

Affiliations

¹ Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231 Guangdong China.
² State Key Laboratory of Animal Nutrition; Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China.

Abstract

Background: RNA editing is a widespread post-transcriptional modification mechanism in mammalian genomes. Although many editing sites have been identified in domestic pigs (Sus scrofa), little is known about the characteristics and dynamic regulation of RNA editing in the pineal gland (PG), a small neuroendocrine gland that synthesizes and secretes melatonin, which is primarily responsible to modulate sleep patterns.

Results: This study analyzed the expression of adenosine-to-inosine (A-to-I) editing regulators and profiled the first dynamic A-to-I RNA editome during postnatal PG development. The results identified ADAR1 as the most abundantly expressed ADAR enzyme, which was down-regulated during postnatal PG development. Furthermore, 47,284 high-confidence RNA editing sites were identified, the majority of which (93.6%) were of the canonical A-to-I editing type, followed by C-to-T editing. Analysis of its characteristics showed that the A-to-I editing sites mostly localized in SINE retrotransposons PRE-1/Pre0_SS. Moreover, a strong deficiency and preference for guanine nucleotides at positions of one base upstream or downstream were found, respectively. The overall editing level at the puberty stage was higher than at both infancy and adulthood stages. Additionally, genome-wide RNA editing was found to exhibit a dynamic stage-specific fashion (postnatally). Genes that underwent developmental changes in RNA editing were associated with catabolic processes as well as protein localization and transport functions, implying that RNA editing might be responsible for the molecular machineries of the postnatal developing PG. Remarkably, RNA editing in 3'-UTRs might regulate gene expression by influencing miRNA binding during PG development.

Conclusions: This study profiles the first comprehensive developmental RNA editome in the pig PG, which contributes to the understanding of the importance of post-transcriptionally mediated regulation during mammalian postnatal PG development. Moreover, this study widely extends RNA editome resources in mammals.

Keywords: A-to-I; Pig; Pineal gland; Postnatal development; RNA editing.