Genome-wide profiling of RNA editing sites in sheep

Zhang, Yuanyuan; Han, Deguo; Dong, Xianggui; Wang, Jiankui; Chen, Jianfei; Yao, Yanzhu; Darwish, Hesham Y. A.; Liu, Wansheng; Deng, Xuemei

doi:10.1186/s40104-019-0331-z

Cited by 13 publications

(15 citation statements)

References 39 publications

(50 reference statements)

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“…Recently, many bioinformatic tools and next-generation sequencing (NGS) techniques have been developed for detecting RNA editing events, which has enabled us to discover genome-wide RNA editing events and their molecular function. Presently, many studies for identification of RNA editing events have been performed in human ( 12 ), cattle ( 13 ), pigs ( 14 ), sheep ( 15 ), and chicken ( 16 ). Many studies have shown that dysregulation of RNA editing is associated with various human diseases, such as the presence of tumors ( 17 ), epilepsy ( 18 ), Alzheimer's disease ( 19 ), and sporadic amyotrophic lateral sclerosis (ALS) ( 20 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of RNA Editing Sites Affecting Muscle Development in Yak

Chen²,

Ma³

et al. 2022

Front. Vet. Sci.

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Skeletal muscle growth and development is a complicated process that is regulated at multiple steps and by numerous myogenesis genes. RNA editing represents one of the events at the post-transcriptional level, which contributes to the diversity of transcriptome and proteome by altering the nucleotides of RNAs. However, RNA editing events in the skeletal muscle of yaks are still not well defined. This study conducted whole-genome RNA-editing identification in skeletal muscle of yaks at embryonic stage (ES) and adult stage (AS). We found a total of 11,168 unique RNA editing sites, most of which were detected in the intergenic region. After annotation, we totally identified 2,718 editing sites within coding regions, among which 858 were missense changes. Moreover, totally 322 editing sites in the 3′ untranslated regions (UTR) were also predicted to alter the set of miRNA target sites, indicating that RNA editing may be involved in translational repression or mRNA degradation. We found 838 RNA editing sites (involving 244 common genes) that are edited differentially in ES as compared to AS. According to the KEGG enrichment analysis, these differentially edited genes were mainly involved in pathways highly related to skeletal muscle development and myogenesis, including MAPK, AMPK, Wnt, and PI3K-Akt signaling pathways. Altogether, our work presents the first characterization of RNA editing sites within yak skeletal muscles on a genome-wide scale and enhances our understanding of the mechanism of skeletal muscle development and myogenesis.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of RNA Editing Sites Affecting Muscle Development in Yak

Chen²,

Ma³

et al. 2022

Front. Vet. Sci.

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“…The advancement of computational methods has enabled elucidating many RNA editing sites in human and mouse [ 6 ]. More recently, a few studies have focused on the function of RNA editing in farm animals, such as cattle [ 7 , 8 ], pig [ 9 , 10 ], sheep [ 11 ], goat [ 12 ], and chicken [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods

Ayalew

Chen

et al. 2022

Animals

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The mammary gland is a complicated organ comprising several types of cells, and it undergoes extensive morphogenetic and metabolic changes during the female reproductive cycle. RNA editing is a posttranscriptional modification event occurring at the RNA nucleotide level, and it drives transcriptomic and proteomic diversities, with potential functional consequences. RNA editing in the mammary gland of yaks, however, remains poorly understood. Here, we used REDItools to identify RNA editing sites in mammary gland tissues in yaks during the lactation period (LP, n = 2) and dry period (DP, n = 3). Totally, 82,872 unique RNA editing sites were identified, most of which were detected in the noncoding regions with a low editing degree. In the coding regions (CDS), we detected 5235 editing sites, among which 1884 caused nonsynonymous amino acid changes. Of these RNA editing sites, 486 were found to generate novel possible miRNA target sites or interfere with the initial miRNA binding sites, indicating that RNA editing was related to gene regulation mediated by miRNA. A total of 14,159 RNA editing sites (involving 3238 common genes) showed a significant differential editing level in the LP when compared with that in the DP through Tukey’s Honest Significant Difference method (p < 0.05). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes that showed different RNA editing levels mainly participated in pathways highly related to mammary gland development, including MAPK, PI3K-Akt, FoxO, and GnRH signaling pathways. Collectively, this work demonstrated for the first time the dynamic RNA editome profiles in the mammary gland of yaks and shed more light on the mechanism that regulates lactation together with mammary gland development.

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“…These data revealed novel insights into molecular pathogenesis at the global RNA level. The NEIL1 editing is also found in chickens and sheep [ 53 , 54 ]. The target duplex secondary structure and A–C mismatch at the recoding site is conserved in other vertebrate NEIL1 mRNAs, including from mouse, horse and dog, suggesting NEIL1 pre-mRNA editing also occurs in these species.…”

Section: Resultsmentioning

confidence: 99%

Conservation of A-to-I RNA editing in bowhead whale and pig

Larsen

Heide‐Jørgensen

2021

PLoS ONE

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RNA editing is a post-transcriptional process in which nucleotide changes are introduced into an RNA sequence, many of which can contribute to proteomic sequence variation. The most common type of RNA editing, contributing to nearly 99% of all editing events in RNA, is A-to-I (adenosine-to-inosine) editing mediated by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. A-to-I editing at ‘recoding’ sites results in non-synonymous substitutions in protein-coding sequences. Here, we present studies of the conservation of A-to-I editing in selected mRNAs between pigs, bowhead whales, humans and two shark species. All examined mRNAs–NEIL1, COG3, GRIA2, FLNA, FLNB, IGFBP7, AZIN1, BLCAP, GLI1, SON, HTR2C and ADAR2 –showed conservation of A-to-I editing of recoding sites. In addition, novel editing sites were identified in NEIL1 and GLI1 in bowhead whales. The A-to-I editing site of human NEIL1 in position 242 was conserved in the bowhead and porcine homologues. A novel editing site was discovered in Tyr244. Differential editing was detected at the two adenosines in the NEIL1 242 codon in both pig and bowhead NEIL1 mRNAs in various tissues and organs. No conservation of editing of KCNB1 and EEF1A mRNAs was seen in bowhead whales. In silico analyses revealed conservation of five adenosines in ADAR2, some of which are subject to A-to-I editing in bowheads and pigs, and conservation of a regulatory sequence in GRIA2 mRNA that is responsible for recognition of the ADAR editing enzyme.

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Genome-wide profiling of RNA editing sites in sheep

Cited by 13 publications

References 39 publications

Genome-Wide Identification of RNA Editing Sites Affecting Muscle Development in Yak

Genome-Wide Identification of RNA Editing Sites Affecting Muscle Development in Yak

Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods

Conservation of A-to-I RNA editing in bowhead whale and pig

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