Systematic analyses reveal RNA editing events involved in skeletal muscle development of goat (Capra hircus)

Liu, Yang; Li, Li; Kyei, Bismark; Guo, Jiazhong; Zhan, Siyuan; Zhao, Wei; Song, Yumo; Zhong, Tao; Wang, Linjie; Xu, Lingyang; Zhang, Hongping

doi:10.1007/s10142-020-00741-0

Cited by 5 publications

(9 citation statements)

References 64 publications

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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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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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“…Identification of new editing sites in repetitive elements does not deepen our understanding of the function of RNA editing because all these editing sites have the same task. This phenomenon, where the repetitive editing sites are highly abundant and act as an immune-protector, is conserved in mammals [11,14,[22][23][24][25]. At the class level, the other animal classes with systematic RNA editing studies in multiple species are the insect class (Insecta) and the cephalopods (Cephalopoda, including octopus, squid, and cuttlefish).…”

Section: A-to-i Rna Editing In Different Animal Clades and The Functi...mentioning

confidence: 99%

Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes

Xu,

Liu,

Zhao

et al. 2023

IJMS

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Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.

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“…RNA editing is affected by many factors, including temperature, tissue context, genotype, feeding conditions, and age [ 14 , 15 ], while RNA editing controls phenotype via editing the sequence of RNA molecules [ 16 , 17 ]. For example, most RNA editing sites (RESs), mainly mediated by the ADAR family, were tissue-specific and enriched in tissue-specific biological functions.…”

Section: Introductionmentioning

confidence: 99%

“…The correlation between editing levels of RESs and their gene expression has been identified [ 18 , 19 ]. Our previous study found a significant difference in RESs counts and editing levels at goat fetal and postnatal periods, whereas SMAD3 , SIAH1 , and CDK13 had embedded functional editing sites and were involved in muscle development [ 17 ]. Furthermore, several studies have identified RESs in farm animals such as pigs [ 19 , 20 , 21 , 22 ], chickens [ 14 ], sheep [ 11 ], and goats [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

“…Our previous study found a significant difference in RESs counts and editing levels at goat fetal and postnatal periods, whereas SMAD3 , SIAH1 , and CDK13 had embedded functional editing sites and were involved in muscle development [ 17 ]. Furthermore, several studies have identified RESs in farm animals such as pigs [ 19 , 20 , 21 , 22 ], chickens [ 14 ], sheep [ 11 ], and goats [ 17 ]. For instance, the brain, subcutaneous fat, heart, liver, muscle, lung, and ovary of pigs had 74,863 RESs [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

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The Profiles and Functions of RNA Editing Sites Associated with High-Altitude Adaptation in Goats

Xing

et al. 2023

IJMS

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High-altitude environments dramatically influenced the genetic evolution of vertebrates. However, little is known about the role of RNA editing on high-altitude adaptation in non-model species. Here, we profiled the RNA editing sites (RESs) of heart, lung, kidney, and longissimus dorsi muscle from Tibetan cashmere goats (TBG, 4500 m) and Inner Mongolia cashmere goats (IMG, 1200 m) to reveal RNA editing-related functions of high-altitude adaptation in goats. We identified 84,132 high-quality RESs that were unevenly distributed across the autosomes in TBG and IMG, and more than half of the 10,842 non-redundant editing sites were clustered. The majority (62.61%) were adenosine-to-inosine (A-to-I) sites, followed by cytidine-to-uridine (C-to-U) sites (19.26%), and 32.5% of them had a significant correlation with the expression of catalytic genes. Moreover, A-to-I and C-to-U RNA editing sites had different flanking sequences, amino acid mutations, and alternative splicing activity. TBG had higher editing levels of A-to-I and C-to-U than IMG in the kidney, whereas a lower level was found in the longissimus dorsi muscle. Furthermore, we identified 29 IMG and 41 TBG population-specific editing sites (pSESs) and 53 population-differential editing sites (pDESs) that were functionally involved in altering RNA splicing or recoding protein products. It is worth noting that 73.3% population-differential, 73.2% TBG-specific, and 80% IMG-specific A-to-I sites were nonsynonymous sites. Moreover, the pSESs and pDESs editing-related genes play critical functions in energy metabolisms such as ATP binding molecular function, translation, and adaptive immune response, which may be linked to goat high-altitude adaptation. Our results provide valuable information for understanding the adaptive evolution of goats and studying plateau-related diseases.

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Systematic analyses reveal RNA editing events involved in skeletal muscle development of goat (Capra hircus)

Cited by 5 publications

References 64 publications

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

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

Identification and Interpretation of A-to-I RNA Editing Events in Insect Transcriptomes

The Profiles and Functions of RNA Editing Sites Associated with High-Altitude Adaptation in Goats

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