Genome-wide profiling of RNA editing sites in sheep

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

Research output: Contribution to journalArticle

Abstract

Background: The widely observed RNA-DNA differences (RDDs) have been found to be due to nucleotide alteration by RNA editing. Canonical RNA editing (i.e., A-to-I and C-to-U editing) mediated by the adenosine deaminases acting on RNA (ADAR) family and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family during the transcriptional process is considered common and essential for the development of an individual. To date, an increasing number of RNA editing sites have been reported in human, rodents, and some farm animals; however, genome-wide detection of RNA editing events in sheep has not been reported. The aim of this study was to identify RNA editing events in sheep by comparing the RNA-seq and DNA-seq data from three biological replicates of the kidney and spleen tissues. Results: A total of 607 and 994 common edited sites within the three biological replicates were identified in the ovine kidney and spleen, respectively. Many of the RDDs were specific to an individual. The RNA editing-related genes identified in the present study might be evolved for specific biological functions in sheep, such as structural constituent of the cytoskeleton and microtubule-based processes. Furthermore, the edited sites found in the ovine BLCAP and NEIL1 genes are in line with those in previous reports on the porcine and human homologs, suggesting the existence of evolutionarily conserved RNA editing sites and they may play an important role in the structure and function of genes. Conclusions: Our study is the first to investigate RNA editing events in sheep. We screened out 607 and 994 RNA editing sites in three biological replicates of the ovine kidney and spleen and annotated 164 and 247 genes in the kidney and spleen, respectively. The gene function and conservation analysis of these RNA editing-related genes suggest that RNA editing is associated with important gene function in sheep. The putative functionally important RNA editing sites reported in the present study will help future studies on the relationship between these edited sites and the genetic traits in sheep.

Original languageEnglish (US)
Article number31
JournalJournal of Animal Science and Biotechnology
Volume10
Issue number1
DOIs
StatePublished - Mar 12 2019

Fingerprint

RNA Editing
RNA editing
Sheep
Genes
Genome
RNA
sheep
genome
spleen
Spleen
kidneys
genes
Kidney
DNA
adenosine deaminase
apolipoprotein B
personal development
Adenosine Deaminase
genetic traits
Domestic Animals

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Food Science
  • Biochemistry
  • Animal Science and Zoology

Cite this

Zhang, Y., Han, D., Dong, X., Wang, J., Chen, J., Yao, Y., ... Deng, X. (2019). Genome-wide profiling of RNA editing sites in sheep. Journal of Animal Science and Biotechnology, 10(1), [31]. https://doi.org/10.1186/s40104-019-0331-z
Zhang, Yuanyuan ; Han, Deping ; Dong, Xianggui ; Wang, Jiankui ; Chen, Jianfei ; Yao, Yanzhu ; Darwish, Hesham Y.A. ; Liu, Wansheng ; Deng, Xuemei. / Genome-wide profiling of RNA editing sites in sheep. In: Journal of Animal Science and Biotechnology. 2019 ; Vol. 10, No. 1.
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abstract = "Background: The widely observed RNA-DNA differences (RDDs) have been found to be due to nucleotide alteration by RNA editing. Canonical RNA editing (i.e., A-to-I and C-to-U editing) mediated by the adenosine deaminases acting on RNA (ADAR) family and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family during the transcriptional process is considered common and essential for the development of an individual. To date, an increasing number of RNA editing sites have been reported in human, rodents, and some farm animals; however, genome-wide detection of RNA editing events in sheep has not been reported. The aim of this study was to identify RNA editing events in sheep by comparing the RNA-seq and DNA-seq data from three biological replicates of the kidney and spleen tissues. Results: A total of 607 and 994 common edited sites within the three biological replicates were identified in the ovine kidney and spleen, respectively. Many of the RDDs were specific to an individual. The RNA editing-related genes identified in the present study might be evolved for specific biological functions in sheep, such as structural constituent of the cytoskeleton and microtubule-based processes. Furthermore, the edited sites found in the ovine BLCAP and NEIL1 genes are in line with those in previous reports on the porcine and human homologs, suggesting the existence of evolutionarily conserved RNA editing sites and they may play an important role in the structure and function of genes. Conclusions: Our study is the first to investigate RNA editing events in sheep. We screened out 607 and 994 RNA editing sites in three biological replicates of the ovine kidney and spleen and annotated 164 and 247 genes in the kidney and spleen, respectively. The gene function and conservation analysis of these RNA editing-related genes suggest that RNA editing is associated with important gene function in sheep. The putative functionally important RNA editing sites reported in the present study will help future studies on the relationship between these edited sites and the genetic traits in sheep.",
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Zhang, Y, Han, D, Dong, X, Wang, J, Chen, J, Yao, Y, Darwish, HYA, Liu, W & Deng, X 2019, 'Genome-wide profiling of RNA editing sites in sheep', Journal of Animal Science and Biotechnology, vol. 10, no. 1, 31. https://doi.org/10.1186/s40104-019-0331-z

Genome-wide profiling of RNA editing sites in sheep. / Zhang, Yuanyuan; Han, Deping; Dong, Xianggui; Wang, Jiankui; Chen, Jianfei; Yao, Yanzhu; Darwish, Hesham Y.A.; Liu, Wansheng; Deng, Xuemei.

In: Journal of Animal Science and Biotechnology, Vol. 10, No. 1, 31, 12.03.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome-wide profiling of RNA editing sites in sheep

AU - Zhang, Yuanyuan

AU - Han, Deping

AU - Dong, Xianggui

AU - Wang, Jiankui

AU - Chen, Jianfei

AU - Yao, Yanzhu

AU - Darwish, Hesham Y.A.

AU - Liu, Wansheng

AU - Deng, Xuemei

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N2 - Background: The widely observed RNA-DNA differences (RDDs) have been found to be due to nucleotide alteration by RNA editing. Canonical RNA editing (i.e., A-to-I and C-to-U editing) mediated by the adenosine deaminases acting on RNA (ADAR) family and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family during the transcriptional process is considered common and essential for the development of an individual. To date, an increasing number of RNA editing sites have been reported in human, rodents, and some farm animals; however, genome-wide detection of RNA editing events in sheep has not been reported. The aim of this study was to identify RNA editing events in sheep by comparing the RNA-seq and DNA-seq data from three biological replicates of the kidney and spleen tissues. Results: A total of 607 and 994 common edited sites within the three biological replicates were identified in the ovine kidney and spleen, respectively. Many of the RDDs were specific to an individual. The RNA editing-related genes identified in the present study might be evolved for specific biological functions in sheep, such as structural constituent of the cytoskeleton and microtubule-based processes. Furthermore, the edited sites found in the ovine BLCAP and NEIL1 genes are in line with those in previous reports on the porcine and human homologs, suggesting the existence of evolutionarily conserved RNA editing sites and they may play an important role in the structure and function of genes. Conclusions: Our study is the first to investigate RNA editing events in sheep. We screened out 607 and 994 RNA editing sites in three biological replicates of the ovine kidney and spleen and annotated 164 and 247 genes in the kidney and spleen, respectively. The gene function and conservation analysis of these RNA editing-related genes suggest that RNA editing is associated with important gene function in sheep. The putative functionally important RNA editing sites reported in the present study will help future studies on the relationship between these edited sites and the genetic traits in sheep.

AB - Background: The widely observed RNA-DNA differences (RDDs) have been found to be due to nucleotide alteration by RNA editing. Canonical RNA editing (i.e., A-to-I and C-to-U editing) mediated by the adenosine deaminases acting on RNA (ADAR) family and apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) family during the transcriptional process is considered common and essential for the development of an individual. To date, an increasing number of RNA editing sites have been reported in human, rodents, and some farm animals; however, genome-wide detection of RNA editing events in sheep has not been reported. The aim of this study was to identify RNA editing events in sheep by comparing the RNA-seq and DNA-seq data from three biological replicates of the kidney and spleen tissues. Results: A total of 607 and 994 common edited sites within the three biological replicates were identified in the ovine kidney and spleen, respectively. Many of the RDDs were specific to an individual. The RNA editing-related genes identified in the present study might be evolved for specific biological functions in sheep, such as structural constituent of the cytoskeleton and microtubule-based processes. Furthermore, the edited sites found in the ovine BLCAP and NEIL1 genes are in line with those in previous reports on the porcine and human homologs, suggesting the existence of evolutionarily conserved RNA editing sites and they may play an important role in the structure and function of genes. Conclusions: Our study is the first to investigate RNA editing events in sheep. We screened out 607 and 994 RNA editing sites in three biological replicates of the ovine kidney and spleen and annotated 164 and 247 genes in the kidney and spleen, respectively. The gene function and conservation analysis of these RNA editing-related genes suggest that RNA editing is associated with important gene function in sheep. The putative functionally important RNA editing sites reported in the present study will help future studies on the relationship between these edited sites and the genetic traits in sheep.

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