Volume 43 Issue 6
Nov.  2022
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Yun-Mei Wang, Ling-Qun Ye, Ming-Shan Wang, Jin-Jin Zhang, Saber Khederzadeh, David M Irwin, Xiao-Die Ren, Ya-Ping Zhang, Dong-Dong Wu. Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics. Zoological Research, 2022, 43(6): 1011-1022. doi: 10.24272/j.issn.2095-8137.2022.331
Citation: Yun-Mei Wang, Ling-Qun Ye, Ming-Shan Wang, Jin-Jin Zhang, Saber Khederzadeh, David M Irwin, Xiao-Die Ren, Ya-Ping Zhang, Dong-Dong Wu. Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics. Zoological Research, 2022, 43(6): 1011-1022. doi: 10.24272/j.issn.2095-8137.2022.331

Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics

doi: 10.24272/j.issn.2095-8137.2022.331
The RNA sequencing data were deposited in the NCBI database (BioProject accession: PRJNA562117) and GSA database (BioProject accession: PRJCA012006). The whole-genome data were from our previous study (Wang et al., 2020), deposited in the Chicken SNP Database (ChickenSD) at http://bigd.big.ac.cn/chickensd/. The gene expression matrices in FPKM are available at the Science Data Bank database (Data doi: 10.57760/sciencedb.j00139.00042). Well-annotated lists of chicken candidate RESs and non-ADAR-editing regulators are also provided in Supplementary Tables S1 and S3, respectively.
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
Y.P.Z., D.D.W., and Y.M.W. designed the study. M.S.W. collected samples. Y.M.W., L.Q.Y., and M.S.W. performed the data analyses. Y.M.W. wrote the manuscript. J.J.Z. performed the experiments related to ADAR knockdown and ADARB2 overexpression and wrote the corresponding methods. D.D.W., L.Q.Y., M.S.W., S.K., and D.M.I. revised the manuscript. X.D.R. deposited the sequencing data into NCBI. All authors read and approved the final version of the manuscript.
#Authors contributed equally to this work
Funds:  This work was supported by the National Natural Science Foundation of China (32100342, U1902204, 31771415, 31801054), Bureau of Science and Technology of Yunnan Province (2015FA026), Youth Innovation Promotion Association, and West Light Foundation of CAS (Y902401081)
More Information
  • The evolutionary and functional features of RNA editing are well studied in mammals, cephalopods, and insects, but not in birds. Here, we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine (A-to-I) RNA editing sites (RESs) in the chicken. In addition, we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication. We detected the lowest editing level in the liver of chickens, compared to muscles in humans, and found higher editing activity and specificity in the brain than in non-neural tissues, consistent with the brain’s functional complexity. To a certain extent, specific editing activity may account for the specific functions of tissues. Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution. Furthermore, the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication, including evolution of nervous and immune systems. Regulation of RNA editing in chickens by adenosine deaminase acting on RNA (ADAR) enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown. Collectively, we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken, thus contributing to our current understanding of the functions and evolution of RNA editing in animals.
  • The RNA sequencing data were deposited in the NCBI database (BioProject accession: PRJNA562117) and GSA database (BioProject accession: PRJCA012006). The whole-genome data were from our previous study (Wang et al., 2020), deposited in the Chicken SNP Database (ChickenSD) at http://bigd.big.ac.cn/chickensd/. The gene expression matrices in FPKM are available at the Science Data Bank database (Data doi: 10.57760/sciencedb.j00139.00042). Well-annotated lists of chicken candidate RESs and non-ADAR-editing regulators are also provided in Supplementary Tables S1 and S3, respectively.
    Supplementary data to this article can be found online.
    The authors declare that they have no competing interests.
    Y.P.Z., D.D.W., and Y.M.W. designed the study. M.S.W. collected samples. Y.M.W., L.Q.Y., and M.S.W. performed the data analyses. Y.M.W. wrote the manuscript. J.J.Z. performed the experiments related to ADAR knockdown and ADARB2 overexpression and wrote the corresponding methods. D.D.W., L.Q.Y., M.S.W., S.K., and D.M.I. revised the manuscript. X.D.R. deposited the sequencing data into NCBI. All authors read and approved the final version of the manuscript.
    #Authors contributed equally to this work
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