类乌齐牦牛全基因组RNA编辑位点预测及剖析

doi:10.11843/j.issn.0366-6964.2021.009

Abstract

Abstract: The study aimed to reveal the variation of transcription products at different RNA expression levels among yak tissues, and provide candidate genes for yak tissue differentiation, systematic genetic regulation and other studies. The cerebrum, cerebellum, buttock fat and buttock muscle tissues of 3 Leiwuqi Yaks with 4.5 years old were collected as experimental material. The expression products of each tissue were scaned through the Illumina 4000 sequencing platform, the SPRINT and JACUSA softwares were used to screen differential RNA editing sites, the classification, annotations and mutation risk assessment of RNA editing sites were analyzed. A total of 24 784 RNA editing sites were found, of which 4 015 sites with editing events were observed in the 4 tissues. The RNA editing sites in the 4 tissues were mainly A-G and T-C editing types. It was found that one of the high-risk editing sites was located in the SON gene, which stopped the translation of the gene prematurely, and caused problems in the binding of RNA to DNA at certain sites in the tissue. The types and distribution of RNA editing sites in cerebrum, cerebellum, buttock fat and buttock muscle tissues of Leiwuqi yaks were predicted and analyzed in this study, which provided a new reference for further study on regulatory genes in yak tissue differentiation and growth.

Key words: Leiwuqi yaks, RNA editing site, SPRINT, JACUSA

CLC Number:

S823.85

WANG Jiabo, SHU Tao, CHAI Zhixin, WANG Jikun, WANG Hui, WU Zhijuan, TANG You, ZHONG Jincheng, JI Qiumei. Prediction and Analysis of RNA Editing Sites in the Whole Genome of Leiwuqi Yaks[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(1): 88-97.

References 36

[1]	QIU Q,ZHANG G J,MA T,et al.The yak genome and adaptation to life at high altitude[J].Nat Genet,2012,44(8):946-949.
[2]	GERALD W, HAN J L, LONG R J. The yak[M].Bangkok, Thailand:The Regional Office for Asia and the Pacific Food and Agriculture Organization of the United Nations, 2003.
[3]	WU D D,DING X D,WANG S,et al.Pervasive introgression facilitated domestication and adaptation in the Bos species complex[J].Nat Ecol Evol,2018,2(7):1139-1145.
[4]	HUANG X D,TAN H Y,LONG R J,et al.Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau,China[J].BMC Microbiol,2012,12:237.
[5]	FU D H,MA X M,JIA C J,et al.A study of genomic prediction of 12 important traits in the domesticated yak (Bos grunniens)[J].Animals (Basel),2019,9(11):927.
[6]	ZHANG Y,WU Q Y,YANG L Q,et al.Characterization of the complete mitochondrial genome sequence of golden wild yak and revealed its phylogenetic relationship with 9 yak subspecies[J].Mitochondrial DNA B:Resources,2019,4(1):660-661.
[7]	王会,柴志欣,朱江江,等.牦牛Linc24063的克隆鉴定及其与miRNAs表达水平的相关性分析[J].中国农业科学,2019,52(14):2538-2547.WANG H,CHAI Z X,ZHU J J,et al. Cloning and identification of long-chain non-coding RNA Linc24063 and its correlation with the expression level of miRNAs in yak[J].Scientia Agricultura Sinica,2019,52(14):2538-2547.(in Chinese)
[8]	梁浩,李敏,董翔宇,等.肉鸡腹脂双向选择系中RNA编辑位点的鉴定研究[J].畜牧兽医学报,2017,48(9):1611-1623.LIANG H,LI M,DONG X Y,et al.Identification of RNA editing sites in chicken lines divergently selected for abdominal fat content[J].Acta Veterinaria et Zootechnica Sinica,2017,48(9):1611-1623.(in Chinese)
[9]	ZHANG Q,XIAO X S.Genome sequence-independent identification of RNA editing sites[J].Nat Methods,2015,12(4):347-350.
[10]	LEE S Y,KIM J H.Bioinformatics approaches for the identification and annotation of RNA editing sites[J].J Genet Med,2013,10(1):27-32.
[11]	HOLMES A P,WOOD S H,MERRY B J,et al.A-to-I RNA editing does not change with age in the healthy male rat brain[J].Biogerontology,2013,14(4):395-400.
[12]	RAMASWAMI G,LI J B.Identification of human RNA editing sites:A historical perspective[J].Methods,2016,107:42-47.
[13]	RAMASWAMI G,ZHANG R,PISKOL R,et al.Identifying RNA editing sites using RNA sequencing data alone[J].Nat Methods,2013,10(2):128-132.
[14]	FUNKHOUSER S A,STEIBEL J P,BATES R O,et al.Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements[J].BMC Genomics,2017,18(1):360.
[15]	LO GIUDICE C,TANGARO M A,PESOLE G,et al.Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal[J].Nat Protoc,2020, 15(3):1098-1131.
[16]	纪会,王会,柴志欣,等.牦牛不同年龄肌肉组织microRNA表达谱及生物信息学分析[J].畜牧兽医学报,2019,50(5):957-971.JI H,WANG H,CHAI Z X,et al.Differential expression profile and bioinformatics analysis of miRNAs in yak muscle tissue during development[J].Acta Veterinaria et Zootechnica Sinica,2019,50(5):957-971.(in Chinese)
[17]	WANG J B,CHAI Z X,DENG L,et al.Detection and integrated analysis of LncRNA and MRNA relevant to plateau adaptation of yak[J].Reprod Domest Anim,2020,doi:10.1111/rda.13767.
[18]	杨玉梅,柴志欣,王会,等.类乌齐牦牛SIRT3基因克隆与生物信息学及差异表达分析[J].中国畜牧杂志,2019,55(6):56-62.YANG Y M,CHAI Z X,WANG H,et al.Cloning,bioinformatics and differential expression analysis of SIRT3 gene in Leiwuqi yak[J].Chinese Journal of Animal Science,2019,55(6):56-62.(in Chinese)
[19]	SOEJIMA T,MINAMI J,IWATSUKI K.Rapid propidium monoazide PCR assay for the exclusive detection of viable Enterobacteriaceae cells in pasteurized milk[J].J Dairy Sci,2012,95(7):3634-3642.
[20]	ZHANG F,LU Y L,YAN S J,et al.SPRINT:An SNP-free toolkit for identifying RNA editing sites[J].Bioinformatics,2017,33(22):3538-3548.
[21]	PIECHOTTA M,WYLER E,OHLER U,et al.JACUSA:Site-specific identification of RNA editing events from replicate sequencing data[J].BMC Bioinformatics,2017,18(1):7.
[22]	CINGOLANI P,PATEL V M,COON M,et al.Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program,SnpSift[J].Front Genet,2012,3:35.
[23]	PORATH H T,CARMI S,LEVANON E Y.A genome-wide map of hyper-edited RNA reveals numerous new sites[J].Nat Commun,2014,5:4726.
[24]	BEHM M,ÖHMAN M.RNA editing:A contributor to neuronal dynamics in the mammalian brain[J].Trends Genet,2016,32(3):165-175.
[25]	ZHANG Y Y,HAN D P,DONG X G,et al.Genome-wide profiling of RNA editing sites in sheep[J].J Anim Sci Biotechnol,2019,10(1):31.
[26]	WU X Y,CHU M,DING X Z,et al.Characterization of the complete mitochondrial genome of Kunlun Mountain type wild yak (Bos mutus)[J].Conserv Genet Resour,2018,10(1):111-113.
[27]	钟金城,柴志欣,马志杰,等.野牦牛线粒体基因组序列测定及其系统进化[J].生态学报,2015,35(5):1564-1572.ZHONG J C,CHAI Z X,MA Z J,et al.Mitochondrial complete genome sequencing and phylogenetic research on wild yak[J].Acta Ecologica Sinica,2015,35(5):1564-1572.(in Chinese)
[28]	GOMMANS W M,MULLEN S P,MAAS S.RNA Editing:A driving force for adaptive evolution?[J].BioEssays,2009,31(10):1137-1145.
[29]	MARTíNEZ-MONTES A M,FERNÁNDEZ A,PÉREZ-MONTARELO D,et al.Using RNA-Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing[J].Anim Genet,2017,48(2):151-165.
[30]	EKDAHL Y,FARAHANI H S,BEHM M,et al.A-to-I editing of MicroRNAs in the mammalian brain increases during development[J].Genome Res,2012,22(8):1477-1487.
[31]	KOSUMI K,BABA Y,ISHIMOTO T,et al.APOBEC3B is an enzymatic source of molecular alterations in esophageal squamous cell carcinoma[J].Med Oncol,2016,33(3):26.
[32]	LU M Z,SZMIDT A E,WANG X R.RNA editing in gymnosperms and its impact on the evolution of the mitochondrial CoxI gene[J].Plant Mol Biol,1998,37(2):225-234.
[33]	WYNN S L,FISHER R A,PAGEL C,et al.Organization and conservation of the GART/SON/DONSON locus in mouse and human genomes[J].Genomics,2000,68(1):57-62.
[34]	LU X Y,NG H H,BUBULYA P A.The role of SON in splicing,development,and disease[J].Wiley Interdiscip Rev:RNA,2014,5(5):637-646.
[35]	GREGORY D J,DELOID G M,SALMON S L,et al.SON DNA-binding protein mediates macrophage autophagy and responses to intracellular infection[J].FEBS Lett,2020,594(17):2782-2799.
[36]	LARKIN D M,DAETWYLER H D,HERNANDEZ A G,et al.Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle[J].Proc Natl Acad Sci U S A,2012,109(20):7693-7698.

Prediction and Analysis of RNA Editing Sites in the Whole Genome of Leiwuqi Yaks

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