1,521
Views
5
CrossRef citations to date
0
Altmetric
Papers

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

, , , ORCID Icon, &
Pages 383-391 | Received 14 Oct 2019, Accepted 17 Feb 2020, Published online: 07 Apr 2020

References

  • Billerey C, Boussaha M, Esquerre D, Rebours E, Djari A, Meersseman C, Klopp C, Gautheret D, Rocha D. 2014. Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics. 15:499.
  • Bolha L, Ravnik-Glavac M, Glavac D. 2017. Long noncoding RNAs as biomarkers in cancer. Dis Markers. 2017:7243968.
  • Bonasio R, Shiekhattar R. 2014. Regulation of transcription by long noncoding RNAs. Annu Rev Genet. 48:433–455.
  • Borsani G, Tonlorenzi R, Simmler MC, Dandolo L, Arnaud D, Capra V, Grompe M, Pizzuti A, Muzny D, Lawrence C, et al. 1991. Characterization of a murine gene expressed from the inactive X chromosome. Nature. 351:325–329.
  • Bush SJ, Muriuki C, McCulloch MEB, Farquhar IL, Clark EL, Hume DA. 2018. Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. Genet Sel Evol. 50:20.
  • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25:1915–1927.
  • Cao M, Zhao J, Hu G. 2019. Genome-wide methods for investigating long noncoding RNAs. Biomed Pharmacother. 111:395–401.
  • Chen M, Li X, Zhang X, Li Y, Zhang J, Liu M, Zhang L, Ding X, Liu X, Guo H. 2019. A novel long non-coding RNA, lncKBTBD10, involved in bovine skeletal muscle myogenesis. In Vitro Cell Dev Biol Anim. 55:25–35.
  • Chen SY, Liu YP, Wang W, Gao CZ, Yao YG, Lai SJ. 2008. Dissecting the matrilineal components of Tongjiang cattle from southwest China. Biochem Genet. 46:206–215.
  • Choi JY, Shin D, Lee HJ, Oh JD. 2019. Comparison of long noncoding RNA between muscles and adipose tissues in Hanwoo beef cattle. Anim Cells Syst (Seoul). 23:50–58.
  • Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22:1775–1789.
  • Fernandes JCR, Acuna SM, Aoki JI, Floeter-Winter LM, Muxel SM. 2019. Long non-coding RNAs in the regulation of gene expression: physiology and disease. ncRNA. 5:17.
  • Huang da W, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57.
  • Huang W, Long N, Khatib H. 2012. Genome-wide identification and initial characterization of bovine long non-coding RNAs from EST data. Anim Genet. 43:674–682.
  • Ibeagha-Awemu EM, Do DN, Dudemaine PL, Fomenky BE, Bissonnette N. 2018. Integration of lncRNA and mRNA transcriptome analyses reveals genes and pathways potentially involved in calf Intestinal growth and development during the early weeks of life. Genes (Basel). 9:142.
  • Ibeagha-Awemu EM, Li R, Dudemaine PL, Do DN, Bissonnette N. 2018. Transcriptome analysis of long non-coding RNA in the bovine mammary gland following dietary supplementation with linseed oil and safflower oil. Int J Mol Sci. 19:3610.
  • Jathar S, Kumar V, Srivastava J, Tripathi V. 2017. Technological developments in lncRNA biology. Adv Exp Med Biol. 1008:283–323.
  • Jin L, Hu SL, Tu T, Huang ZQ, Tang QZ, Ma JD, Wang X, Li XW, Zhou X, Shuai SR, et al. 2018. Global long noncoding RNA and mRNA expression changes between prenatal and neonatal lung tissue in pigs. Genes (Basel). 9:443.
  • Jin CF, Li Y, Ding XB, Li X, Zhang LL, Liu XF, Guo H. 2017. lnc133b, a novel, long non-coding RNA, regulates bovine skeletal muscle satellite cell proliferation and differentiation by mediating miR-133b. Gene. 630:35–43.
  • Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, et al. 2018. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 19:684.
  • Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 12:357–360.
  • Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G. 2007. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35:W345–W349.
  • Kopp F, Mendell JT. 2018. Functional classification and experimental dissection of long noncoding RNAs. Cell. 172:393–407.
  • Koufariotis LT, Chen YP, Chamberlain A, Vander Jagt C, Hayes BJ. 2015. A catalogue of novel bovine long noncoding RNA across 18 tissues. PLoS One. 10:e0141225.
  • Li D, Li F, Jiang K, Zhang M, Han R, Jiang R, Li Z, Tian Y, Yan F, Kang X, et al. 2019. Integrative analysis of long noncoding RNA and mRNA reveals candidate lncRNAs responsible for meat quality at different physiological stages in Gushi chicken. PLoS One. 14:e0215006.
  • Li Q, Qiao J, Zhang Z, Shang X, Chu Z, Fu Y, Chu M. 2018. Identification and analysis of differentially expressed long non-coding RNAs of Chinese Holstein cattle responses to heat stress. Anim Biotechnol. 31:9–16.
  • Li B, Ruotti V, Stewart RM, Thomson JA, Dewey CN. 2010. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 26:493–500.
  • Ling YH, Xu LN, Zhu L, Sui MH, Zheng Q, Li WY, Liu Y, Fang FG, Zhang XR. 2017. Identification and analysis of differentially expressed long non-coding RNAs between multiparous and uniparous goat (Capra hircus) ovaries. PLoS One. 12:e0183163.
  • Liu XF, Ding XB, Li X, Jin CF, Yue YW, Li GP, Guo H. 2017. An atlas and analysis of bovine skeletal muscle long noncoding RNAs. Anim Genet. 48:278–286.
  • Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15:550.
  • Marchese FP, Raimondi I, Huarte M. 2017. The multidimensional mechanisms of long noncoding RNA function. Genome Biol. 18:206.
  • Mattick JS, Makunin IV. 2006. Non-coding RNA. Hum Mol Genet. 15:R17–29.
  • Meseure D, Alsibai KD, Nicolas A, Bieche I, Morillon A. 2015. Long noncoding RNAs as new architects in cancer epigenetics, prognostic biomarkers, and potential therapeutic targets. Biomed Res Int. 2015:320214.
  • Muret K, Klopp C, Wucher V, Esquerre D, Legeai F, Lecerf F, Desert C, Boutin M, Jehl F, Acloque H, et al. 2017. Long noncoding RNA repertoire in chicken liver and adipose tissue. Genet Sel Evol. 49:6.
  • Niknafs YS, Pandian B, Iyer HK, Chinnaiyan AM, Iyer MK. 2017. TACO produces robust multisample transcriptome assemblies from RNA-seq. Nat Methods. 14:68–70.
  • Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 33:290–295.
  • Ponting CP, Oliver PL, Reik W. 2009. Evolution and functions of long noncoding RNAs. Cell. 136:629–641.
  • Ren HX, Wang GF, Chen L, Jiang J, Liu LJ, Li NF, Zhao JH, Sun XY, Zhou P. 2016. Genome-wide analysis of long non-coding RNAs at early stage of skin pigmentation in goats (Capra hircus). BMC Genomics. 17:67.
  • Schmitz SU, Grote P, Herrmann BG. 2016. Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci. 73:2491–2509.
  • Sun X, Li M, Sun Y, Cai H, Lan X, Huang Y, Bai Y, Qi X, Chen H. 2016. The developmental transcriptome sequencing of bovine skeletal muscle reveals a long noncoding RNA, lncMD, promotes muscle differentiation by sponging miR-125b. Biochim Biophys Acta. 1863:2835–2845.
  • Sulayman A, Tian K, Huang X, Tian Y, Xu X, Fu X, Zhao B, Wu W, Wang D, Yasin A, et al. 2019. Genome-wide identification and characterization of long non-coding RNAs expressed during sheep fetal and postnatal hair follicle development. Sci Rep. 9:8501.
  • Taylor DH, Chu ET, Spektor R, Soloway PD. 2015. Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev. 82:932–956.
  • Tong C, Chen Q, Zhao L, Ma J, Ibeagha-Awemu EM, Zhao X. 2017. Identification and characterization of long intergenic noncoding RNAs in bovine mammary glands. BMC Genomics. 18:468.
  • Wang GZ, Du K, Hu SQ, Chen SY, Jia XB, Cai MC, Shi Y, Wang J, Lai SJ. 2018. Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue. Lipids Health Dis. 17:271.
  • Wang X, Yang C, Guo F, Zhang Y, Ju Z, Jiang Q, Zhao X, Liu Y, Zhao H, Wang J, et al. 2019. Integrated analysis of mRNAs and long noncoding RNAs in the semen from Holstein bulls with high and low sperm motility. Sci Rep. 9:2092.
  • Weikard R, Hadlich F, Hammon HM, Frieten D, Gerbert C, Koch C, Dusel G, Kuehn C. 2018. Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets. Oncotarget. 9:21052–21069.
  • Weikard R, Hadlich F, Kuehn C. 2013. Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing. BMC Genomics. 14:789.
  • Wu Z, Gao S, Zhao X, Chen J, Keyvanfar K, Feng X, Kajigaya S, Young NS. 2019. Long noncoding RNAs of single hematopoietic stem and progenitor cells in healthy and dysplastic human bone marrow. Haematologica. 104:894–906.
  • Xu J, Bai J, Zhang X, Lv Y, Gong Y, Liu L, Zhao H, Yu F, Ping Y, Zhang G, et al. 2017. A comprehensive overview of lncRNA annotation resources. Brief Bioinform. 18:236–249.
  • Xu X, Ji S, Li W, Yi B, Li H, Zhang H, Ma W. 2017. LncRNA H19 promotes the differentiation of bovine skeletal muscle satellite cells by suppressing Sirt1/FoxO1. Cell Mol Biol Lett. 22:10.
  • Yang B, Jiao B, Ge W, Zhang X, Wang S, Zhao H, Wang X. 2018. Transcriptome sequencing to detect the potential role of long non-coding RNAs in bovine mammary gland during the dry and lactation period. BMC Genomics. 19:605.
  • Yang Y, Zhou R, Zhu S, Li X, Li H, Yu H, Li K. 2017. Systematic identification and molecular characteristics of long noncoding RNAs in pig tissues. Biomed Res Int. 2017:6152582.
  • Yue B, Li H, Liu M, Wu J, Li M, Lei C, Huang B, Chen H. 2019. Characterization of lncRNA-miRNA-mRNA network to reveal potential functional ceRNAs in bovine skeletal muscle. Front Genet. 10:91.
  • Zhan S, Dong Y, Zhao W, Guo J, Zhong T, Wang L, Li L, Zhang H. 2016. Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. BMC Genomics. 17:666.
  • Zhao Y, Chen M, Lian D, Li Y, Li Y, Wang J, Deng S, Yu K, Lian Z. 2019. Non-coding RNA regulates the myogenesis of skeletal muscle satellite cells, injury repair and diseases. Cells. 8:988.
  • Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, Li Z, Bu D, Sun N, Zhang MQ, et al. 2016. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res. 44:D203–D208.d