Analysis of m⁶A methylation in skin tissues of different sex Liaoning cashmere goats

References

• Wei CM, Gershowitz A, Moss B. Methylated nucleotides block 5' terminus of HeLa cell messenger RNA. Cell. 1975;4(4):379–386.
   PubMed Web of Science ®Google Scholar
• Yue Y, Liu J, He C. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 2015;29(13):1343–1355.
   PubMed Web of Science ®Google Scholar
• Chen W, Tran H, Liang Z, Lin H, Zhang L. Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome. Sci Rep. 2015;5:13859.
   PubMed Web of Science ®Google Scholar
• Deng X, Chen K, Luo G-Z, et al. Widespread occurrence of N6-methyladenosine in bacterial mRNA. Nucleic Acids Res. 2015;43(13):6557–6567.
   PubMed Web of Science ®Google Scholar
• Huang W, Xiong J, Yang Y, et al. Determination of DNA adenine methylation in genomes of mammals and plants by liquid chromatography/mass spectrometry. RSC Adv. 2015;5(79):64046–64054.
   Web of Science ®Google Scholar
• Wan Y, Tang K, Zhang D, et al. Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana. Genome Biol. 2015;16:272.
   PubMed Web of Science ®Google Scholar
• Boccaletto P, Machnicka MA, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 2018;46(D1):D303–D307.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Liu X, Liu L, et al. Expression and prognostic significance of m6A-related genes in lung adenocarcinoma. Med Sci Monit. 2020;26:e919644.
   PubMed Web of Science ®Google Scholar
• Chen J, Zhang Y-C, Huang C, et al. m6A regulates neurogenesis and neuronal development by modulating histone methyltransferase Ezh2. Genomics Proteomics Bioinformatics. 2019;17(2):154–168.
   PubMed Web of Science ®Google Scholar
• Fustin J-M, Doi M, Yamaguchi Y. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell. 2013;155:793–806.
   PubMed Web of Science ®Google Scholar
• Batista PJ, Molinie B, Wang J, et al. m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. 2014;15(6):707–719.
   PubMed Web of Science ®Google Scholar
• Zhao X, Yang Y, Sun B-F, et al. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 2014;24(12):1403–1419.
   PubMed Web of Science ®Google Scholar
• Wang Y, Li Y, Toth JI, et al. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat Cell Biol. 2014;16(2):191–198.
   PubMed Web of Science ®Google Scholar
• Li H-B, Tong J, Zhu S, et al. m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature. 2017;548(7667):338–342.
   PubMed Web of Science ®Google Scholar
• Zhang C, Chen Y, Sun B, et al. m6A modulates haematopoietic stem and progenitor cell specification. Nature. 2017;549(7671):273–276.
   PubMed Web of Science ®Google Scholar
• Hibar DP, Stein JL, Renteria ME, et al. Common genetic variants influence human subcortical brain structures. Nature. 2015;520(7546):224–229.
   PubMed Web of Science ®Google Scholar
• Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012;485(7397):201–206.
   PubMed Web of Science ®Google Scholar
• Bai J, Zhang Q, Li J, Dao EJ, Jia X. Estimates of genetic parameters and genetic trends for production traits of Inner Mongolian white cashmere goat. Asian Australas J Anim Sci. 2005;19(1):13–18.
   Web of Science ®Google Scholar
• Song XC, Gao JC. The factors affecting the fineness of Liaoning cashmere and the ways to reduce the fineness of cashmere. Liaoning Anim Husband Vet. 1999;000:3–5.
   Google Scholar
• Zhu YC. Factors affecting cashmere fineness and research status of cashmere fineness control. Contemp Anim Husband. 2003;24(003): 35–37.
   Google Scholar
• Stenn KS, Paus R. Controls of hair follicle cycling. Physiol Rev. 2001;81(1):449–494.
   PubMed Web of Science ®Google Scholar
• Liu B, Gao F, Guo J, et al. A microarray-based analysis reveals that a short photoperiod promotes hair growth in the Arbas cashmere goat. PLoS One. 2016;11(1):e0147124.
   PubMed Web of Science ®Google Scholar
• Bai WL, Yin RH, Yin RL, et al. IGF1 mRNA splicing variants in Liaoning cashmere goat: identification, characterization, and transcriptional patterns in skin and visceral organs. Anim Biotechnol. 2013;24(2):81–93.
   PubMed Web of Science ®Google Scholar
• Fan YX, Wu RB, Qiao X, et al. Hair follicle transcriptome profiles during the transition from anagen to catagen in cashmere goat (Capra hircus). Genet Mol Res. 2015;14(4):17904–17915.
   PubMed Web of Science ®Google Scholar
• Bai WL, Wang JJ, Yin RH, et al. Molecular characterization of HOXC8 gene and methylation status analysis of its exon 1 associated with the length of cashmere fiber in Liaoning cashmere goat. Genetica. 2017;145(1):115–126.
   PubMed Web of Science ®Google Scholar
• Meyer KD, Saletore Y, Zumbo P, et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell. 2012;149(7):1635–1646.
   PubMed Web of Science ®Google Scholar
• Yang Y, Hsu PJ, Chen YS, Yang YG. Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism. Cell Res. 2018;28(6):616–624.
   PubMed Web of Science ®Google Scholar
• Wang Y, Zheng Y, Guo D, et al. m6A methylation analysis of differentially expressed genes in skin tissues of coarse and fine type Liaoning cashmere goats. Front Genet. 2019;10:1318.
   PubMed Web of Science ®Google Scholar
• Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:3.
   Google Scholar
• Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357–360.
   PubMed Web of Science ®Google Scholar
• Meng J, Lu Z, Liu H, et al. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. Methods. 2014;69(3):274–281.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, He QY. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics. 2015;31(14):2382–2383.
   PubMed Web of Science ®Google Scholar
• Bailey TL, Boden M, Buske FA, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202–208.
   PubMed Web of Science ®Google Scholar
• Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–589.
   PubMed Web of Science ®Google Scholar
• Pertea M, Pertea GM, Antonescu CM, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290–295.
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–140.
   PubMed Web of Science ®Google Scholar
• Fan Y, Zhang C, Zhu G. Profiling of RNA N6-methyladenosine methylation during follicle selection in chicken ovary. Poult Sci. 2019;98(11):6117–6124.
   PubMed Web of Science ®Google Scholar
• Wang Y, Mao J, Wang X, et al. Genome-wide screening of altered m6A-tagged transcript profiles in the hippocampus after traumatic brain injury in mice. Epigenomics. 2019;11(7):805–819.
   PubMed Web of Science ®Google Scholar
• Keum DI, Pi LQ, Hwang ST, Lee WS. Protective effect of Korean Red Ginseng against chemotherapeutic drug-induced premature catagen development assessed with human hair follicle organ culture model. J Ginseng Res. 2016;40(2):169–175.
   PubMed Web of Science ®Google Scholar
• Mendoza MN, Raudsepp T, Alshanbari F, Gutierrez G, Ponce de Leon FA. Chromosomal Localization of candidate genes for fiber growth and color in alpaca (Vicugna pacos). Front Genet. 2019;10:583.
   PubMed Web of Science ®Google Scholar
• Huang Z, Xu A, Cheung BMY. The potential role of fibroblast growth factor 21 in lipid metabolism and hypertension. Curr Hypertens Rep. 2017;19(4):28.
   PubMed Web of Science ®Google Scholar
• Maiese K. Novel applications of trophic factors, Wnt and WISP for neuronal repair and regeneration in metabolic disease. Neural Regen Res. 2015;10(4):518–528.
   PubMed Web of Science ®Google Scholar
• Lin W-h, Xiang L-J, Shi H-X, et al. Fibroblast growth factors stimulate hair growth through β-catenin and Shh expression in C57BL/6 mice. Biomed Res Int. 2015;2015:730139.
   PubMed Web of Science ®Google Scholar
• Ariza de Schellenberger A, Horland R, Rosowski M, et al. Cartilage oligomeric matrix protein (COMP) forms part of the connective tissue of normal human hair follicles. Exp Dermatol. 2011;20(4):361–366.
   PubMed Web of Science ®Google Scholar
• Akilli Öztürk Ö, Pakula H, Chmielowiec J, et al. Gab1 and Mapk signaling are essential in the hair cycle and hair follicle stem cell quiescence. Cell Rep. 2015;13(3):561–572.
   PubMed Web of Science ®Google Scholar
• Chang M, et al. Region-specific RNA m(6)A methylation represents a new layer of control in the gene regulatory network in the mouse brain. Open Biol. 2017;7:170166.
   PubMed Web of Science ®Google Scholar