Giải trình tự bisulfite toàn bộ bộ gen của da dê xác định các dấu hiệu liên quan đến chu kỳ phát triển lông
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#nang lông #metyl hóa DNA #chu kỳ lông #dê cashmere #trình tự bisulfite toàn bộ genTài liệu tham khảo
Gudjonsson JE, Krueger G. A role for epigenetics in psoriasis: methylated cytosine-guanine sites differentiate lesional from nonlesional skin and from normal skin. J Invest Dermatol. 2012;132:506–8.
Botchkarev VA, Fessing MY, Botchkareva NV, Westgate G, Tobin DJ. First international symposium “epigenetic control of skin development and regeneration”: how chromatin regulators orchestrate skin functions. J Invest Dermatol. 2013;133:1918–21.
Plikus MV, Guerrero-Juarez CF, Treffeisen E, Gay DL. Epigenetic control of skin and hair regeneration after wounding. Exp Dermatol. 2015;24:167–70.
Bormann F, Rodríguez-Paredes M, Hagemann S, Manchanda H, Kristof B, Gutekunst J, et al. Reduced DNA methylation patterning and transcriptional connectivity define human skin aging. Aging Cell. 2016;15:563–71.
Stojanova ZP, Kwan T, Segil N. Epigenetic regulation of Atoh1 guides hair cell development in the mammalian cochlea. Development. 2015;142:3529–36.
He Y, Waqas M, Chai R, Li H. Epigenetic and signaling pathway regulation in hair cell regeneration. Cell Mol Med 2015;1:1.
Li J, Jiang T-X, Hughes MW, Wu P, Widelitz RB, Fan G, et al. Progressive alopecia reveals decreasing stem cell activation probability during aging of mice with epidermal deletion of DNA methyltransferase 1. J Invest Dermatol. 2012;132:2681–90.
LeBoeuf M, Terrell A, Trivedi S, Sinha S, Epstein JA, Olson EN, et al. Hdac1 and Hdac2 act redundantly to control p63 and p53 functions in epidermal progenitor cells. Dev Cell. 2010;19:807–18.
Lien W-H, Guo X, Polak L, Lawton LN, Young RA, Zheng D, et al. Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage. Cell Stem Cell. 2011;9:219–32.
Grönniger E, Weber B, Heil O, Peters N, Stäb F, Wenck H, et al. Aging and chronic sun exposure cause distinct epigenetic changes in human skin. PLoS Genet. 2010;6:e1000971.
Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, et al. Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol. 2015;16:80.
Baker RE, Murray PJ. Understanding hair follicle cycling: a systems approach. Curr Opin Genet Dev. 2012;22:607–12.
Xu T, Guo X, Wang H, Hao F, Du X, Gao X, et al. Differential gene expression analysis between anagen and telogen of Capra hircus skin based on the de novo assembled transcriptome sequence. Gene. 2013;520:30–8.
Geng R, Yuan C, Chen Y. Exploring differentially expressed genes by RNA-Seq in cashmere goat (Capra hircus) skin during hair follicle development and cycling. PLoS One. 2013;8:e62704.
Yuan C, Wang X, Geng R, He X, Qu L, Chen Y. Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing. BMC Genomics. 2013;14:511.
Gao Y, Wang X, Yan H, Zeng J, Ma S, Niu Y, et al. Comparative transcriptome analysis of fetal skin reveals key genes related to hair follicle morphogenesis in cashmere goats. PLoS One. 2016;11:e0151118.
Zhou G, Kang D, Ma S, Wang X, Gao Y, Yang Y, et al. Integrative analysis reveals ncRNA-mediated molecular regulatory network driving secondary hair follicle regression in cashmere goats. BMC Genomics. 2018;19:222.
Dong Y, Xie M, Jiang Y, Xiao N, Du X, Zhang W, et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotech. 2013;31:135–41.
Su J, Wang Y, Xing X, Liu J, Zhang Y. Genome-wide analysis of DNA methylation in bovine placentas. BMC Genomics. 2014;15:12.
Zhang Y, Li F, Feng X, Yang H, Zhu A, Pang J, et al. Genome-wide analysis of DNA methylation profiles on sheep ovaries associated with prolificacy using whole-genome bisulfite sequencing. BMC Genomics. 2017;18:759.
Jin L, Jiang Z, Xia Y, Lou P, Chen L, Wang H, et al. Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs. BMC Genomics. 2014;15:653.
Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012;13:R83.
Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat Genet. 2017;49:643–50.
Reimand J, Arak T, Adler P, Kolberg L, Reisberg S, Peterson H, et al. G:profiler—a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 2016;44:W83–9.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Li Y, Zhou G, Zhang R, Guo J, Li C, Martin G, et al. Comparative proteomic analyses using iTRAQ-labeling provides insights into fiber diversity in sheep and goats. J Proteome. 2018;172:82–8.
Flanagan JM, Wild L. An epigenetic role for noncoding RNAs and intragenic DNA methylation. Genome Biol. 2007;8:307.
Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D’Souza C, Fouse SD, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466:253.
Zhang S, Qin C, Cao G, Guo L, Feng C, Zhang W. Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing. Bioinformatics. 2017;33:1591–5.
Zheng Z, Wei X, Hildebrandt A, Schmidt B. A computational method for studying the relation between alternative splicing and DNA methylation. Nucleic Acids Res. 2016;44:e19.
Schneider MR, Schmidt-Ullrich R, Paus R. The hair follicle as a dynamic Miniorgan. Curr Biol. 2009;19:R132–42.
Frattini S, Capra E, Lazzari B, McKay SD, Coizet B, Talenti A, et al. Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus. BMC Genomics. 2017;18:476.
Lee J-R, Hong CP, Moon J-W, Jung Y-D, Kim D-S, Kim T-H, et al. Genome-wide analysis of DNA methylation patterns in horse. BMC Genomics. 2014;15:598.
Yang L, Liu B, Li Y, Wang S, Yuan X, Wang D, et al. iRhom2 mutation leads to aberrant hair follicle differentiation in mice. PLoS One. 2014;9:e115114.
Bock C, Beerman I, Lien W-H, Smith ZD, Gu H, Boyle P, et al. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell. 2012;47:633–47.
Sennett R, Wang Z, Rezza A, Grisanti L, Roitershtein N, Sicchio C, et al. An integrated transcriptome atlas of embryonic hair follicle progenitors, their niche, and the developing skin. Dev Cell. 2015;34:577–91.
Lin KK, Kumar V, Geyfman M, Chudova D, Ihler AT, Smyth P, et al. Circadian clock genes contribute to the regulation of hair follicle cycling. PLoS Genet. 2009;5:e1000573.
Kobielak A, Pasolli HA, Fuchs E. Mammalian formin-1 participates in adherens junctions and polymerization of linear actin cables. Nat Cell Biol. 2004;6:21–30.
O’Shaughnessy RFL, Yeo W, Gautier J, Jahoda CAB, Christiano AM. The WNT Signalling modulator, wise, is expressed in an interaction-dependent manner during hair-follicle cycling. J Invest Dermatol. 2004;123:613–21.
Hulmes DJS, Mould AP, Kessler E. The CUB domains of procollagen C-proteinase enhancer control collagen assembly solely by their effect on procollagen C-proteinase/bone morphogenetic protein-1. Matrix Biol. 1997;16:41–5.
Linde N, Sosa MS, Aguirre-Ghiso JA. Integration of microenvironmental and stress signaling antagonizes colorectal cancer progression. EMBO J. 2014;33:1737–9.
Li S, Teegarden A, Bauer EM, Choi J, Messaddeq N, Hendrix DA, et al. Transcription factor CTIP1/BCL11A regulates epidermal differentiation and lipid metabolism during skin development. Sci Rep. 2017;7:13427.
Bancelin S, Lynch B, Bonod-Bidaud C, Ducourthial G, Psilodimitrakopoulos S, Dokládal P, et al. Ex vivo multiscale quantitation of skin biomechanics in wild-type and genetically-modified mice using multiphoton microscopy. Sci Rep. 2015;5:17635.
Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.