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PLOS ONE  2013 

Exploring Differentially Expressed Genes by RNA-Seq in Cashmere Goat (Capra hircus) Skin during Hair Follicle Development and Cycling

DOI: 10.1371/journal.pone.0062704

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Abstract:

Cashmere goat (Capra hircus) hair follicle development and cycling can be divided into three stages: anagen, catagen and telogen. To elucidate the genes involved in hair follicle development and cycling in cashmere goats, transcriptome profiling of skin was carried out by analysing samples from three hair follicle developmental stages using RNA-Seq. The RNA-Seq analysis generated 8487344, 8142514 and 7345335 clean reads in anagen, catagen and telogen stages, respectively, which provided abundant data for further analysis. A total of 1332 differentially expressed genes (DEGs) were identified, providing evidence that the development of hair follicles among the three distinct stages changed considerably. A total of 683 genes with significant differential expression were detected between anagen and catagen, 530 DEGs were identified between anagen and telogen, and 119 DEGs were identified between catagen and telogen. A large number of DEGs were predominantly related to cellular process, cell & cell part, binding, biological regulation and metabolic process among the different stages of hair follicle development. In addition, the Wnt, Shh, TGF-β and Notch signaling pathways may be involved in hair follicle development and the identified DEGs may play important roles in these signaling pathways. These results will expand our understanding of the complex molecular mechanisms of hair follicle development and cycling in cashmere goats and provide a foundation for future studies.

References

[1]  Ryder ML (1966) Coat structure and seasonal shedding in goats. Animal Production 8: 289–302.
[2]  Nixon AJ, Gurnsey MP, Betteridge K, Mitchell RJ, Welch RAS (1991) Seasonal hair follicle activity and fibre growth in some New Zealand cashmere-bearing goats&LPKT Capra hircus&RPKT. Journal of Zoology 224: 589–598.
[3]  Ansari-Renani HR, Ebadi Z, Moradi S, Baghershah HR, Ansari-Renani MY, et al. (2011) Determination of hair follicle characteristics, density and activity of Iranian cashmere goat breeds. Small Ruminant Research 95(2–3): 128–132.
[4]  Hardy MH (1992) The secret life of the hair follicle. Trends Genet 8: 55–61.
[5]  Stenn KS, Paus R (2001) Controls of hair follicle cycling. Physiol Rev 81: 449–494.
[6]  Botchkarev VA, Kishimoto J (2003) Molecular control of epithelial-mesenchymal interactions during hair follicle cycling. J Investig Dermatol Symp Proc 8(1): 46–55.
[7]  Millar SE (2002) Molecular mechanisms regulating hair follicle development. Journal of Investigative Dermatology 118: 216–225.
[8]  Schmidt-Ullrich R, Paus R (2005) Molecular principles of hair follicle induction and morphogenesis. Bioessays 27(3): 247–261.
[9]  Schneider MR, Schmidt-Ullrich R, Paus R (2009) The hair follicle as a dynamic miniorgan. Current Biology 19(3): R132–R142.
[10]  Geyfman M, Andersen B (2010) Clock genes, hair growth and aging. Aging (Albany N Y) 2(3): 122–128.
[11]  Nathalie Le Bot (2011) Hair follicles run by clockwork. Nature Cell Biology 13: 1394.
[12]  Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57–63.
[13]  Wilhelm BT, Landry JR (2009) RNA-Seq quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48: 249–257.
[14]  Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12(2): 87–98.
[15]  Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics 25 (15): 1966–1967.
[16]  Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7): 621–628.
[17]  Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Research 7: 986–995.
[18]  Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I (2001) Controlling the false discovery rate in behavior genetics research. Behavioural Brain Research 125: 279–284.
[19]  de Hoon MJL, Imoto S, Nolan J, Miyano S (2004) Open Source Clustering Software. Bioinformatics 20 (9): 1453–1454.
[20]  Saldanha AJ (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20(17): 3246–3248.
[21]  Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al. (2009) ClueGO: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091–1093.
[22]  Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25: 402–408.
[23]  Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25): 14863–14868.
[24]  Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: 480–484.
[25]  Fuchs E (2007) Scratching the surface of skin development. Nature 445: 834–842.
[26]  Mikkola ML (2007) Genetic basis of skin appendage development. Semin Cell Dev Biol 18: 225–236.
[27]  Huntzicker EG, Oro AE (2008) Controlling hair follicle signaling pathways through polyubiquitination. J Invest Dermatol 128(5): 1081–1087.
[28]  Botchkarev VA, Fessing MY (2005) Edar signaling in the control of hair follicle development. J Investig Dermatol Symp Proc 10: 247–251.
[29]  Mou C, Jackson B, Schneider P, Overbeek PA, Headon DJ (2006) Generation of the primary hair follicle pattern. Proc Natl Acad Sci USA 103: 9075–9080.
[30]  Zhang Y, Tomann P, Andl T, Gallant NM, Huelsken J, et al. (2009) Reciprocal requirements for EDA/EDAR/NF-κB and Wnt/β-catenin signaling pathways in hair follicle induction. Dev Cell 17(1): 49–61.
[31]  Huelsken J, Vogel R, Erdmann B, Cotsarelis G, Birchmeier W (2001) Beta-catenin controls hair follicle morphogenesis and stem cell differentiation in the skin. Cell 105: 533–545.
[32]  Van Mater D, Kolligs FT, Dlugosz AA, Fearon ER (2003) Transient activation of beta-catenin signaling in cutaneous keratinocytes is sufficient to trigger the active growth phase of the hair cycle in mice. Genes Dev 17: 1219–1224.
[33]  Fu J, Hsu W (2012) Epidermal Wnt controls hair follicle induction by orchestrating dynamic signaling crosstalk between the epidermis and dermis. J Invest Dermatol 29. doi:10.1038/jid.2012.407.
[34]  Chen D, Jarrell A, Guo C, Lang R, Atit R (2012) Dermal β-catenin activity in response to epidermal Wnt ligands is required for fibroblast proliferation and hair follicle initiation. Development 139(8): 1522–1533.
[35]  Oro AE, Higgins K (2003) Hair cycle regulation of Hedgehog signal reception. Dev Biol 255: 238–248.
[36]  Levy V, Lindon C, Harfe BD, Morgan BA (2005) Distinct stem cell populations regenerate the follicle and interfollicular epidermis. Dev Cell 9: 855–861.
[37]  Woo WM, Zhen HH, Oro AE (2012) Shh maintains dermal papilla identity and hair morphogenesis via a Noggin-Shh regulatory loop. Genes Dev 26(11): 1235–1246.
[38]  Fuchs E (2007) Scratching the surface of skin development. Nature 445: 834–842.
[39]  Little JC, Westgate GE, Evans A, Granger SP (1994) Cytokine gene expression in intact anagen rat hair follicles. J Invest Dermatol 103(5): 715–720.
[40]  Danilenko DM, Ring BD, Pierce GF (1996) Growth factors and cytokines in hair follicle development and cycling: recent insights from animal models and the potentials for clinical therapy. Mol Med Today 2(11): 460–467.
[41]  Paus R, Cotsarelis G (1999) The biology of hair follicles. N Engl J Med 341(7): 491–497.
[42]  Krause K, Foitzik K (2006) Biology of the hair follicle: the basics. Semin Cutan Med Surg 25(1): 2–10.
[43]  Donet E, Bayo P, Calvo E, Labrie F, Pérez P (2008) Identification of novel glucocorticoid receptor-regulated genes involved in epidermal homeostasis and hair follicle differentiation. J Steroid Biochem Mol Biol 108(1–2): 8–16.
[44]  Lindner G, Menrad A, Gherardi E, Merlino G, Welker P, et al. (2000) Involvement of hepatocyte growth factor/scatter factor and met receptor signaling in hair follicle morphogenesis and cycling. FASEB J 4(2): 319–332.
[45]  McElwee KJ, Huth A, Kissling S, Hoffmann R (2004) Macrophage-stimulating protein promotes hair growth ex vivo and induces anagen from telogen stage hair follicles in vivo. J Invest Dermatol 123(1): 34–40.
[46]  Everts HB (2012) Endogenous retinoids in the hair follicle and sebaceous gland. Biochim Biophys Acta 1821(1): 222–229.
[47]  Napoli JL (2012) Physiological insights into all-trans-retinoic acid biosynthesis. Biochim Biophys Acta 1821(1): 152–167.
[48]  Nuutila K, Siltanen A, Peura M, Bizik J, Kaartinen I, et al. (2012) Human skin transcriptome during superficial cutaneous wound healing. Wound Repair Regen 20(6): 830–839.
[49]  Fredholm BB, Jzerman AP, Jacobson KA, Klotz KN, Linden J (2001) International union of pharmacology. XXV. Nomenclature and classification of adenosine receptors. Pharmacol Rev 53: 527–552.
[50]  Li M, Marubayashi A, Nakaya Y, Fukui K, Arase S (2001) Minoxidil-induced hair growth is mediated by adenosine in cultured dermal papilla cells: possible involvement of sulfonylurea receptor 2B as a target of minoxidil. J Invest Dermatol 117: 1594–1600.
[51]  Oura H, Iino M, Nakazawa Y, Tajima M, Ideta R, et al. (2008) Adenosine increases anagen hair growth and thick hairs in Japanese women with female pattern hair loss: a pilot, double-blind, randomized, placebo-controlled trial. J Dermatol 35(12): 763–7.
[52]  Hwang KA, Hwang YL, Lee MH, Kim NR, Roh SS, et al. (2012) Adenosine stimulates growth of dermal papilla and lengthens the anagen phase by increasing the cysteine level via fibroblast growth factors 2 and 7 in an organ culture of mouse vibrissae hair follicles. Int J Mol Med 29(2): 195–201.
[53]  Iino M, Ehama R, Nakazawa Y, Iwabuchi T, Ogo M, et al. (2007) Adenosine stimulates fibroblast growth factor-7 gene expression via adenosine A2b receptor signaling in dermal papilla cells. J Invest Dermatol 127(6): 1318–1325.

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