Discovery of genes and proteins possibly regulating mean wool fibre diameter using cDNA microarray and proteomic approaches.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
07 05 2020
07 05 2020
Historique:
received:
27
02
2017
accepted:
30
03
2020
entrez:
9
5
2020
pubmed:
10
5
2020
medline:
24
11
2020
Statut:
epublish
Résumé
Wool fibre diameter (WFD) is one of the wool traits with higher economic impact. However, the main genes specifically regulating WFD remain unidentified. In this current work we have used Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin, bearing more wool, in Aohan fine wool sheep, a Chinese indigenous breed, and compared them with that of small tail Han sheep, a sheep bread with coarse wool. Microarray analyses showed that most of the genes likely determining wool diameter could be classified into a few categories, including immune response, regulation of receptor binding and growth factor activity. Certain gene families might play a role in hair growth regulation. These include growth factors, immune cytokines, solute carrier families, cellular respiration and glucose transport amongst others. Proteomic analyses also identified scores of differentially expressed proteins.
Identifiants
pubmed: 32382132
doi: 10.1038/s41598-020-64903-7
pii: 10.1038/s41598-020-64903-7
pmc: PMC7206055
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7726Références
Purvis, I. W. & Franklin, I. R. Major genes and QTL influencing wool production and quality: a review. Genet. Sel. Evol. 37(Suppl 1), S97–107 (2005).
pubmed: 15601598
pmcid: 3226268
doi: 10.1186/1297-9686-37-S1-S97
Bidinost, F. et al. Wool quantitative trait loci in Merino sheep. Small Rumin. Res. 74, 113–118 (2008).
doi: 10.1016/j.smallrumres.2007.04.005
Itenge, T. O., Hickford, J. G. H., Forrest, R. H. J., McKenzie, G. W. & Frampton, C. M. Improving the quality of wool through the use of gene markers. South. Afr. J. Anim. Sci. 39, 219–223 (2009).
Beh, K. J. et al. A genome scan for QTL affecting fleece and wool traits in Merino sheep. Wool. Technol. Sheep Breed. 49, 88–89 (2001).
Cano, E. M. et al. QTL affecting fleece traits in Angora goats. Small Rumin. Res. 71, 158–164 (2007).
doi: 10.1016/j.smallrumres.2006.06.002
Schmidt-Ullrich, R. & Paus, R. Molecular principles of hair follicle induction and morphogenesis. Bioessays 27, 247–261 (2005).
pubmed: 15714560
doi: 10.1002/bies.20184
Galbraith, H. Fundamental hair follicle biology and fine fibre production in animals. Animal 4, 1490–1509 (2010).
pubmed: 22444696
doi: 10.1017/S175173111000025X
McGrice, H. A. Molecular Characterisation of Primary Wool Follicle Initiation in Merino Sheep PhD thesis, University of Adelaide, (2010).
Rhee, H., Polak, L. & Fuchs, E. Lhx2 maintains stem cell character in hair follicles. Science 312, 1946–1949 (2006).
pubmed: 16809539
pmcid: 2405918
doi: 10.1126/science.1128004
Janich, P. et al. The circadian molecular clock creates epidermal stem cell heterogeneity. Nature 480, 209–214 (2011).
pubmed: 22080954
doi: 10.1038/nature10649
Ohyama, M. et al. Characterization and isolation of stem cell-enriched human hair follicle bulge cells. J. Clin. Invest. 116, 249–260 (2006).
pubmed: 16395407
pmcid: 1323261
doi: 10.1172/JCI26043
Cotsarelis, G. Gene expression profiling gets to the root of human hair follicle stem cells. J. Clin. Invest. 116, 19–22 (2006).
pubmed: 16395398
pmcid: 1323274
doi: 10.1172/JCI27490
Ollier, S., Robert-Granie, C., Bernard, L., Chilliard, Y. & Leroux, C. Mammary transcriptome analysis of food-deprived lactating goats highlights genes involved in milk secretion and programmed cell death. J. Nutr. 137, 560–567 (2007).
pubmed: 17311940
doi: 10.1093/jn/137.3.560
Faucon, F. et al. Terminal differentiation of goat mammary tissue during pregnancy requires the expression of genes involved in immune functions. Physiol. Genomics 40, 61–82 (2009).
pubmed: 19843654
doi: 10.1152/physiolgenomics.00032.2009
Bongiorni, S. et al. A Tool for Sheep Product Quality: Custom Microarrays from Public Databases. nutrients, 235–250 (2009).
Norris, B. J., Bower, N. I., Smith, W. J. M., Cam, G. R. & Reverter, A. Gene expression profiling of ovine skin and wool follicle development using a combined ovine-bovine skin cDNA microarray. Australian J. Exp. Agriculture 45, 867–877 (2005).
doi: 10.1071/EA05050
Smith, W. J. et al. A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep. BMC Vet. Res. 6, 27 (2010).
pubmed: 20500888
pmcid: 2886023
doi: 10.1186/1746-6148-6-27
Penagaricano, F., Zorrilla, P., Naya, H., Robello, C. & Urioste, J. I. Gene expression analysis identifies new candidate genes associated with the development of black skin spots in Corriedale sheep. J Appl Genet (2012).
MacKinnon, K. M., Burton, J. L., Zajac, A. M. & Notter, D. R. Microarray analysis reveals difference in gene expression profiles of hair and wool sheep infected with Haemonchus contortus. Vet. Immunol. Immunopathol. 130, 210–220 (2009).
pubmed: 19346008
doi: 10.1016/j.vetimm.2009.02.013
Keane, O. M. et al. Gene expression profiling of naive sheep genetically resistant and susceptible to gastrointestinal nematodes. BMC Genomics 7, 42 (2006).
pubmed: 16515715
pmcid: 1450279
doi: 10.1186/1471-2164-7-42
Wenguang, Z., Jianghong, W., Jinquan, L. & Yashizawa, M. A subset of skin-expressed microRNAs with possible roles in goat and sheep hair growth based on expression profiling of mammalian microRNAs. OMICS 11, 385–396 (2007).
pubmed: 18092910
doi: 10.1089/omi.2006.0031
Liu, G. et al. Identification of microRNAs in wool follicles during anagen, catagen, and telogen phases in Tibetan sheep. PLoS One 8, e77801 (2013).
pubmed: 24204975
pmcid: 3804049
doi: 10.1371/journal.pone.0077801
Yuan, C. et al. Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing. BMC Genomics 14, 511 (2013).
pubmed: 23889850
pmcid: 3765263
doi: 10.1186/1471-2164-14-511
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 8, e62704 (2013).
pubmed: 23638136
pmcid: 3640091
doi: 10.1371/journal.pone.0062704
Dong, Y. et al. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat. Biotechnol. 31, 135–141 (2013).
pubmed: 23263233
doi: 10.1038/nbt.2478
Jiang, Y. et al. The sheep genome illuminates biology of the rumen and lipid metabolism. Science 344, 1168–1173, https://doi.org/10.1126/science.1252806 (2014).
doi: 10.1126/science.1252806
pubmed: 24904168
pmcid: 4157056
Yue, Y. et al. Exploring Differentially Expressed Genes and Natural Antisense Transcripts in Sheep (Ovis aries) Skin with Different Wool Fiber Diameters by Digital Gene Expression Profiling. PLoS One 10, e0129249 (2015).
pubmed: 26076016
pmcid: 4468096
doi: 10.1371/journal.pone.0129249
Liu, N. et al. Identification of skin-expressed genes possibly associated with wool growth regulation of Aohan fine wool sheep. BMC Genet. 15, 144 (2014).
pubmed: 25511509
pmcid: 4272822
doi: 10.1186/s12863-014-0144-1
Liu, N. et al. Differential expression of genes and proteins associated with wool follicle cycling. Mol. Biol. Rep. 41, 5343–5349 (2014).
pubmed: 24847760
doi: 10.1007/s11033-014-3405-1
Yu, Z. D. et al. Micro-arrays as a discovery tool for wool genomics. Proc. N. Zealand Soc. Anim. Prod. 66, 129–133 (2006).
Yu, Z. D. et al. Gene expression profiling of wool follicle growth cycles by cDNA microarray. Proc. N. Zealand Soc. Anim. Prod. 68, 39–42 (2008).
Zhao, J. et al. Identification of genes and proteins associated with anagen wool growth. Anim. Genet. 48, 67–79 (2017).
pubmed: 27611105
doi: 10.1111/age.12480
Adelson, D. L., Cam, G. R., DeSilva, U. & Franklin, I. R. Gene expression in sheep skin and wool (hair). Genomics 83, 95–105 (2004).
pubmed: 14667813
doi: 10.1016/S0888-7543(03)00210-6
Rogers, G. E. Biology of the wool follicle: an excursion into a unique tissue interaction system waiting to be re-discovered. Exp. Dermatol. 15, 931–949 (2006).
pubmed: 17083360
doi: 10.1111/j.1600-0625.2006.00512.x
Nagorcka, B. The reaction-diffusion (RD) theory of wool (hair) follicle initiation and development. I. Primary follicles. Australian J. Agric. Res. 46, 333–355 (1995).
doi: 10.1071/AR9950333
Nagorcka, B. The reaction-diffusion (RD) theory of wool (hair) follicle initiation and development. II. Original secondary follicles. Australian J. Agric. Res. 46, 357–378 (1995).
doi: 10.1071/AR9950357
Sick, S., Reinker, S., Timmer, J. & Schlake, T. WNT and DKK determine hair follicle spacing through a reaction-diffusion mechanism. Science 314, 1447–1450 (2006).
pubmed: 17082421
doi: 10.1126/science.1130088
Gibbs, S. et al. Molecular characterization and evolution of the SPRR family of keratinocyte differentiation markers encoding small proline-rich proteins. Genomics 16, 630–637, https://doi.org/10.1006/geno.1993.1240 (1993).
doi: 10.1006/geno.1993.1240
pubmed: 8325635
Ishida-Yamamoto, A., Kartasova, T., Matsuo, S., Kuroki, T. & Iizuka, H. Involucrin and SPRR are synthesized sequentially in differentiating cultured epidermal cells. J. Invest. Dermatol. 108, 12–16 (1997).
pubmed: 8980279
doi: 10.1111/1523-1747.ep12285611
Candi, E. et al. Biochemical, structural, and transglutaminase substrate properties of human loricrin, the major epidermal cornified cell envelope protein. J. Biol. Chem. 270, 26382–26390 (1995).
pubmed: 7592852
doi: 10.1074/jbc.270.44.26382
Wang, L. & Baldwin, R. L. t. & Jesse, B. W. Identification of two cDNA clones encoding small proline-rich proteins expressed in sheep ruminal epithelium. Biochem. J. 317(Pt 1), 225–233 (1996).
pubmed: 8694768
pmcid: 1217467
doi: 10.1042/bj3170225
Akiyama, M., Smith, L. T., Yoneda, K., Holbrook, K. A. & Shimizu, H. Transglutaminase and major cornified cell envelope precursor proteins, loricrin, small proline-rich proteins 1 and 2, and involucrin are coordinately expressed in the sites defined to form hair canal in developing human hair follicle. Exp. Dermatol. 8, 313–314 (1999).
pubmed: 10439243
doi: 10.1111/j.1600-0625.1999.tb00368.x
Bodo, E. et al. Dissecting the impact of chemotherapy on the human hair follicle: a pragmatic in vitro assay for studying the pathogenesis and potential management of hair follicle dystrophy. Am. J. Pathol. 171, 1153–1167 (2007).
pubmed: 17823286
pmcid: 1988866
doi: 10.2353/ajpath.2007.061164
Yoshikawa, Y. et al. Upregulation of genes orchestrating keratinocyte differentiation, including the novel marker gene ID2, by contact sensitizers in human bulge-derived keratinocytes. J. Biochem. Mol. Toxicol. 24, 10–20 (2010).
pubmed: 20146380
doi: 10.1002/jbt.20307
Aubert, J. et al. Gene expression profiling in psoriatic scalp hair follicles: clobetasol propionate shampoo 0.05% normalizes psoriasis disease markers. J. Eur. Acad. Dermatol. Venereol. 24, 1304–1311 (2010).
pubmed: 20337827
doi: 10.1111/j.1468-3083.2010.03637.x
French, A. T. et al. Up-regulation of intelectin in sheep after infection with Teladorsagia circumcincta. Int. J. Parasitol. 38, 467–475 (2008).
pubmed: 17983620
doi: 10.1016/j.ijpara.2007.08.015
Mistry, D. H. & Medrano, J. F. Cloning and localization of the bovine and ovine lysophosphatidic acid acyltransferase (LPAAT) genes that codes for an enzyme involved in triglyceride biosynthesis. J. Dairy. Sci. 85, 28–35 (2002).
pubmed: 11860120
doi: 10.3168/jds.S0022-0302(02)74049-6
Karnik, P. et al. Hair follicle stem cell-specific PPARgamma deletion causes scarring alopecia. J. Invest. Dermatol. 129, 1243–1257 (2009).
pubmed: 19052558
doi: 10.1038/jid.2008.369
Rowe, J. M. et al. Illuminating role of CYP1A1 in skin function. J. Invest. Dermatol. 128, 1866–1868 (2008).
pubmed: 18185528
doi: 10.1038/sj.jid.5701236
Liu, B. et al. A Microarray-Based Analysis Reveals that a Short Photoperiod Promotes Hair Growth in the Arbas Cashmere Goat. PLoS One 11, e0147124 (2016).
pubmed: 26814503
pmcid: 4731399
doi: 10.1371/journal.pone.0147124
Christoph, T. et al. The human hair follicle immune system: cellular composition and immune privilege. Br. J. Dermatol. 142, 862–873 (2000).
pubmed: 10809841
doi: 10.1046/j.1365-2133.2000.03464.x
Osaka, N. et al. ASK1-dependent recruitment and activation of macrophages induce hair growth in skin wounds. J. Cell Biol. 176, 903–909 (2007).
pubmed: 17389227
pmcid: 2064076
doi: 10.1083/jcb.200611015
Kawano, M. et al. Comprehensive analysis of FGF and FGFR expression in skin: FGF18 is highly expressed in hair follicles and capable of inducing anagen from telogen stage hair follicles. J. Invest. Dermatol. 124, 877–885 (2005).
pubmed: 15854025
doi: 10.1111/j.0022-202X.2005.23693.x
Powell, B. C. & Beltrame, J. S. Characterization of a hair (wool) keratin intermediate filament gene domain. J. Invest. Dermatol. 102, 171–177 (1994).
pubmed: 7508962
doi: 10.1111/1523-1747.ep12371758
Horner, M. E., Parkinson, K. E., Kaye, V. & Lynch, P. J. Dowling-Degos disease involving the vulva and back: case report and review of the literature. Dermatol. Online J. 17, 1 (2011).
pubmed: 21810386
Rosenquist, T. A. & Martin, G. R. Fibroblast growth factor signalling in the hair growth cycle: expression of the fibroblast growth factor receptor and ligand genes in the murine hair follicle. Dev. Dyn. 205, 379–386 (1996).
pubmed: 8901049
doi: 10.1002/(SICI)1097-0177(199604)205:4<379::AID-AJA2>3.0.CO;2-F
Menzies, M., Stockwell, S., Brownlee, A., Cam, G. & Ingham, A. Gene expression profiles of BMP4, FGF10 and cognate inhibitors, in the skin of foetal Merino sheep, at the time of secondary follicle branching. Exp. Dermatol. 18, 877–879 (2009).
pubmed: 19469906
doi: 10.1111/j.1600-0625.2008.00837.x
Botchkarev, V. A. et al. Noggin is a mesenchymally derived stimulator of hair-follicle induction. Nat. Cell Biol. 1, 158–164 (1999).
pubmed: 10559902
doi: 10.1038/11078
Yuan, C. et al. The up-regulation of 14-3-3 proteins in Smad4 deficient epidermis and hair follicles at catagen. Proteomics 8, 2230–2243 (2008).
pubmed: 18446800
doi: 10.1002/pmic.200700760
Hammond, N. L., Headon, D. J. & Dixon, M. J. The cell cycle regulator protein 14-3-3sigma is essential for hair follicle integrity and epidermal homeostasis. J. Invest. Dermatol. 132, 1543–1553 (2012).
pubmed: 22377760
pmcid: 3378636
doi: 10.1038/jid.2012.27
Zhou, P. et al. Molecular characterization of transcriptome-wide interactions between highly pathogenic porcine reproductive and respiratory syndrome virus and porcine alveolar macrophages in vivo. Int. J. Biol. Sci. 7, 947–959 (2011).
pubmed: 21850204
pmcid: 3157269
doi: 10.7150/ijbs.7.947
Tang, Z. et al. LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs. Genome Biol. 8, R115 (2007).
pubmed: 17573972
pmcid: 2394763
doi: 10.1186/gb-2007-8-6-r115
Nacht, M. et al. Molecular characteristics of non-small cell lung cancer. Proc. Natl Acad. Sci. USA 98, 15203–15208 (2001).
pubmed: 11752463
doi: 10.1073/pnas.261414598
Dennis, G. Jr. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, P3 (2003).
pubmed: 12734009
doi: 10.1186/gb-2003-4-5-p3
Berndt, P., Hobohm, U. & Langen, H. Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints. Electrophoresis 20, 3521–3526 (1999).
pubmed: 10612278
doi: 10.1002/(SICI)1522-2683(19991201)20:18<3521::AID-ELPS3521>3.0.CO;2-8