Animal Bioscience

  • 제37권12호
  • /
  • Pages.2066-2080
  • /
  • 2024
  • /
  • 2765-0189(pISSN)
  • /
  • 2765-0235(eISSN)
아세아태평양축산학회 (Asian Australasian Association of Animal Production Societies)
권호 표지
DOI QR코드

DOI QR Code

N6-methyladenosine (m6A)-circHECA from secondary hair follicle of cashmere goats: identification, regulatory network and expression regulated potentially by methylation of its host gene promoter

  • Jincheng Shen (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Taiyu Hui (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Man Bai (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Yixing Fan (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Yubo Zhu (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Qi Zhang (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Ruqing Xu (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Jialiang Zhang (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Zeying Wang (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University) ;
  • Wenxin Zheng (State Key Laboratory for Herbivorous Livestock Genetic Improvement and Germplasm Innovation of Ministry of Science and Technology and Xinjiang Uygur Autonomous Region) ;
  • Wenlin Bai (College of Animal Science and Veterinary Medicine, Shenyang Agricultural University)
  • 투고 : 2024.02.07
  • 심사 : 2024.05.11
  • 발행 : 2024.12.01
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Objective: The objective of this study was to identify the N6-methyladenosine (m6A)-circHECA molecule in secondary hair follicles (SHFs) of cashmere goats, and generate its potential regulatory network, as well as explore the potential relationship between transcriptional pattern of m6A-circHECA and promoter methylation of its host gene (HECA). Methods: The validation of circHECA m6A sites was performed using methylation immunoprecipitation (Me-RIP) along with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) technique. The nucleus and cytoplasm localizations of m6A-circHECA were performed using SHF stem cells of cashmere goats with RT-qPCR analysis. Based on in-silico analysis, the regulatory networks of m6A-circHECA were generated with related signal pathway enrichment. The methylation level of promoter region of m6A-circHECA host gene (HECA) was assessed by the bisulfite sequencing PCR (BSP-PCR) technique. Results: The m6A-circHECA was confirmed to contain four m6A modification sites including m6A-213, m6A-297, m6A-780, and m6A-927, and it was detected mainly in cytoplasm of the SHF stem cells of cashmere goats. The integrated regulatory network analysis showed directly or indirectly complex regulatory relationships between m6A-circHECA of cashmere goats and its potential target molecules: miRNAs, mRNAs, and proteins. The regulatory network and pathway enrichment indicated that m6A-circHECA might play multiple roles in the SHF physiology process of cashmere goats through directly or indirectly interacting or regulating its potential target molecules. A higher methylation level of promoter region of HECA gene in SHFs of cashmere goats might cause the lower expression of m6A-circHECA. Conclusion: The m6A-circHECA might play multiple roles in SHF physiology process of cashmere goats through miRNA mediated pathways along with directly or indirectly interaction with its target proteins. The promoter methylation of m6A-circHECA host gene (HECA) most likely was implicated in its expression inhibition in SHFs of cashmere goats.

키워드

과제정보

The authors thank Di Han for help in collecting skin samples from the goats.

참고문헌

  1. Zhu Y, Wang Y, Zhao J, et al. CircRNA-1967 participates in the differentiation of goat SHF-SCs into hair follicle lineage by sponging miR-93-3p to enhance LEF1 expression. Anim Biotechnol 2023;34:482-94. https://doi.org/10.1080/10495398.2021.1975729 
  2. Jiao Q, Wang YR, Zhao JY, Wang ZY, Guo D, Bai WL. Identification and molecular analysis of cashmere goat lncRNAs reveal their integrated regulatory network and potential roles in secondary hair follicle. Anim Biotechnol 2021;32:719-32. https://doi.org/10.1080/10495398.2020.1747477 
  3. 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. https://doi.org/10.1371/journal.pone.0062704 
  4. Geng R, Wang L, Wang X, Chen Y. Cyclic expression of Lhx2 is involved in secondary hair follicle development in cashmere goat. Gene Expr Patterns 2014;16:31-5. https://doi.org/10.1016/j.gep.2014.07.004 
  5. Bai WL, Dang YL, Yin RH, et al. Differential expression of microRNAs and their Regulatory networks in skin tissue of liaoning cashmere goat during hair follicle cycles. Anim Biotechnol 2016;27:104-12. https://doi.org/10.1080/10495398.2015.1105240 
  6. Zhao J, Shen J, Wang Z, et al. CircRNA-0100 positively regulates the differentiation of cashmere goat SHF-SCs into hair follicle lineage via sequestering miR-153-3p to heighten the KLF5 expression. Arch Anim Breed 2022;65:55-67. https://doi.org/10.5194/aab-65-55-2022 
  7. Shirokova V, Biggs LC, Jussila M, Ohyama T, Groves AK, Mikkola ML. Foxi3 deficiency compromises hair follicle stem cell specification and activation. Stem Cells 2016;34:1896-908. https://doi.org/10.1002/stem.2363 
  8. Yin R, Wang Y, Wang Z, et al. Discovery and molecular analysis of conserved circRNAs from cashmere goat reveal their integrated regulatory network and potential roles in secondary hair follicle. Electron J Biotechnol 2019;41:37-47. https://doi.org/10.1016/j.ejbt.2019.06.004 
  9. Yang Y, Fan X, Mao M, et al. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res 2017;27:626-41. https://doi.org/10.1038/cr.2017.31 
  10. Rao X, Lai L, Li X, Wang L, Li A, Yang Q. N6 -methyladenosine modification of circular RNA circ-ARL3 facilitates Hepatitis B virus-associated hepatocellular carcinoma via sponging miR-1305. IUBMB Life 2021;73:408-17. https://doi.org/10.1002/iub.2438 
  11. Hui T, Zhu Y, Shen J, et al. Identification and molecular analysis of m6A-circRNAs from cashmere goat reveal their integrated regulatory network and putative functions in secondary hair follicle during anagen stage. Animals (Basel) 2022;12:694. https://doi.org/10.3390/ani12060694 
  12. Yin R, Yin R, Bai M, et al. N6-Methyladenosine modification (m6A) of circRNA-ZNF638 contributes to the induced activation of SHF stem cells through miR-361-5p/Wnt5a axis in cashmere goats. Anim Biosci 2023;36:555-69. https://doi.org/10.5713/ab.22.0211 
  13. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999;41:95-8. 
  14. Chen Z, Ling K, Zhu Y, Deng L, Li Y, Liang Z. circ0000069 promotes cervical cancer cell proliferation and migration by inhibiting miR-4426. Biochem Biophys Res Commun 2021;551:114-20. https://doi.org/10.1016/j.bbrc.2021.03.020 
  15. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011;27:431-2. https://doi.org/10.1093/bioinformatics/btq675 
  16. Bindea G, Galon J, Mlecnik B. CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics 2013;29:661-3. https://doi.org/10.1093/bioinformatics/btt019 
  17. Muppirala UK, Lewis BA, Dobbs D. Computational tools for investigating RNAprotein interaction partners. J Comput Sci Syst Biol 2013;6:182-7. https://doi.org/10.4172/jcsb.1000115 
  18. Tang D, Chen M, Huang X, et al. SRplot: A free online platform for data visualization and graphing. PLoS One 2023;18:e0294236. https://doi.org/10.1371/journal.pone.0294236 
  19. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-∆∆Ct method. Methods 2001;25:402-8. https://doi.org/10.1006/meth.2001.1262 
  20. Kumaki Y, Oda M, Okano M. QUMA: quantification tool for methylation analysis. Nucleic Acids Res 2008;36:W170-5. https://doi.org/10.1093/nar/gkn294 
  21. Wang S, Chai P, Jia R, Jia R. Novel insights on m6A RNA methylation in tumorigenesis: a double-edged sword. Mol Cancer 2018;17:101. https://doi.org/10.1186/s12943-018-0847-4 
  22. Su R, Fan Y, Qiao X, et al. Transcriptomic analysis reveals critical genes for the hair follicle of Inner Mongolia cashmere goat from catagen to telogen. PLoS One 2018;13:e0204404. https://doi.org/10.1371/journal.pone.0204404 
  23. Sinha T, Panigrahi C, Das D, Chandra Panda A. Circular RNA translation, a path to hidden proteome. Wiley Interdiscip Rev RNA 2022;13:e1685. https://doi.org/10.1002/wrna.1685 
  24. Lin YC, Wang YC, Lee YC, et al. CircVIS: a platform for circRNA visual presentation. BMC Genomics 2022;22:921. https://doi.org/10.1186/s12864-022-08650-1 
  25. 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. https://doi.org/10.1186/1471-2164-14-511 
  26. Geyfman M, Plikus MV, Treffeisen E, Andersen B, Paus R. Resting no more: re-defining telogen, the maintenance stage of the hair growth cycle. Biol Rev Camb Philos Soc 2015;90:1179-96. https://doi.org/10.1111/brv.12151 
  27. Zhang Y, Yu J, Shi C, et al. Lef1 contributes to the differentiation of bulge stem cells by nuclear translocation and cross-talk with the Notch signaling pathway. Int J Med Sci 2013;10:738-46. https://doi.org/10.7150/ijms.5693 
  28. Yu BD, Becker-Hapak M, Snyder EL, Vooijs M, Denicourt C, Dowdy SF. Distinct and nonoverlapping roles for pRB and cyclin D:cyclin-dependent kinases 4/6 activity in melanocyte survival. Proc Natl Acad Sci USA 2003;100:14881-6. https://doi.org/10.1073/pnas.2431391100 
  29. Lay K, Kume T, Fuchs E. FOXC1 maintains the hair follicle stem cell niche and governs stem cell quiescence to preserve long-term tissue-regenerating potential. Proc Natl Acad Sci USA 2016;113:E1506-15. https://doi.org/10.1073/pnas.1601569113 
  30. Kim J, Kim SR, Choi YH, et al. Quercitrin stimulates hair growth with enhanced expression of growth factors via activation of MAPK/CREB signaling pathway. Molecules 2020;25:4004. https://doi.org/10.3390/molecules25174004 
  31. Lu Q, Gao Y, Fan Z, et al. Amphiregulin promotes hair regeneration of skin-derived precursors via the PI3K and MAPK pathways. Cell Prolif 2021;54:e13106. https://doi.org/10.1111/cpr.13106 
  32. Sennett R, Wang Z, Rezza A, et al. An integrated transcriptome atlas of embryonic hair follicle progenitors, their niche, and the developing skin. Dev Cell 2015;34:577-91. https://doi.org/10.1016/j.devcel.2015.06.023 
  33. Kang JI, Choi YK, Han SC, et al. 5-bromo-3,4-dihydroxybenzaldehyde promotes hair growth through activation of Wnt/β-catenin and autophagy pathways and inhibition of TGF-β pathways in dermal papilla cells. Molecules 2022;27:2176. https://doi.org/10.3390/molecules27072176 
  34. Muppirala UK, Honavar VG, Dobbs D. Predicting RNA-protein interactions using only sequence information. BMC Bioinformatics 2011;12:489. https://doi.org/10.1186/1471-2105-12-489 
  35. Chi C, Hou W, Zhang Y, et al. PDHB-AS suppresses cervical cancer progression and cisplatin resistance via inhibition on Wnt/β-catenin pathway. Cell Death Dis 2023;14:90. https://doi.org/10.1038/s41419-022-05547-5 
  36. Shahbazian D, Roux PP, Mieulet V, et al. The mTOR/PI3K and MAPK pathways converge on eIF4B to control its phosphorylation and activity. EMBO J 2006;25:2781-91. https://doi.org/10.1038/sj.emboj.7601166 
  37. Wang G, Wu H, Liang P, He X, Liu D. Fus knockdown inhibits the profibrogenic effect of cardiac fibroblasts induced by angiotensin II through targeting Pax3 thereby regulating TGF-β1/Smad pathway. Bioengineered 2021;12:1415-25. https://doi.org/10.1080/21655979.2021.1918522 
  38. Polycarpou-Schwarz M, Gunderson SI, Kandels-Lewis S, Seraphin B, Mattaj IW. Drosophila SNF/D25 combines the functions of the two snRNP proteins U1A and U2B' that are encoded separately in human, potato, and yeast. RNA 1996;2:11-23 
  39. Luo Y, Lin J, Zhang Y, Dai G, Li A, Liu X. LncRNA PCAT6 predicts poor prognosis in hepatocellular carcinoma and promotes proliferation through the regulation of cell cycle arrest and apoptosis. Cell Biochem Funct 2020;38:895-904. https://doi.org/10.1002/cbf.3510 
  40. Lien WH, Polak L, Lin M, Lay K, Zheng D, Fuchs E. In vivo transcriptional governance of hair follicle stem cells by canonical Wnt regulators. Nat Cell Biol 2014;16:179-90. https://doi.org/10.1038/ncb2903 
  41. Dai Z, Sezin T, Chang Y, Lee EY, Wang EHC, Christiano AM. Induction of T cell exhaustion by JAK1/3 inhibition in the treatment of alopecia areata. Front Immunol 2022;13:955038. https://doi.org/10.3389/fimmu.2022.955038 
  42. Yang X, Han F, Hu X, et al. EIF4A3-induced Circ_0001187 facilitates AML suppression through promoting ubiquitin-proteasomal degradation of METTL3 and decreasing m6A modification level mediated by miR-499a-5p/RNF113A pathway. Biomark Res 2023;11:59. https://doi.org/10.1186/s40364-023-00495-4 
  43. Daugela L, Nusgen N, Walier M, Oldenburg J, Schwaab R, El-Maarri O. Measurements of DNA methylation at seven loci in various tissues of CD1 mice. PLoS One 2012;7:e44585. https://doi.org/10.1371/journal.pone.0044585 
  44. Xu J, Wang Z, Li S, et al. Combinatorial epigenetic regulation of non-coding RNAs has profound effects on oncogenic pathways in breast cancer subtypes. Brief Bioinform 2018;19:52-64. https://doi.org/10.1093/bib/bbw099 
  45. Jakobsen T, Dahl M, Dimopoulos K, Gronbaek K, Kjems J, Kristensen LS. Genome-wide circular RNA expression patterns reflect resistance to immunomodulatory drugs in multiple myeloma cells. Cancers (Basel) 2021;13:365. https://doi.org/10.3390/cancers13030365 
  46. Yang Z, Xu F, Teschendorff AE, et al. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022;9:1067406. https://doi.org/10.3389/fmolb.2022.1067406 
  47. Chen N, Zhao G, Yan X, et al. A novel FLI1 exonic circular RNA promotes metastasis in breast cancer by coordinately regulating TET1 and DNMT1. Genome Biol 2018;19:218. https://doi.org/10.1186/s13059-018-1594-y 
  48. Han W, Yang F, Wu Z, et al. Inner mongolian cashmere goat secondary follicle development regulation research based on mRNA-miRNA Co-analysis. Sci Rep 2020;10:4519. https://doi.org/10.1038/s41598-020-60351-5