Integrative and comparative analysis of whole-transcriptome sequencing in circCOL1A1-knockdown and circCOL1A1-overexpressing goat hair follicle stem cells

Abstract

Objective: Hair morphogenesis is tightly related to hair follicle stem cells (HFSCs) proliferation and hair follicle (HF) development. Yangtze River Delta white goats (YRDWG) HFSCs are important for producing superior-quality brush hair (SQBH). Nonetheless, the known regulatory mechanisms are not sufficient to explain YRDWG gHFSCs growth, HF development, and SQBH formation. Methods: To deeply investigate the interaction networks and mechanisms of circCOL1A1 in the HF development and SQBH formation of YRDWG in detail, we applied wholetranscriptome sequencing and bioinformatics analysis of circCOL1A1-knockdown and circCOL1A1-overexpressing HFSCs from YRDWG. STRING and other databases were used to construct multiple interaction networks. Differentially expressed (DE) genes, DEmiRNAs, and DE-circRNAs were further confirmed via real-time quantitative polymerase chain reaction and Sanger sequencing. Results: A total of 87 genes, 96 miRNAs, and 135 circRNAs were DE between circCOL1A1-knockdown and circCOL1A1-overexpressing gHFSCs. Functional enrichment, gene ontology annotation and Kyoto encyclopedia of genes and genomes analyses identified marked enrichment of these DE- genes, DE-miRNAs, and DE-circRNAs in the MAPK, PI3K/Akt, and focal adhesion signaling pathways, which are closely associated with gHFSCs growth and HF development. In addition, through interaction network construction, four important regulatory axes were obtained, namely, the chi-circCOL1A1- miR-149-5p-CMTM3-AR, chi-circACTN1- miR-671-5p-MAPK3/COL13A1, chi-circITGA6-miR-18a-5p-FGF1/MAP3K1 and chi-circ COBLL1-miR-30a-5p/miR-128-3pITGA6/MAPK14/FGF14 axes. Conclusion: These novel findings provide a valuable and comprehensive basis for investigating the complex mechanism by which circRNAs participate in and regulate HF development and SQBH formation in YRDWG.