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. 2022 Dec 8;23(1):813.
doi: 10.1186/s12864-022-09003-8.

Construction of transcriptome atlas of white yak hair follicle during anagen and catagen using single-cell RNA sequencing

Qingbo Zheng  1   2   3 , Na Ye  1   2   3 , Pengjia Bao  1   2 , Xiaolan Zhang  1   2 , Fubin Wang  1   2   3 , Lanhua Ma  1   2   3 , Min Chu  1   2 , Xian Guo  1   2 , Chunnian Liang  1   2 , Heping Pan  4 , Ping Yan  5   6
Affiliations

Construction of transcriptome atlas of white yak hair follicle during anagen and catagen using single-cell RNA sequencing

Qingbo Zheng et al. BMC Genomics. .

Erratum in

Abstract

Background: As the direct organ of villus, hair follicles have obvious seasonal cycles. The hair follicle cycle is orchestrated by multiple cell types that together direct cell renewal and differentiation. But the regulation property of hair follicle cells from anagen to catagen in yak is still unknown.

Results: In this study, single-cell RNA sequencing was performed on 24,124 single cells of the scapular skin from white yak. Based on tSNE cluster analysis, the cell types of IFE-DC, epidermal cell lines, fibroblasts, keratinocytes, IRS, DS, INFU, and other cells in yak hair follicles during anagen and catagen were successfully identified, and the gene expression profiles were described. The GO enrichment analysis indicated the different cells characteristic genes to be mainly enriched in the epidermal development, epithelial cell differentiation and wound healing pathways. The pseudotime trajectory analysis described the differentiation trajectory of the epidermal lineage and dermal lineage of the hair follicle during anagen and catagen. Moreover, the dynamic changes of the genes like LHX2, KRT25, and KRT71 were found to be highly expressed in HS and IRS, but not in the IFE-DC, INFU, and keratinocyte during differentiation.

Conclusions: Our results analyzed the time-varying process of gene expression in the dermal cell lineage and epidermal cell lineage of hair follicles during anagen and catagen during fate differentiation was expounded at the single cell level, revealing the law of fate specialization of different types of cells. In addition, based on the enrichment analysis, the transcriptional regulatory factors involved in the different cell fates were also revealed. These results will help to enhance our understanding of yak hair follicle cycle and promote the development and utilization of yak villus.

Keywords: Anagen; Catagen; Hair follicle; Yak; scRNA-seq.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
High-variable gene analysis and cell heterogeneity identification of the hair follicle during anagen and catagen. a scRNA-seq process; b Gene dispersion distribution map; c Characterization of the major cell types in the tSNE; d Main cell type proportion during anagen and catagen; e Comparison of the differential genes in the different cell groups; f Expression of the different cell markers in all the cells
Fig. 2
Fig. 2
Enrichment analysis of multiple cell clusters. a Analysis of the different IFE-DC clusters enriched GO terms; b Analysis of the epidermal cell lineage enriched GO terms; c Analysis of different the fibroblasts clusters enriched GO terms; d GO enrichment network diagram of the different cell types; e Gene overlap among the different cell types
Fig. 3
Fig. 3
Enrichment analysis of some cell types. a The GO enrichment analysis of the HS characteristic genes; b GO enrichment analysis of the INFU characteristic genes; c GO enrichment analysis of the keratinocyte characteristic genes; d GO enrichment analysis of the DS characteristic genes
Fig. 4
Fig. 4
Construction of the pseudotime trajectory of epidermal cell lineage and IFE-DC heterogeneity analysis. a Construction of pseudotime trajectories of the epidermal cell lineages during anagen and anagen of yak hair follicles; b Gene expression dynamics during IFE-DC specialization; c GO analysis of differential genes in the process of IFE-DC specialization; d Expression of characteristic genes in different stages of IFE-DC; e Interaction analysis of the characteristic genes; f Immunofluorescence analysis of skin tissue
Fig. 5
Fig. 5
Dynamic changes in the gene expression during the specialization of keratinocyte, HS, and IRS. a Expression of the keratinocyte characteristic genes in pseudotime trajectory; b Expression of the characteristic genes in different stages of keratinocyte; c Gene expression during keratinocyte specialization; d Enrichment analysis of differential genes in keratinocyte cell specialization; e Gene expression during the specialization of HS and IRS; f GO enrichment analysis of the characteristic genes in the process of HS and IRS specialization; g Immunofluorescence analysis of the hair follicles; h Interaction analysis of characteristic genes in the specialization of HS and IRS
Fig. 6
Fig. 6
Dynamic changes in the gene expression during specialization of hair follicle fibroblasts and DS. a Construction of the pseudotime differentiation trajectory between the fibroblasts and DS; b Gene expression during fibroblast specialization; c Expression of the characteristic genes in different stages of fibroblast; d GO enrichment analysis of fibroblast characteristic genes; e Gene expression during DS specialization; f GO enrichment analysis of the characteristic genes in DS; g Interaction analysis of the characteristic genes in DS; h Immunofluorescence analysis of the hair follicles
Fig. 7
Fig. 7
Analysis of the immunohistochemistry of the key protein of yak hair follicles
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