Analysis of differential expression of hair follicle tissue transcriptome in Hetian sheep undergoing different periodic changes.

Background: This study provides new information on long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in the hair follicles of Hetian sheep the sequencing and analysis of the transcriptome of skin hair follicles during three periods of periodicity change. This is important for improving the quality of carpet wool, providing a preliminary basis for further research on the targeting relationship of these mRNAs and their target genes, and providing a scientific basis for marker-assisted selection of Hetian sheep.

Methods: The periodic variation of anagen (P I, May,  = 3), catagen (p II, October,  = 3), and telogen (p III, January,  = 3) of the skin hair follicle tissue of three Hetian sheep ewes were selected. Skin samples were collected from the right mid-side of each sampled sheep at three hair follicle developmental stages. The three sheep were used for each developmental stage as biological and technical replicates for transcriptome sequencing and analysis.

Results: The statistical power of this experimental design, calculated in RNASeqPower, was 0.92. Differential expression analysis revealed 81 lncRNAs that were differentially expressed (46 up-regulated and 35 down-regulated) and 129 mRNAs that were differentially expressed (46 up-regulated and 83 down-regulated) during the PI and PII periods. Between the PI and PIII periods, a total of 144 differentially expressed lncRNAs and 693 differentially expressed mRNAs were identified. Of these, 73 lncRNAs were significantly up-regulated and 71 were significantly down-regulated, while 474 mRNAs were significantly up-regulated and 219 were down-regulated. Additionally, a total of 87 lncRNAs were found to be differentially expressed, with 40 up-regulated and 47 down-regulated, along with 39 differentially expressed mRNAs (23 up-regulated and 16 down-regulated), between the PII and PIII stages. The functional assessment revealed that the mRNA expressed in the cells is related to the membrane, cell processes, metabolism, extracellular region, and other GO items. It is enriched in thyroid hormone synthesis, choline metabolism, cancer, AMPK, Hedgehog, and other signaling pathways.

Conclusion: A total of 2,286 lncRNAs (including 965 known and 1,321 novel lncRNAs) and 20,879 mRNAs were identified. These co-expressed differentially expressed genes could be used as candidate genes for studying the periodic changes of the hair follicles in Hetian sheep.