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. 2022 Mar 28;13(4):606.
doi: 10.3390/genes13040606.

Transcriptome Analysis Revealed Long Non-Coding RNAs Associated with mRNAs in Sheep Thyroid Gland under Different Photoperiods

Wei Wang  1 , Xiaoyun He  1 , Ran Di  1 , Xiangyu Wang  1 , Mingxing Chu  1
Affiliations

Transcriptome Analysis Revealed Long Non-Coding RNAs Associated with mRNAs in Sheep Thyroid Gland under Different Photoperiods

Wei Wang et al. Genes (Basel). .

Abstract

The thyroid gland is a vital endocrine organ involved in the reproduction of animals via the regulation of hormone synthesis and secretion. LncRNAs have been proven to play important roles in reproductive regulation; however, the associated mechanism in the thyroid gland has not been clarified. In this study, we investigated to identify photoperiod-induced lncRNAs and mRNAs in the thyroid gland in Sunite ewes by comparing the expression profiles of short photoperiod (SP) and long photoperiods (LP). A total of 41,088 lncRNAs were identified in the thyroid gland through RNA-Seq. Functional analysis of differentially expressed lncRNAs using the R package revealed that reproductive hormone- and photoperiod response-related pathways, including the prolactin signaling, cAMP signaling, and circadian rhythm pathways, were significantly enriched. An mRNA-lncRNA interaction analysis suggested that the lncRNA LOC1056153S88 trans targets ARG2 and CCNB3, and the lncRNA LOC105607004 trans targets DMXL2, both of these might be involved in seasonal sheep breeding reproduction. Together, these results will provide resources for further studies on seasonal reproduction in sheep.

Keywords: lncRNA; mRNA; photoperiod; sheep; thyroid gland.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Identification of lncRNAs and mRNAs in the ewes thyroid gland. (A) Venn shows the common and unique number of novel lncRNAs by four methods, including CNCI, CPC, PFAM, and CPAT. (B) The expression level of lncRNAs and mRNAs. (C) FPKM distribution of each sample. (D) The length statistics of lncRNA and mRNA. (E) The statistics of lncRNA and mRNA exon number.
Figure 2
Figure 2
Analysis of differentially expressed transcripts. (A) Differentially expressed transcripts were assessed based on a volcano map of the DE-lncRNAs in SP42 and LP42. (B) Differentially expressed transcripts were assessed based on a volcano map of the DE-lncRNAs in SP42 and SPLP42. (C) Differentially expressed transcripts were assessed based on a volcano map of the DE-lncRNAs in LP42 and SPLP42. (D) Differentially expressed transcripts were assessed based on a volcano map of the DE-mRNAs in SP42 and LP42. (E) Differentially expressed transcripts were assessed based on a volcano map of the DE-mRNAs in SP42 and SPLP42. (F) Differentially expressed transcripts were assessed based on a volcano map of the DE-mRNAs in LP42 and SPLP42. Blue and red represent up-regulated and down-regulated transcripts, respectively (Table S2).
Figure 3
Figure 3
An analysis of GO and KEGG enrichment in the thyroid gland was performed. (A) An analysis of GO function of DE-mRNAs in SP42 and LP42. (B) Ten major KEGG enrichment pathways of DE-mRNAs were observed between SP42 and LP42. (C) An analysis of GO function of DE-mRNAs in SP42 and SPLP42. (D) Ten major KEGG enrichment pathways of DE-mRNAs were observed betweenSP42 and SPLP42.
Figure 4
Figure 4
An analysis of GO and KEGG enrichment in the thyroid gland was performed. (A) Analysis of GO function of DE-mRNAs in LP42 and SPLP42. (B) Ten major KEGG enrichment pathways of DE-mRNAs were observed between LP42 and SPLP42. (C) Analysis of GO function of DE-lncRNAs in SP42 and LP42. (D) Ten major KEGG enrichment pathways of DE-lncRNAs were observed between SP42 and LP42.
Figure 5
Figure 5
An analysis of GO and KEGG enrichment in the thyroid gland was performed. (A) Analysis of GO function of DE-lncRNAs in SP42 and SPLP42. (B) Ten major KEGG enrichment pathways of DE-lncRNAs were observed between SP42 and SPLP42. (C) Analysis of GO function of DE-lncRNAs in LP42 and SPLP42. (D) Ten major KEGG enrichment pathways of DE-lncRNAs were observed between LP42 and SPLP42.
Figure 6
Figure 6
The interaction networks were identified for lncRNAs and their corresponding target genes. (A) The networks for SP42 and LP42; (B) the networks for SP42 and SPLP42; (C) the networks for LP42 and SPLP42. Blue and purple represent up and downregulation, respectively. Triangle and Ellipse represent mRNAs and lncRNAs, respectively.
Figure 7
Figure 7
Validation of RNA sequencing (RNA-seq) data using RT-qPCR. (A) RNA-Seq and RT-qPCR results of three selected differentially expressed lncRNAs in the thyroid gland of Sunite sheep at different photoperiods. (B) RNA-Seq and RT-qPCR results of three selected differentially expressed mRNAs in the thyroid gland of Sunite sheep at different photoperiods.
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