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. 2018 Jun 26;19(1):495.
doi: 10.1186/s12864-018-4864-x.

Genome-wide Discovery of lincRNAs With Spatiotemporal Expression Patterns in the Skin of Goat During the Cashmere Growth Cycle

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Free PMC article

Genome-wide Discovery of lincRNAs With Spatiotemporal Expression Patterns in the Skin of Goat During the Cashmere Growth Cycle

Shen Song et al. BMC Genomics. .
Free PMC article

Abstract

Background: Long intergenic noncoding RNAs (lincRNAs) have been recognized in recent years as key regulators of biological processes. However, lincRNAs in goat remain poorly characterized both across various tissues and during different developmental stages in goat (Capra hircus).

Results: We performed the genome-wide discovery of the lincRNAs in goat by combining the RNA-seq dataset that were generated from 28 cashmere goat skin samples and the 12 datasets of goat tissues downloaded from the NCBI database. We identified a total of 5546 potential lincRNA transcripts that overlapped 3641 lincRNA genes. These lincRNAs exhibited a tissue-specific pattern. Specifically, there are 584 lincRNAs expressed exclusively in only one tissue, and 91 were highly expressed in hair follicle (HF). In addition, 2350 protein-coding genes and 492 lincRNAs were differentially expressed in the skin of goat. The majority exhibited the remarkable differential expression during the transition of the goat skin from the May-June to August-October time point, which covered the different seasons. Fundamental biological processes, such as skin development, were significantly enriched in these genes. Furthermore, we identified several lincRNAs highly expressed in the HF, which exhibited not only the co-expression pattern with the key factors to the HF development but also the activated expression in the August to October time point. Intriguingly, one of spatiotemporal lincRNAs, linc-chig1598 could be a potential regulator of distal-less homeobox 3 expression during the secondary hair follicle growth.

Conclusions: This study will facilitate future studies aimed at unravelling the function of lincRNAs in hair follicle development.

Keywords: Cashmere growth cycle; Goat skin; Hair follicle; Transcriptome; lincRNA.

Conflict of interest statement

Ethics approval

The experimental cashmere goats were from the Inner Mongolia White Cashmere Goat Farm, located in Inner Mongolia Autonomous Region of China (latitude 38°23’N, longitude 108°07′E, altitude 1378 m) and were raised by feeding practices according to the Cashmere goat standard. All experimental procedures in this study were approved by and performed according to the guidelines for the care and use of experimental animals that have been established by the Animal Care and Use Committee of the Ministry of Agriculture of the People’s Republic of China.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Genomic structure characteristics of lincRNAs compared to protein-coding genes. a. Distribution of exon number for predicted lincRNAs and protein-coding genes. b. Distribution of the number of transcripts in the predicted lincRNAs and protein-coding genes. c. Distribution of the transcript lengths of the predicted lincRNAs and protein-coding genes
Fig. 2
Fig. 2
Tissue-wide distributions and expression level of lincRNAs. a. Heatmap of 5546 lincRNAs across 10 tissues. Each row represents the expression levels of all detected lincRNAs, and each column contains all expressed transcripts. We transformed the FPKM values into the log2 (FPKM+ 1) values and then calculated the Z-score for every log 2 (FPKM+ 1) value within each tissue. b. Histograms indicating the number of tissue-specific lincRNAs in each tissue. c. Expression level indicated by log10 (FPKM+ 1) in lincRNAs and protein-coding genes in each tissue
Fig. 3
Fig. 3
PCA of all expressed genes and lincRNAs. PCA based on all genes: all differentially expressed genes (a) and PCA based on the lincRNAs: differentially expressed lincRNAs (b). Blue dots represent May and June, whereas red dots represent Aug, Sep, and Oct
Fig. 4
Fig. 4
Hierarchical clustering of all differentially expressed genes (a) and lincRNAs (b). We transformed the RPKM values into the log10 (FPKM+ 1) values and then calculated the Z-score for every log10 (FPKM+ 1) value within each tissue. The five main clusters (K1-K5) are presented on the left panel a
Fig. 5
Fig. 5
Expression patterns of the differentially expressed genes (including protein-coding genes and lincRNAs) in the five main clusters (K1-K5) corresponding to the Fig. 4a and the significantly enriched GO terms in different clusters

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