Exploring Differentially Expressed Genes and Natural Antisense Transcripts in Sheep (Ovis aries) Skin with Different Wool Fiber Diameters by Digital Gene Expression Profiling

Abstract

Wool fiber diameter (WFD) is the most important economic trait of wool. However, the genes specifically controlling WFD remain elusive. In this study, the expression profiles of skin from two groups of Gansu Alpine merino sheep with different WFD (a super-fine wool group [FD = 18.0 ± 0.5 μm, n= 3] and a fine wool group [FD=23.0±0.5μm, n=3]) were analyzed using next-generation sequencing–based digital gene expression profiling. A total of 40 significant differentially expressed genes (DEGs) were detected, including 9 up-regulated genes and 31 down-regulated genes. Further expression profile analysis of natural antisense transcripts (NATs) showed that more than 30% of the genes presented in sheep skin expression profiles had NATs. A total of 7 NATs with significant differential expression were detected, and all were down-regulated. Among of 40 DEGs, 3 DEGs (AQP8, Bos d2, and SPRR) had significant NATs which were all significantly down-regulated in the super-fine wool group. In total of DEGs and NATs were summarized as 3 main GO categories and 38 subcategories. Among the molecular functions, cellular components and biological processes categories, binding, cell part and metabolic process were the most dominant subcategories, respectively. However, no significant enrichment of GO terms was found (corrected P-value >0.05). The pathways that were significantly enriched with significant DEGs and NATs were mainly the lipoic acid metabolism, bile secretion, salivary secretion and ribosome and phenylalanine metabolism pathways (P < 0.05). The results indicated that expression of NATs and gene transcripts were correlated, suggesting a role in gene regulation. The discovery of these DEGs and NATs could facilitate enhanced selection for super-fine wool sheep through gene-assisted selection or targeted gene manipulation in the future.

Molecular and Cellular Mechanisms of Apoptosis during Dissociated Spermatogenesis

“…Recently, the NGS-based RNA-Seq approach has been widely employed for the identification and profiling of apoptosis-related genes in many species (Deng et al, 2014; Liu et al, 2015; Yue et al, 2015). In this study, using RNA-Seq technology, many DEGs involved in apoptosis regulation were identified and characterized at the different stages of spermatogenesis in P. sinensis .…”

Integrated Analysis of the Roles of Long Noncoding RNA and Coding RNA Expression in Sheep (Ovis aries) Skin during Initiation of Secondary Hair Follicle

“…Although the precise nature of the epidermal placode-inducing “first dermal message” remains poorly understood, several studies have suggested that HF initiation is an orchestrated interaction between mesenchymal and epithelial cells mediated through the secretion of stimulator and inhibitor signaling molecules, such as Wnt / β-catenin , EDA / EDAR / NF-κB , Noggin / Lef-1 , Shh , BMP-2 / 4 / 7 and FGF [ 9 , 14 ]. Recent studies looking beyond protein-coding genes have shown that non-coding RNA (ncRNA), such as microRNA(miRNA),natural antisense transcripts (NAT) and long non-coding RNA (lncRNA), can show higher specificity as biomarkers for some applications than protein coding genes [ 15 – 19 ]. Among these ncRNAs, lncRNAs are not only large in quantity but also play important roles in gene expression regulation in organisms [ 20 – 22 ].…”

Avustralya Merinosu ve Çin Merinosu Hibritlerinde Yün Miktarı İle Mikrosatellit Arasındaki İlişkinin Araştırılması

“…The phenotypic mean of microsatellites was analyzed by the generalized linear model (GLM) of SAS (V6.12) software, and multiple comparisons between genotypes were performed using the least significant difference method (LSD) [26] .…”