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Ran M.,Hunan University | Ran M.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | Chen B.,Hunan University | Chen B.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | And 9 more authors.
Biology of Reproduction | Year: 2016

Thousands of long noncoding RNAs (lncRNAs) have been identified in mouse, rat, and human testes, some of which play important roles in testis development and spermatogenesis. However, systematic analysis of lncRNAs expressed in postnatal pig testes has not been reported. Thus, in this study, we present the expression and characterization of lncRNAs in immature (30-day-old [D30]) and mature (180-day-old [D180]) pig testes. A total of 90 440 168 (85.75%) and 97 001 700 (95.35%) 150-base-pair paired-end clean reads were generated in D30 and D180 cDNA libraries, respectively, using the Illumina HiSeq 4000 platform; 36 727 transcripts were assembled in those two libraries, 777 lncRNA transcripts from 752 lncRNA gene loci were identified using the highly stringent pipeline, and 101 of those lncRNA transcripts were significantly differentially expressed. Those lncRNAs shared some characteristics with other mammals, including fewer exons, shorter length and exon length, and lower expression level compared with those of protein-coding genes; 402 protein-coding genes (<10 kb) were found as nearest neighbors of 294 out of 752 lncRNA genes, and gene ontology enrichment showed that they were enriched in transcription- and development-related processes. Fifteen differentially expressed and 10 novel lncRNAs were randomly selected and validated by quantitative polymerase chain reaction (PCR) and reverse transcriptase PCR. In addition, one of the 10 novel lncRNAs was further confirmed using RACE clone technology. This study provides a catalog of porcine testes lncRNAs for further understanding their regulation roles in pig testis development and spermatogenesis. © 2016 by the Society for the Study of Reproduction, Inc.


Ran M.,Hunan University | Ran M.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | Chen B.,Hunan University | Chen B.,Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal | And 12 more authors.
RSC Advances | Year: 2015

To understand the complex physiological process underlying pig testis development and spermatogenesis, this study aims to characterize the change in miRNA and mRNA profiles at four developmental stages of embryonic and postnatal testes, including 60 dpc (days post coitus, E60), 90 dpc (E90), 30-day-old (D30) and 180-day-old (D180). A total of 304 mature, 50 novel miRNAs, and 8343 differentially-expressed genes were identified. 93 (48 up and 45 down), 104 (49 up and 55 down), 122 (49 up and 73 down) differentially-expressed miRNAs, as well as 1007 (646 up and 361 down), 1929 (911 up and 1018 down), 7420 (3998 up and 3422 down) differentially-expressed genes were identified in E90 vs. E60, D30 vs. E90 and D180 vs. D30, respectively. Integrating analysis of miRNA and mRNA expression profiles predicted more than 5000 miRNA-mRNA interaction sites. GO and KEGG pathway analysis of the predicted target genes illustrated the likely roles of differentially expressed miRNAs in testis development and spermatogenesis. For example, PI3K-Akt signaling pathway and Hippo signaling pathway related development, and carbon metabolism, fatty acid metabolism, protein digestion and absorption, were involved in metabolite synthesis. These integrated high-throughput expression data show that miRNA is a critical factor in porcine testis development, providing a useful resource to understand global genome expression change in porcine testis development and spermatogenesis. © 2015 The Royal Society of Chemistry.

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