Long Non-Coding RNA Expression Profiling of Mouse Testis during Postnatal Development

PLOS ONE, Dec 2019

Mammalian testis development and spermatogenesis play critical roles in male fertility and continuation of a species. Previous research into the molecular mechanisms of testis development and spermatogenesis has largely focused on the role of protein-coding genes and small non-coding RNAs, such as microRNAs and piRNAs. Recently, it has become apparent that large numbers of long (>200 nt) non-coding RNAs (lncRNAs) are transcribed from mammalian genomes and that lncRNAs perform important regulatory functions in various developmental processes. However, the expression of lncRNAs and their biological functions in post-natal testis development remain unknown. In this study, we employed microarray technology to examine lncRNA expression profiles of neonatal (6-day-old) and adult (8-week-old) mouse testes. We found that 8,265 lncRNAs were expressed above background levels during post-natal testis development, of which 3,025 were differentially expressed. Candidate lncRNAs were identified for further characterization by an integrated examination of genomic context, gene ontology (GO) enrichment of their associated protein-coding genes, promoter analysis for epigenetic modification, and evolutionary conservation of elements. Many lncRNAs overlapped or were adjacent to key transcription factors and other genes involved in spermatogenesis, such as Ovol1, Ovol2, Lhx1, Sox3, Sox9, Plzf, c-Kit, Wt1, Sycp2, Prm1 and Prm2. Most differentially expressed lncRNAs exhibited epigenetic modification marks similar to protein-coding genes and tend to be expressed in a tissue-specific manner. In addition, the majority of differentially expressed lncRNAs harbored evolutionary conserved elements. Taken together, our findings represent the first systematic investigation of lncRNA expression in the mammalian testis and provide a solid foundation for further research into the molecular mechanisms of lncRNAs function in mammalian testis development and spermatogenesis.

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Long Non-Coding RNA Expression Profiling of Mouse Testis during Postnatal Development

Citation: Sun J, Lin Y, Wu J ( Long Non-Coding RNA Expression Profiling of Mouse Testis during Postnatal Development Jin Sun 0 Yi Lin 0 Ji Wu 0 Wei Yan, University of Nevada School of Medicine, United States of America 0 1 Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University , Shanghai , China , 2 Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University , Yinchuan, Ningxia , China , 3 The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai , China Mammalian testis development and spermatogenesis play critical roles in male fertility and continuation of a species. Previous research into the molecular mechanisms of testis development and spermatogenesis has largely focused on the role of protein-coding genes and small non-coding RNAs, such as microRNAs and piRNAs. Recently, it has become apparent that large numbers of long (.200 nt) non-coding RNAs (lncRNAs) are transcribed from mammalian genomes and that lncRNAs perform important regulatory functions in various developmental processes. However, the expression of lncRNAs and their biological functions in post-natal testis development remain unknown. In this study, we employed microarray technology to examine lncRNA expression profiles of neonatal (6-day-old) and adult (8-week-old) mouse testes. We found that 8,265 lncRNAs were expressed above background levels during post-natal testis development, of which 3,025 were differentially expressed. Candidate lncRNAs were identified for further characterization by an integrated examination of genomic context, gene ontology (GO) enrichment of their associated protein-coding genes, promoter analysis for epigenetic modification, and evolutionary conservation of elements. Many lncRNAs overlapped or were adjacent to key transcription factors and other genes involved in spermatogenesis, such as Ovol1, Ovol2, Lhx1, Sox3, Sox9, Plzf, c-Kit, Wt1, Sycp2, Prm1 and Prm2. Most differentially expressed lncRNAs exhibited epigenetic modification marks similar to proteincoding genes and tend to be expressed in a tissue-specific manner. In addition, the majority of differentially expressed lncRNAs harbored evolutionary conserved elements. Taken together, our findings represent the first systematic investigation of lncRNA expression in the mammalian testis and provide a solid foundation for further research into the molecular mechanisms of lncRNAs function in mammalian testis development and spermatogenesis. - Funding: This work was supported by National Basic Research Program of China (grant numbers 2013CB967401 and 2010CB945001; http://www.most.gov.cn) and the National Nature Science Foundation of China (grant number 81121001; http://www.nsfc.gov.cn). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. The mammalian testis is the site of spermatogenesis and testosterone production, so it plays a central role in the male reproductive system. Spermatogenesis is the primary biological process in the testis and produces mature haploid spermatozoa from diploid spermatogonia. This developmental process is complicated, and involves a series of cellular differentiation and cell biological events, including spermatogonial proliferation, meiosis of spermatocytes and morphological changes of round spermatids [1,2]. Elucidation of the molecular mechanisms underlying spermatogenesis is important for our understanding of the genetic regulation of normal male germ cell development. Importantly, this understanding can also direct strategies for clinical diagnosis and therapy of male infertility. Therefore, investigations into the molecular mechanisms of testis development and spermatogenesis are prominent in the field of reproductive biology. To date, these investigations have largely focused on the role of protein-coding genes and small non-coding RNAs, including microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs). The unprecedented advances in high-throughput technologies, such as microarray screening and transcriptome sequencing, have delivered significant advances in the exploration of testis development and spermatogenesis. So far, gene expression profiling, proteome profiling, miRNA profiling, piRNA profiling during testis development or spermatogenesis in mouse have been investigated [37]. Long non-coding RNAs (lncRNAs) represent a novel class of regulatory molecule, which are arbitrarily defined as transcripts of more than 200 nucleotides (nt) in length that lack significant open reading frames [8]. Advances in genome-wide analyses of the mammalian transcriptome have revealed lncRNAs as a major class of transcript, that is pervasively transcribed [9]. Most lncRNA (...truncated)


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Jin Sun, Yi Lin, Ji Wu. Long Non-Coding RNA Expression Profiling of Mouse Testis during Postnatal Development, PLOS ONE, 2013, Volume 8, Issue 10, DOI: 10.1371/journal.pone.0075750