Transcriptome profiling of the murine testis during the first wave of spermatogenesis.
Transcriptome profiling of the murine testis during the first wave of spermatogenesis.
复制标题
DOI：
10.1371/journal.pone.0061558
复制
发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Sironen A
中科院分区：
文献类型：
--
作者：
Laiho A;Kotaja N;Gyenesei A;Sironen A
正确的基因表达模式构成了男性生殖细胞分化和男性生育能力的基础。尽管之前的研究已经阐明了睾丸特异性基因表达的重要性，但确切的转录本和全面的基因表达模式仍然未知。大规模测序技术使得基因表达和异构体研究的成本有效的分析成为可能。使用 SOLiD 4 下一代测序平台，我们研究了小鼠精子发生第一波期间五个不同时间点的基因表达模式。我们的结果强调了精子发生相关生物过程和相关细胞成分的上调。阐明精子发育过程中重要时间点的差异基因表达强调了生物过程中基因表达正确时机的重要性。使用 R/Bioconductor 的 Limma 软件包分析差异基因水平表达，并使用 Cufflinks 管道进行亚型分析。在基因水平上，总共鉴定了 2494 个差异表达基因，Cufflinks 表征了超过 160,000 个基因亚型，其中 29% 是分配给已知基因的新转录本。 57% 的表达基因被检测到同工型，睾丸中总共表达了超过 26,000 个基因。差异启动子和转录起始位点的使用似乎也在精子发生过程中基因表达的调节中发挥作用。此外，我们在第一波精子发生过程中发现了 947 个上调的长非编码 RNA。这些 RNA 似乎对不同时间点具有高度特异性。由于存在大量表达基因和已鉴定的亚型，因此睾丸组织样本的转录组分析具有很高的信息量。我们的研究为研究基因亚型和调控以及影响男性生育力的因素提供了非常有价值的基础。
Correct gene expression patterns form the basis for male germ cell differentiation and male fertility. Although previous studies have elucidated the importance of testis specific gene expression, the exact transcripts and comprehensive gene expression patterns remain unknown. Large scale sequencing techniques have enabled cost effective analysis of gene expression and isoform studies. Using the SOLiD 4 next-generation sequencing platform we have investigated the gene expression patterns at five different time points during the first wave on murine spermatogenesis. Our results highlight the upregulation of spermatogenesis related biological processes and associated cellular components. Elucidation of differential gene expression at important time points during the sperm development emphasizes the importance of correct timing of gene expression within biological processes. Differential gene level expression was analyzed with R/Bioconductor’s Limma package and isoform analysis was conducted with the Cufflinks pipeline. At gene level total of 2494 differentially expressed genes were identified and Cufflinks characterized over 160 000 gene isoforms, of which 29% were novel transcripts assigned to known genes. Isoforms were detected for 57% of expressed genes and in a total over 26 000 genes were expressed in the testis. Differential promoter and transcription start site usage appears also to play a role in regulation of gene expression during spermatogenesis. Furthermore, we identified 947 upregulated long non-coding RNAs during the first wave of spermatogenesis. These RNAs appeared to be highly specific to different time points. Transcriptomic analysis of testis tissue samples is highly informative due to the large number of expressed genes and identified isoforms. Our study provides a very valuable basis for investigation of gene isoforms and regulation and factors contributing to male fertility.
登录
查看更多内容
影响因子：
4.3
作者：
Eden E;Lipson D;Yogev S;Yakhini Z
通讯作者：
Yakhini Z
DOI：
10.1073/pnas.1635054100
发表时间：
2003-10-14
影响因子：
11.1
作者：
Schultz, N;Hamra, FK;Garbers, DL
通讯作者：
Garbers, DL
影响因子：
3.3
作者：
Schlecht, U;Demougin, P;Primig, M
通讯作者：
Primig, M
DOI：
10.1007/978-1-61779-436-0_7
发表时间：
2012-01-01
期刊：
GERMLINE DEVELOPMENT: METHODS AND PROTOCOLS
影响因子：
--
作者：
Lee, Tin-Lap;Rennert, Owen M.;Chan, Wai-Yee
通讯作者：
Chan, Wai-Yee
影响因子：
3
作者：
Eden, Eran;Navon, Roy;Yakhini, Zohar
通讯作者：
Yakhini, Zohar