title: Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells.
abstract: Among all tissues of the metazoa, the transcritpome of testis displays the highest diversity and specificity. However, its composition and dynamics during spermatogenesis have not been fully understood. Here, we have identified 20,639 message RNAs (mRNAs), 7,168 long non-coding RNAs (lncRNAs) and 15,101 circular RNAs (circRNAs) in mouse spermatogenic cells, and found many of them were specifically expressed in testes. lncRNAs are significantly more testis-specific than mRNAs. At all stages, mRNAs are generally more abundant than lncRNAs, and linear transcripts are more abundant than circRNAs. We showed that the productions of circRNAs and piRNAs were highly regulated instead of random processes. Based on the results of a small-scale functional screening experiment using cultured mouse spermatogonial stem cells, many evolutionarily conserved lncRNAs are likely to play roles in spermatogenesis. Typical classes of transcription factor binding sites are enriched in the promoters of testis-specific m/lncRNA genes. Target genes of CREM and RFX2, 2 key TFs for spermatogenesis, were further validated by using ChIP-chip assays and RNA-seq on RFX2-knockout spermatogenic cells. Our results contribute to the current understanding of the transcriptomic complexity of spermatogenic cells and provide a valuable resource from which many candidate genes may be selected for further functional studies.
authors: a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.
authors: Xiwen
authors: X
authors: Lin
authors: b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China.
authors: Miao
authors: M
authors: Han
authors: c Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai , China.
authors: Lu
authors: L
authors: Cheng
authors: a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.|d Graduate University of Chinese Academy of Sciences , Beijing , China.
authors: Jian
authors: J
authors: Chen
authors: a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.|d Graduate University of Chinese Academy of Sciences , Beijing , China.
authors: Zhuqiang
authors: Z
authors: Zhang
authors: b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China.
authors: Ting
authors: T
authors: Shen
authors: a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.
authors: Min
authors: M
authors: Wang
authors: b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China.|c Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai , China.
authors: Bo
authors: B
authors: Wen
authors: b State Key Laboratory of Genetic Engineering & Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University , Shanghai , China.
authors: Ting
authors: T
authors: Ni
authors: a State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China.
authors: Chunsheng
authors: C
authors: Han
keywords: circRNAs; expression; lncRNAs; mRNAs; spermatogenesis; testis; transcription