Project description:Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genomewide investigations of transcriptome complexities in major mammalian organs and their underlying cellular sources, transcriptional mechanisms, and functional relevance have been scarce. Here we first show, using extensive RNAseq data, that transcription of both functional and nonfunctional genomic elements is substantially more widespread in the testis than in other organs across representative mammals. By scrutinizing the transcriptomes of all main testicular cell types in the mouse, we then reveal that meiotic spermatocytes and especially postmeiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein coding genes and long noncoding RNA genes but also poorly conserved intergenic sequences, suggesting that much of it is not of immediate functional relevance. Rather, our analyses of genomewide epigenetic data show that this prevalent transcription, which apparently promoted the birth of new genes during evolution, results from a highly permissive chromatin state during and after meiosis that may ultimately facilitate the replacement of histones by protamines during late spermatogenesis. To study the cellular source and mechanisms of high transcriptome complexity in the mammalian testis, we generated strand-specific deep coverage RNASeq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa as well as for brain, liver and the whole testis from the mouse. We prepared 8 sequencing libraries for the polyadenylated RNA fraction of each sample and sequenced each library in 3 lanes of the Illumina Genome Analyser IIx platform, yielding a total of >60 millions strand-specific reads of 76 base pairs per sample. In addition, we generated ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids. RNA-seq, ChIP-seq and RRBS data were generated from the same individual or pool of individuals, in the case of purified cells. RNASeq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa

Project description:Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome‐wide investigations of transcriptome complexities in major mammalian organs and their underlying cellular sources, transcriptional mechanisms, and functional relevance have been scarce. Here we first show, using extensive RNA‐seq data, that transcription of both functional and nonfunctional genomic elements is substantially more widespread in the testis than in other organs across representative mammals. By scrutinizing the transcriptomes of all main testicular cell types in the mouse, we then reveal that meiotic spermatocytes and especially post‐meiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein‐coding genes and long noncoding RNA genes but also poorly conserved intergenic sequences, suggesting that much of it is not of immediate functional relevance. Rather, our analyses of genome‐wide epigenetic data show that this prevalent transcription, which apparently promoted the birth of new genes during evolution, results from a highly permissive chromatin state during and after meiosis that may ultimately facilitate the replacement of histones by protamines during late spermatogenesis. To study the cellular source and mechanisms of high transcriptome complexity in the mammalian testis, we generated strand-specific deep coverage RNA‐Seq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa as well as for brain, liver and the whole testis from the mouse. We prepared 8 sequencing libraries for the polyadenylated RNA fraction of each sample and sequenced each library in 3 lanes of the Illumina Genome Analyser IIx platform, yielding a total of >60 millions strand-specific reads of 76 base pairs per sample. In addition, we generated ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids. RNA-seq, ChIP-seq and RRBS data were generated from the same individual or pool of individuals, in the case of purified cells. ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids

Project description:Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. We identify ~11,000 primate- specific lncRNA families, which show evidence for selective constraint during recent evolution, and ~2,400 highly conserved lncRNAs (including ~400 genes that likely originated more than 300 million years ago). We find that lncRNAs, in particular ancient ones, are generally actively regulated and may predominantly function in embryonic development. lncRNA X-inactivation patterns reveal an extremely female-biased monotreme-specific lncRNA, which may partially compensate X-dosage in this lineage. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but global patterns like tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network, which surprisingly contains many lncRNA hubs, suggests potential functions for lncRNAs in fundamental processes like spermatogenesis or synaptic transmission, but also in more specific mechanisms such as placenta growth suppression through miRNA production. [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis.

Project description:Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome‐wide investigations of transcriptome complexities in major mammalian organs and their underlying cellular sources, transcriptional mechanisms, and functional relevance have been scarce. Here we first show, using extensive RNA‐seq data, that transcription of both functional and nonfunctional genomic elements is substantially more widespread in the testis than in other organs across representative mammals. By scrutinizing the transcriptomes of all main testicular cell types in the mouse, we then reveal that meiotic spermatocytes and especially post‐meiotic round spermatids have remarkably diverse transcriptomes, which explains the high transcriptome complexity of the testis as a whole. The widespread transcriptional activity in spermatocytes and spermatids encompasses protein‐coding genes and long noncoding RNA genes but also poorly conserved intergenic sequences, suggesting that much of it is not of immediate functional relevance. Rather, our analyses of genome‐wide epigenetic data show that this prevalent transcription, which apparently promoted the birth of new genes during evolution, results from a highly permissive chromatin state during and after meiosis that may ultimately facilitate the replacement of histones by protamines during late spermatogenesis. To study the cellular source and mechanisms of high transcriptome complexity in the mammalian testis, we generated strand-specific deep coverage RNA‐Seq data for purified sertoli cells, spermatogonia, spermatocytes, spermatids and spermatozoa as well as for brain, liver and the whole testis from the mouse. We prepared 8 sequencing libraries for the polyadenylated RNA fraction of each sample and sequenced each library in 3 lanes of the Illumina Genome Analyser IIx platform, yielding a total of >60 millions strand-specific reads of 76 base pairs per sample. In addition, we generated ChIP-Seq data for the H3K4me2 modification as well as RRBS data for brain, liver, testis, spermatocytes and spermatids. RNA-seq, ChIP-seq and RRBS data were generated from the same individual or pool of individuals, in the case of purified cells.

Dataset Information

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis (RNA-Seq organs)

Publications

Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets