Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

Abstract

Understanding the extent of genomic transcription and its functional relevance is a central goal in genomics research. However, detailed genome-wide investigations of transcriptome complexity in major mammalian organs have been scarce. Here, using extensive RNA-seq data, we show that transcription of the genome is substantially more widespread in the testis than in other organs across representative mammals. Furthermore, we 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 and long noncoding RNA genes but also poorly conserves intergenic sequences, suggesting that it may not be of immediate functional relevance. Rather, our analyses of genome-wide epigenetic data suggest that this prevalent transcription, which most likely promoted the birth of new genes during evolution, is facilitated by an overall permissive chromatin in these germ cells that results from extensive chromatin remodeling.

E2F1 controls germ cell apoptosis during the first wave of spermatogenesis

“…8A). A previously published data set on the transcriptomes of the different testicular cell types (Sertoli cell, spermatogonia, spermatocytes, and spermatids) after primary cell extraction was used for the analysis (Soumillon et al ., 2013). Differential expression of genes in the different testicular cell types was analyzed.…”

“…This example depicts the shortcomings of the experimental and analytical procedures: contamination of unwanted cells in the primary cell extractions or a specificity issue in the differential expression analysis of the RNA‐seq data. Furthermore, the varied transcriptional complexity between the different germ‐cell populations may cause biases in the RNA‐seq‐analysis (Soumillon et al ., 2013). Moreover, it would have been ideal if all the samples used in this comparative analysis were from the same time points, since gene expression in spermatogenesis and testicular development is highly dynamic.…”

MPC1-like Is a Placental Mammal-specific Mitochondrial Pyruvate Carrier Subunit Expressed in Postmeiotic Male Germ Cells

“…The transcriptome of germ cells varies greatly during the course of spermatogenesis (30,33), indicating that transcriptional regulation is crucial for spermatogenesis to ensure the availability of appropriate precursor pools, progression of meiosis, and differentiation of haploid cells into fully mature spermatozoa. As part of this process, MPC1L and MPC2 levels increase during spermiogenesis (Fig.…”

Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa

“…This approach is not only costly, but importantly, it increases the number of factors (variance components) to consider when analyzing data derived from such studies. Several recent studies, however, have shown that fairly complete transcriptomes can also be reconstructed from single tissues such as gill (Kelley et al 2012) and testis (Soumillon et al 2013). Kelley et al (2012) speculated that the gill may contain exceptionally high numbers of transcripts, making it a good tissue for transcriptome assembly.…”