An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

Abstract

The parts of the genome transcribed by a cell or tissue reflect the biological processes and functions it carries out. We characterized the features of mammalian tissue transcriptomes at the gene level through analysis of RNA deep sequencing (RNA-Seq) data across human and mouse tissues and cell lines. We observed that roughly 8,000 protein-coding genes were ubiquitously expressed, contributing to around 75% of all mRNAs by message copy number in most tissues. These mRNAs encoded proteins that were often intracellular, and tended to be involved in metabolism, transcription, RNA processing or translation. In contrast, genes for secreted or plasma membrane proteins were generally expressed in only a subset of tissues. The distribution of expression levels was broad but fairly continuous: no support was found for the concept of distinct expression classes of genes. Expression estimates that included reads mapping to coding exons only correlated better with qRT-PCR data than estimates which also included 3′ untranslated regions (UTRs). Muscle and liver had the least complex transcriptomes, in that they expressed predominantly ubiquitous genes and a large fraction of the transcripts came from a few highly expressed genes, whereas brain, kidney and testis expressed more complex transcriptomes with the vast majority of genes expressed and relatively small contributions from the most expressed genes. mRNAs expressed in brain had unusually long 3′UTRs, and mean 3′UTR length was higher for genes involved in development, morphogenesis and signal transduction, suggesting added complexity of UTR-based regulation for these genes. Our results support a model in which variable exterior components feed into a large, densely connected core composed of ubiquitously expressed intracellular proteins.

Dual Specificity Phosphatase 4 Mediates Cardiomyopathy Caused by Lamin A/C (LMNA) Gene Mutation

“…We used ventricular tissue from 8-week-old male mice, which is prior to observable signs of cardiomyopathy, to minimize potential secondary effects of disease. Of 22,310 mapped genes, ϳ10,700 genes (cutoff based on fragments/kilobase of exons/million bases mapped Ͼ 1) were expressed in heart samples (see supplemental data), consistent with previous RNAseq results using mouse heart tissue (23,24). At 8 weeks of age, Dusp4 overexpression led to significant (q Ͻ 0.05) up-regulation of 410 genes, with Dusp4 and fetal isoforms of myosin light chains among the highest scoring and significant downregulation of 212 genes (Fig.…”

Functional transcriptomics of a migrating cell in Caenorhabditis elegans

“…We ran single-cell RT-PCRs (13) on wild-type LCs from the mid-L3 and mid-L4 larval stages, as well as mid-L4 LCs with RNAi-inactivated nhr-67 (3). As a control for housekeeping genes (15) and genes expressed in other differentiated cell types (16), we also amplified RNA from whole mixed-stage hermaphrodites (primarily larvae). To minimize variable amplification of transcripts from five individual cells, we initially pooled aliquots of RT-PCRs from each cell type before sequencing.…”

Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle

“…Gene expression was calculated as 'reads per kilobase of exon model per million mapped reads' (RPKM). A published method was used to determine the expression value cutoff, which removes the background expression level noise [25]. Therefore, the definition herein is based on the presence of a transcript and not expression level variability among the tissues and cells.…”

“…Only the uniquely-mapped reads were used for further analyses. According to various tissue-based transcriptomic studies [25], greater than six million reads are sufficient for detecting most of the expressed genes in the human mammary gland. Hence, we are confident that our sequencing depth is adequate and the RNA-seq data provide objective profiling of the transcriptomes of the mouse mammary gland at the different developmental stages that we studied.…”