The transcriptome is the set of all messenger RNA (mRNA) and other expressed RNA molecules, or "transcripts", produced in one or a population of cells. Simply, it is the omics study of transcriptomes.
The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type.
Unlike the genome, which is roughly fixed for a given cell line (excluding mutations), the transcriptome can vary with external environmental conditions and epigenetic regulations.
Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being actively expressed at any given time, with the exception of mRNA degradation phenomena such as transcriptional attenuation. The study of transcriptomics examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on full transcriptome sequencing (RNA-seq) and DNA microarray technology.
Applications and analysis
The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the processes of cellular differentiation and carcinogenesis. A number of organism-specific transcriptome databases have been constructed and annotated to aid in the identification of genes that are differentially expressed in distinct cell populations or subtypes; however, the analysis of relative mRNA expression levels can be complicated by the fact that relatively small changes in mRNA expression can produce large changes in the total amount of the corresponding protein present in the cell. One analysis method, known as Gene Set Enrichment Analysis, identifies coregulated gene networks rather than individual genes that are up- or down-regulated in different cell populations.
Although microarray studies can reveal the relative amounts of different mRNAs in the cell, levels of mRNA are not directly proportional to the expression level of the proteins they code for. The number of protein molecules synthesized using a given mRNA molecule as a template is highly dependent on translation-initiation features of the mRNA sequence; in particular, the ability of the translation initiation sequence is a key determinant in the recruiting of ribosomes for protein translation. The complete protein complement of a cell or organism is known as the proteome.
A study of 158,807 mouse transcripts revealed that 4520 of these transcripts form antisense partners that are base pair complementary to the exons of genes. These results raise the possibility that significant numbers of "antisense RNA-coding genes" might participate in the regulation of the levels of expression of protein-coding mRNAs.
- ^ Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102(43):15545-50.
- ^ "Antisense Transcription in the Mammalian Transcriptome" by the RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium: S. Katayama et al. in Science, Vol 309, Issue 5740, 1564-1566 , 2 September 2005.
- ^ Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, Kinzler KW. Characterization of the yeast transcriptome. Cell. 1997 Jan 24;88(2):243-51.
- ^ Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W, and P Zimmermann. (2006) Web-based analysis of the mouse transcriptome using Genevestigator. BMC Bioinformatics 7:311
- List of omics topics in biology
- DNA microarrays (a.k.a. DNA chips)
- Gene expression and Expressome (a.k.a. array expression)
- Serial analysis of gene expression