Premium
The complexity of the mammalian transcriptome
Author(s) -
Gustincich Stefano,
Sandelin Albin,
Plessy Charles,
Katayama Shintaro,
Simone Roberto,
Lazarevic Dejan,
Hayashizaki Yoshihide,
Carninci Piero
Publication year - 2006
Publication title -
the journal of physiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.802
H-Index - 240
eISSN - 1469-7793
pISSN - 0022-3751
DOI - 10.1113/jphysiol.2006.115568
Subject(s) - transcriptome , biology , gene , genome , computational biology , in silico , genetics , transcription (linguistics) , gene expression , linguistics , philosophy
A comprehensive understanding of protein and regulatory networks is strictly dependent on the complete description of the transcriptome of cells. After the determination of the genome sequence of several mammalian species, gene identification is based on in silico predictions followed by evidence of transcription. Conservative estimates suggest that there are about 20 000 protein‐encoding genes in the mammalian genome. In the last few years the combination of full‐length cDNA cloning, cap‐analysis gene expression (CAGE) tag sequencing and tiling arrays experiments have unveiled unexpected additional complexities in the transcriptome. Here we describe the current view of the mammalian transcriptome focusing on transcripts diversity, the growing non‐coding RNA world, the organization of transcriptional units in the genome and promoter structures. In‐depth analysis of the brain transcriptome has been challenging due to the cellular complexity of this organ. Here we present a computational analysis of CAGE data from different regions of the central nervous system, suggesting distinctive mechanisms of brain‐specific transcription.