The complexity of the mammalian transcriptome

Stefano Gustincich, Albin Sandelin, Charles Plessy, Shintaro Katayama, Roberto Simone, Dejan Lazarevic, Yoshihide Hayashizaki, Piero Carninci

Research output: Contribution to journalArticle

81 Citations (Scopus)

Abstract

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. 2006 The Authors. Journal compilation

Original languageEnglish
Pages (from-to)321-332
Number of pages12
JournalJournal of Physiology
Volume575
Issue number2
DOIs
Publication statusPublished - Sep 2006

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Transcriptome
Genome
Gene Expression
Untranslated RNA
Brain
Gene Expression Profiling
Computer Simulation
Sequence Analysis
Organism Cloning
Proteins
Central Nervous System
Complementary DNA
Genes

ASJC Scopus subject areas

  • Physiology

Cite this

Gustincich, S., Sandelin, A., Plessy, C., Katayama, S., Simone, R., Lazarevic, D., ... Carninci, P. (2006). The complexity of the mammalian transcriptome. Journal of Physiology, 575(2), 321-332. https://doi.org/10.1113/jphysiol.2006.115568

The complexity of the mammalian transcriptome. / Gustincich, Stefano; Sandelin, Albin; Plessy, Charles; Katayama, Shintaro; Simone, Roberto; Lazarevic, Dejan; Hayashizaki, Yoshihide; Carninci, Piero.

In: Journal of Physiology, Vol. 575, No. 2, 09.2006, p. 321-332.

Research output: Contribution to journalArticle

Gustincich, S, Sandelin, A, Plessy, C, Katayama, S, Simone, R, Lazarevic, D, Hayashizaki, Y & Carninci, P 2006, 'The complexity of the mammalian transcriptome', Journal of Physiology, vol. 575, no. 2, pp. 321-332. https://doi.org/10.1113/jphysiol.2006.115568
Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D et al. The complexity of the mammalian transcriptome. Journal of Physiology. 2006 Sep;575(2):321-332. https://doi.org/10.1113/jphysiol.2006.115568
Gustincich, Stefano ; Sandelin, Albin ; Plessy, Charles ; Katayama, Shintaro ; Simone, Roberto ; Lazarevic, Dejan ; Hayashizaki, Yoshihide ; Carninci, Piero. / The complexity of the mammalian transcriptome. In: Journal of Physiology. 2006 ; Vol. 575, No. 2. pp. 321-332.
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