Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality.
In studies of their transcriptional activity, genomes have shown a high order of organization. We assessed the question of how genomically neighboring genes are transcriptionally coupled across tissues and what could be the driving force behind their coupling. We focused our analysis on the transcriptome information for 13 tissues of Mus musculus and 79 tissues of Homo sapiens. The analysis of coexpression patterns of genomically adjacent genes across tissues revealed 2619 and 1275 clusters of highly coexpressed genes, respectively. Most of these clusters consist of pairs and triplets of genes. They span a limited genomic length and are phylogenetically conserved between human and mouse. These clusters consist mainly of nonparalogous genes and show a decreased functional and similar regulatory relationship to one another compared to general genomic neighbors. We hypothesize that these clusters trace back to large-scale, qualitative, persistent reorganizations of the transcriptome, while transcription factor regulation is likely to handle fine-tuning of transcription on shorter time scales. Our data point to so far uncharacterized cis-acting units and reject cofunctionality as a driving force.
Purmann
Antje
A
Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
Toedling
Joern
J
Schueler
Markus
M
Carninci
Piero
P
Lehrach
Hans
H
Hayashizaki
Yoshihide
Y
Huber
Wolfgang
W
Sperling
Silke
S
D000818:Animals; D017124:Conserved Sequence / Q000502:physiology; D020869:Gene Expression Profiling / Q000145:classification*; D005786:Gene Expression Regulation / Q000502:physiology*; D053263:Gene Regulatory Networks / Q000502:physiology; D015894:Genome, Human / Q000502:physiology*; D023281:Genomics; D006796:Household Work; D006801:Humans; D051379:Mice; D005810:Multigene Family / Q000502:physiology*; D010802:Phylogeny; D014158:Transcription, Genetic / Q000502:physiology*