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          Institute: MPI für molekulare Genetik     Collection: Department of Vertebrate Genomics     Display Documents



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ID: 335525.0, MPI für molekulare Genetik / Department of Vertebrate Genomics
Genomic organization of transcriptomes in mammals: coregulation and cofunctionality
Authors:Purmann, Antje; Toedling, Joern; Schueler, Markus; Carninci, Piero; Lehrach, Hans; Hayashizaki, Yoshihide; Huber, Wolfgang; Sperling, Silke
Language:English
Date of Publication (YYYY-MM-DD):2007-05
Title of Journal:Genomics
Volume:89
Issue / Number:5
Start Page:580
End Page:587
Copyright:© 2007 Elsevier Inc.
Review Status:not specified
Audience:Experts Only
Abstract / Description: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.
Free Keywords:Genomics; Gene expression; Transcription regulation; Regulatory elements; Mammals
External Publication Status:published
Document Type:Article
Communicated by:Hans Lehrach
Affiliations:MPI für molekulare Genetik
External Affiliations:EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK;
Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan;
Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Identifiers:ISSN:0888-7543
DOI:10.1016/j.ygeno.2007.01.010
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