Chromosomal clustering of a human transcriptome reveals regulatory background

BMC Bioinformatics. 2005 Sep 19:6:230. doi: 10.1186/1471-2105-6-230.

Abstract

Background: There has been much evidence recently for a link between transcriptional regulation and chromosomal gene order, but the relationship between genomic organization, regulation and gene function in higher eukaryotes remains to be precisely defined.

Results: Here, we present evidence for organization of a large proportion of a human transcriptome into gene clusters throughout the genome, which are partly regulated by the same transcription factors, share biological functions and are characterized by non-housekeeping genes. This analysis was based on the cardiac transcriptome identified by our genome-wide array analysis of 55 human heart samples. We found 37% of these genes to be arranged mainly in adjacent pairs or triplets. A significant number of pairs of adjacent genes are putatively regulated by common transcription factors (p = 0.02). Furthermore, these gene pairs share a significant number of GO functional classification terms. We show that the human cardiac transcriptome is organized into many small clusters across the whole genome, rather than being concentrated in a few larger clusters.

Conclusion: Our findings suggest that genes expressed in concert are organized in a linear arrangement for coordinated regulation. Determining the relationship between gene arrangement, regulation and nuclear organization as well as gene function will have broad biological implications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Chromosome Mapping
  • Gene Expression
  • Gene Order / genetics*
  • Humans
  • Models, Biological
  • Multigene Family / physiology*
  • Myocardium / chemistry
  • Myocardium / metabolism*
  • Transcription Factors / physiology*

Substances

  • Transcription Factors