Clustering of Highly Expressed Genes in the Human Genome

Abstract

A dual mechanism of gene regulation exists in the human genome: Transcription factors determine whether a gene will be expressed and establish a basic level of transcription. In addition, the chromosomal domain in which a gene is positioned exerts a substantial effect and potentiates the ultimate expression level.

Keywords: chromosomal domains; gene expression; transcription; genome organization; gene clustering

Figure 1.

Physically mapped transcriptome profile of the q‐arm of human chromosome 1. Giemsa banding is illustrated below each transcriptome map (centromere/heterochromatic region is marked ‘cen’). RIDGEs are marked with an ‘R’, anti‐RIDGEs are marked ‘AR’. Black vertical bars represent genes and their height indicates domain activity for a window of 49 genes (median expression of the surrounding 49 genes in 133 pooled SAGE libraries from different tissues). Below is the chromosomal position in megabases (UCSC Genome Build HG15). Illustration by Jan Koster and Hinco Gierman.

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References

Barski A, Cuddapah S, Cui K et al. (2007) High‐resolution profiling of histone methylations in the human genome. Cell 129: 823–837.

Caron H, van Schaik B, van der Mee M et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291: 1289–1292.

Gierman HJ, Indemans MH, Koster J et al. (2007) Domain‐wide regulation of gene expression in the human genome. Genome Research 17: 1286–1295.

Gilbert N, Boyle S, Fiegler H et al. (2004) Chromatin architecture of the human genome: gene‐rich domains are enriched in open chromatin fibers. Cell 118: 555–566.

Goetze S, Mateos‐Langerak J, Gierman HJ et al. (2007) The three‐dimensional structure of human interphase chromosomes is related to the transcriptome map. Molecular and Cellular Biology 27: 4475–4487.

Lercher MJ, Urrutia AO and Hurst LD (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genetics 31: 180–183.

Mijalski T, Harder A, Halder T et al. (2005) Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. Proceedings of the National Academy of Sciences of the USA 102: 8621–8626.

Roh TY, Cuddapah S and Zhao K (2005) Active chromatin domains are defined by acetylation islands revealed by genome‐wide mapping. Genes & Development 19: 542–552.

Stransky N, Vallot C, Reyal F et al. (2006) Regional copy number‐independent deregulation of transcription in cancer. Nature Genetics 38: 1386–1396.

Versteeg R, van Schaik BD, van Batenburg MF et al. (2003) The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Research 13: 1998–2004.

Further Reading

Bernstein BE, Kamal M, Lindblad‐Toh K et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120: 169–181.

Cremer T and Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Reviews. Genetics 2: 292–301.

Hurst LD, Pal C and Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nature Reviews. Genetics 5: 299–310.

Semon M and Duret L (2006) Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Molecular Biology and Evolution 23: 1715–1723.

Singer GA, Lloyd AT, Huminiecki LB and Wolfe KH (2005) Clusters of co‐expressed genes in mammalian genomes are conserved by natural selection. Molecular Biology and Evolution 22: 767–775.

Sproul D, Gilbert N and Bickmore WA (2005) The role of chromatin structure in regulating the expression of clustered genes. Nature Reviews. Genetics 6: 775–781.

Turner BM (2001) Chromatin and Gene Regulation. Mechanisms in Epigenetics. Oxford: Blackwell Science.

Web Links

The Human Transcriptome Map. A Web application that gives the gene expression profiles for any chromosomal region: http://bioinfo.amc.uva.nl/HTMseq/

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How to Cite close
Gierman, Hinco J, and Versteeg, Rogier(Apr 2008) Clustering of Highly Expressed Genes in the Human Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005931.pub2]