Bidirectional Gene Pairs in the Human Genome

Kanako O Koyanagi, Hokkaido University, Sapporo, Hokkaido, Japan
Tadashi Imanishi, AIST, Koto‐ku, Tokyo, Japan
Takashi Gojobori, National Institute of Genetics, Mishima, Shizuoka, Japan

Published online: July 2008

DOI: 10.1002/9780470015902.a0020776

Bidirectional gene pairs, also called head-to-head gene pairs, are defined as two genes on different strands with adjacent 5¢-ends. They are transcribed divergently in a variety of coordinated fashion. The region between two transcription start sites of a bidirectional gene pair is designated as a putative bidirectional promoter.

Keywords: genome organization; coexpression; promoter

Figure 1. Organization of neighbouring gene pairs. Three possible patterns are shown. Lines represent the genome sequence and arrows indicate the directions of the transcription of the genes. Reproduced with permission from Koyanagi et al. (2005), Copyright Elsevier (2005).
Figure 2. Conservation of the closely located human bidirectional gene pairs (<1 kb apart) in other eukaryotic genomes (Koyanagi et al., 2005). The number of human pairs corresponding to the homologous pairs in the genomes of other species is shown. White bars represent the total number of homologous pairs in the genomes of other species. Black bars represent the homologous pairs that are adjacent in a bidirectional arrangement on the chromosome of other species. Reproduced with permission from Koyanagi et al. (2005), Copyright Elsevier (2005).
close
 References
    Adachi N and Lieber MR (2002) Bidirectional gene organization: a common architectural feature of the human genome. Cell 109: 807–809.
    Burbelo PD, Martin GR and Yamada Y (1988) Alpha 1(IV) and alpha 2(IV) collagen genes are regulated by a bidirectional promoter and a shared enhancer. Proceedings of the National Academy of Sciences of the USA 85: 9679–9682.
    Chen PY, Chang WS, Chou RH et al. (2007) Two non-homologous brain diseases-related genes, SERPINI1 and PDCD10, are tightly linked by an asymmetric bidirectional promoter in an evolutionarily conserved manner. BMC Molecular Biology 8: 2.
    Guarguaglini G, Battistoni A, Pittoggi C et al. (1997) Expression of the murine RanBP1 and Htf9-c genes is regulated from a shared bidirectional promoter during cell cycle progression. The Biochemical Journal 325(Pt 1): 277–286.
    Hansen JJ, Bross P, Westergaard M et al. (2003) Genomic structure of the human mitochondrial chaperonin genes: HSP60 and HSP10 are localised head to head on chromosome 2 separated by a bidirectional promoter. Human Genetics 112: 71–77.
    Koyanagi KO, Hagiwara M, Itoh T, Gojobori T and Imanishi T (2005) Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system. Gene 353: 169–176.
    Kruglyak S and Tang H (2000) Regulation of adjacent yeast genes. Trends in Genetics 16: 109–111.
    Lengronne A, Katou Y, Mori S et al. (2004) Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature 430: 573–578.
    Lercher MJ, Blumenthal T and Hurst LD (2003) Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Research 13: 238–243.
    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.
    Li YY, Yu H, Guo ZM et al. (2006) Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Computational Biology 2: e74.
    Lin JM, Collins PJ, Trinklein ND et al. (2007) Transcription factor binding and modified histones in human bidirectional promoters. Genome Research 17: 818–827.
    Okazaki Y, Furuno M, Kasukawa T et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563–573.
    Orii KE, Orii KO, Souri M et al. (1999) Genes for the human mitochondrial trifunctional protein alpha- and beta-subunits are divergently transcribed from a common promoter region. The Journal of Biological Chemistry 274: 8077–8084.
    Schuettengruber B, Doetzlhofer A, Kroboth K, Wintersberger E and Seiser C (2003) Alternate activation of two divergently transcribed mouse genes from a bidirectional promoter is linked to changes in histone modification. The Journal of Biological Chemistry 278: 1784–1793.
    Shearwin KE, Callen BP and Egan JB (2005) Transcriptional interference – a crash course. Trends in Genetics 21: 339–345.
    Takai D and Jones PA (2004) Origins of bidirectional promoters: computational analyses of intergenic distance in the human genome. Molecular Biology and Evolution 21: 463–467.
    Takeda J, Suzuki Y, Nakao M et al. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Research 34: 3917–3928.
    Trappe R, Doenecke D and Albig W (1999) The expression of human H2A-H2B histone gene pairs is regulated by multiple sequence elements in their joint promoters. Biochimica et Biophysica Acta 1446: 341–351.
    Trinklein ND, Aldred SF, Hartman SJ et al. (2004) An abundance of bidirectional promoters in the human genome. Genome Research 14: 62–66.
    Williams EJ and Bowles DJ (2004) Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Research 14: 1060–1067.
    Yang MQ, Koehly LM and Elnitski LL (2007) Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Computational Biology 3: e72.
 Further Reading
    Hurst LD, Pal C and Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nature Reviews Genetics 5(4): 299–310.
    Kapranov P, Willingham AT and Gingeras TR (2007) Genome-wide transcription and the implications for genomic organization. Nature Reviews Genetics 8(6): 413–423.
    Lawrence JG (2002) Shared strategies in gene organization among prokaryotes and eukaryotes. Cell 110(4): 407–413.
    Wray GA, Hahn MW, Abouheif E et al. (2003) The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution 20(9): 1377–1419.

Related Sub-Topics:

Evolutionary Genomics | Molecular Evolution | Human Evolution | Transcription of DNA | Evolution of Coding and Functional Modules
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Bidirectional Gene Pairs in the Human Genome
 
How to Cite close
Koyanagi, Kanako O, Imanishi, Tadashi, and Gojobori, Takashi(Jul 2008) Bidirectional Gene Pairs in the Human Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020776]