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Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA

Nature Immunology volume 5, pages 768–774 (2004)Cite this article

The combination of bioinformatic and biological approaches constitutes a powerful method for identifying gene regulatory elements. High-quality genome sequences are available in public databases for several vertebrate species. Comparative cross-species sequence analysis of these genomes shows considerable conservation of noncoding sequences in DNA. Biological analyses show that an unexpectedly high number of the conserved sequences correspond to functional cis-regulatory regions that influence gene transcription. Because research biologists are often unfamiliar with the bioinformatic resources at their disposal, this commentary discusses how to integrate biological and bioinformatic methods in the discovery of gene regulatory regions and includes a tutorial on widely available comparative genomics programs.

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Figure 1: TH2 cytokine locus on mouse chromosome 11.
Figure 2: Identification of orthologs.
Figure 3: Alignment of a section of the IL4 locus on mouse chromosome 11 with the corresponding region of human chromosome 5.

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Authors and Affiliations

  1. Department of Pathology, Harvard Medical School and the CBR Institute for Biomedical Research, Boston, 02115, Massachusetts, USA

    Julie Nardone, K Mark Ansel & Anjana Rao

  2. Department of Pathology and the Graduate Program in Immunology, Harvard Medical School, and the CBR Institute for Biomedical Research, Boston, 02115, Massachusetts, USA

    Dong U Lee

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Nardone, J., Lee, D., Ansel, K. et al. Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA. Nat Immunol 5, 768–774 (2004). https://doi.org/10.1038/ni0804-768

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