Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA.
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.
Nardone
Julie
J
Department of Pathology, Harvard Medical School and the CBR Institute for Biomedical Research, Boston, Massachusetts 02115, USA.
Lee
Dong U
DU
Ansel
K Mark
KM
Rao
Anjana
A
D000818:Animals; D019295:Computational Biology; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics*; D016678:Genome; D015698:Genomic Library; D023281:Genomics; D006801:Humans; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014158:Transcription, Genetic
D004247:DNA