Computational approaches to finding and analyzing cis-regulatory elements.
The transcription of almost all developmental genes is driven by tissue- and time-specific regulatory elements. These transcriptional regulatory elements lie in the genomic DNA proximal to the gene, and hence are cis-regulatory (as opposed to trans-regulatory elements like transcription factor genes). Over the past three decades, a number of techniques have been applied to the problem of finding and characterizing these regulatory elements. In this chapter, I discuss some computational approaches that have been particularly useful in identifying developmental cis-regulatory regions, and provide a tutorial on how to apply these approaches to the study of chick development.
Brown
C Titus
CT
Beckman Institute, Caltech, Pasadena, CA 91125, USA.
D000818:Animals; D001665:Binding Sites; D002642:Chick Embryo; D002645:Chickens / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D030541:Databases, Genetic; D050436:Regulatory Elements, Transcriptional / Q000502:physiology; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
D014157:Transcription Factors