TY - JOUR
T1 - Evolution of cis-regulatory sequences in Drosophila.
AU - He, Xin
AU - Sinha, Saurabh
PY - 2010
Y1 - 2010
N2 - Cross-species comparison is an emerging paradigm for identifying cis-regulatory sequences and understanding their function and evolution. In this chapter, we review probabilistic models of evolution of transcription factor binding sites, which provide the theoretical basis for a number of new bioinformatics tools for comparative sequence analysis. We illustrate how important functional and evolutionary insights on binding site gain and loss can be acquired through sequence comparison. This includes the observation that binding site turnover follows a molecular clock and that its rate correlates with the strength of binding sites and the presence of other sites in the neighborhood. We also comment on emerging trends that go beyond individual binding sites to a more holistic study of regulatory evolution. We point out common technical challenges, such as reliable sequence alignment and binding site prediction, when doing comparative regulatory sequence analysis and note some potential solutions thereof.
AB - Cross-species comparison is an emerging paradigm for identifying cis-regulatory sequences and understanding their function and evolution. In this chapter, we review probabilistic models of evolution of transcription factor binding sites, which provide the theoretical basis for a number of new bioinformatics tools for comparative sequence analysis. We illustrate how important functional and evolutionary insights on binding site gain and loss can be acquired through sequence comparison. This includes the observation that binding site turnover follows a molecular clock and that its rate correlates with the strength of binding sites and the presence of other sites in the neighborhood. We also comment on emerging trends that go beyond individual binding sites to a more holistic study of regulatory evolution. We point out common technical challenges, such as reliable sequence alignment and binding site prediction, when doing comparative regulatory sequence analysis and note some potential solutions thereof.
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U2 - 10.1007/978-1-60761-854-6_18
DO - 10.1007/978-1-60761-854-6_18
M3 - Review article
C2 - 20827599
AN - SCOPUS:79952111359
SN - 1064-3745
VL - 674
SP - 283
EP - 296
JO - Methods in molecular biology (Clifton, N.J.)
JF - Methods in molecular biology (Clifton, N.J.)
ER -