RT Journal
A1 Johnson, David S.
A1 Davidson, Brad
A1 Brown, Christopher D.
A1 Smith, William C.
A1 Sidow, Arend
T1 Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance
JF Genome Research 
JO Genome Research 
YR 2004 
FD December 01 
VO 14 
IS 12 
SP 2448 
OP 2456 
DO 10.1101/gr.2964504 
UL http://genome.cshlp.org/content/14/12/2448.abstract 
AB We show that sequence comparisons at different levels of resolution can efficiently guide functional analyses of regulatory regions in the ascidians Ciona savignyi and Ciona intestinalis. Sequence alignments of several tissue-specific genes guided discovery of minimal regulatory regions that are active in whole-embryo reporter assays. Using the Troponin I (TnI) locus as a case study, we show that more refined local sequence analyses can then be used to reveal functional substructure within a regulatory region. A high-resolution saturation mutagenesis in conjunction with comparative sequence analyses defined essential sequence elements within the TnI regulatory region. Finally, we found a significant, quantitative relationship between function and sequence divergence of noncoding functional elements. This work demonstrates the power of comparative sequence analysis between the two Ciona species for guiding gene regulatory experiments.