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Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance

    • 1 Department of Pathology and Department of Genetics, Stanford University Medical Center, Stanford, California 94305-5324, USA
    • 2 Department of Molecular and Cell Biology, Division of Genetics and Development, Center for Integrative Genomics, University of California–Berkeley, California 94720, USA
    • 3 Molecular Cellular and Developmental Biology Department, Neuroscience Research Institute, University of California–Santa Barbara, California 93106, USA
Published November 15, 2004. Vol 14 Issue 12, pp. 2448-2456. https://doi.org/10.1101/gr.2964504
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Abstract

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.

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