ArticleGenome research2004
Noncoding regulatory sequences of Ciona exhibit strong correspondence between evolutionary constraint and functional importance.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Toward a comprehensive catalog of regulatory elements.Human genetics · 2023Review
- Heart Enhancers: Development and Disease Control at a Distance.Frontiers in genetics · 2021Review
- Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos.eLife · 2020Article
- Universality of the DNA methylation codes in Eucaryotes.Scientific reports · 2019Article
- Article
- Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.Genome research · 2016Article
- Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.PLoS genetics · 2015Article
- Article
- Evolutionary genomics of fast evolving tunicates.Genome biology and evolution · 2014Review
- Histone H3 K27 acetylation marks a potent enhancer element on the adipogenic master regulator gene Pparg2.Cell cycle (Georgetown, Tex.) · 2014Article
- Parallel evolution of chordate cis-regulatory code for development.PLoS genetics · 2013Article
- Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord.PLoS biology · 2013Article
- Functional studies of the Ciona intestinalis myogenic regulatory factor reveal conserved features of chordate myogenesis.Developmental biology · 2013Article
- Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis.Current genomics · 2013Article
- Vascular Endothelial Growth Factor Receptor Family in Ascidians, Halocynthia roretzi (Sea Squirt). Its High Expression in Circulatory System-Containing Tissues.International journal of molecular sciences · 2013Article
- Initial deployment of the cardiogenic gene regulatory network in the basal chordate, Ciona intestinalis.Developmental biology · 2012Article
- Genomic approaches towards finding cis-regulatory modules in animals.Nature reviews. Genetics · 2012Review
- Article
- Article
- Distinct functional constraints partition sequence conservation in a cis-regulatory element.PLoS genetics · 2011Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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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