Genome-wide identification of tissue-specific enhancers in the Ciona tadpole

Naoe Harafuji, David N. Keys, Michael Levine

Research output: Contribution to journalArticlepeer-review

89 Scopus citations


Less than 100 cis-regulatory DNAs have been characterized in the context of transgenic metazoan embryos. Here we investigate the feasibility of conducting a genome-wide search for tissue-specific enhancers in the ascidian Ciona intestinalis. A total of 138 random genomic DNA fragments with an average size of 1.7 kb were separately placed 5′ of a lacZ reporter gene. Eleven of the lacZ fusion genes displayed localized patterns of expression in tadpole-stage Ciona embryos. At least five of these transgenes appear to contain bona fide tissue-specific enhancers that direct expression in the cerebral vesicle, neural tube, primordial adhesive organ, notochord, and tail epidermis. One of the enhancers maps near Distalless (Ci-DII-A) and recapitulates most aspects of the endogenous expression pattern, including localized expression in the anterior-most regions of the neurogenic ectoderm. We discuss the prospects of creating a regulatory atlas of the Ciona genome, whereby every enhancer is identified for every gene.

Original languageEnglish (US)
Pages (from-to)6802-6805
Number of pages4
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number10
StatePublished - May 14 2002
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General


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