A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis

David N. Keys; Byung In Lee; Anna Di Gregorio; Naoe Harafuji; J. Chris Detter; Mei Wang; Orsalem Kahsai; Sylvia Ahn; Cindy Zhang; Sharon A. Doyle; Noriyuki Satoh; Yutaka Satou; Hidetoshi Saiga; Allen T. Christian; Dan S. Rokhsar; Trevor L. Hawkins; Mike Levine; Paul M. Richardson

doi:10.1073/pnas.0408952102

A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis

David N. Keys, Byung In Lee, Anna Di Gregorio, Naoe Harafuji, J. Chris Detter, Mei Wang, Orsalem Kahsai, Sylvia Ahn, Cindy Zhang, Sharon A. Doyle, Noriyuki Satoh, Yutaka Satou, Hidetoshi Saiga, Allen T. Christian, Dan S. Rokhsar, Trevor L. Hawkins, Mike Levine, Paul M. Richardson

Molecular Pathobiology

Research output: Contribution to journal › Article › peer-review

Abstract

A screen for the systematic identification of cis-regulatory elements within large (> 100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.

Original language	English (US)
Pages (from-to)	679-683
Number of pages	5
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	102
Issue number	3
DOIs	https://doi.org/10.1073/pnas.0408952102
State	Published - Jan 18 2005

Keywords

Ascidian
Cis-regulation
Hox cluster

ASJC Scopus subject areas

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Keys, D. N., Lee, B. I., Di Gregorio, A., Harafuji, N., Detter, J. C., Wang, M., Kahsai, O., Ahn, S., Zhang, C., Doyle, S. A., Satoh, N., Satou, Y., Saiga, H., Christian, A. T., Rokhsar, D. S., Hawkins, T. L., Levine, M., & Richardson, P. M. (2005). A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Proceedings of the National Academy of Sciences of the United States of America, 102(3), 679-683. https://doi.org/10.1073/pnas.0408952102

Keys, DN, Lee, BI, Di Gregorio, A, Harafuji, N, Detter, JC, Wang, M, Kahsai, O, Ahn, S, Zhang, C, Doyle, SA, Satoh, N, Satou, Y, Saiga, H, Christian, AT, Rokhsar, DS, Hawkins, TL, Levine, M & Richardson, PM 2005, 'A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis', Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 3, pp. 679-683. https://doi.org/10.1073/pnas.0408952102

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title = "A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis",

abstract = "A screen for the systematic identification of cis-regulatory elements within large (> 100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.",

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AU - Keys, David N.

AU - Lee, Byung In

AU - Di Gregorio, Anna

AU - Harafuji, Naoe

AU - Detter, J. Chris

AU - Wang, Mei

AU - Kahsai, Orsalem

AU - Ahn, Sylvia

AU - Zhang, Cindy

AU - Doyle, Sharon A.

AU - Satoh, Noriyuki

AU - Satou, Yutaka

AU - Saiga, Hidetoshi

AU - Christian, Allen T.

AU - Rokhsar, Dan S.

AU - Hawkins, Trevor L.

AU - Levine, Mike

AU - Richardson, Paul M.

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AB - A screen for the systematic identification of cis-regulatory elements within large (> 100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.

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A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis

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Keywords

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