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.
authors.affiliation: U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: David N
authors.initials: DN
authors.lastname: Keys
authors.forename: Byung-in
authors.initials: BI
authors.lastname: Lee
authors.forename: Anna
authors.initials: A
authors.lastname: Di Gregorio
authors.forename: Naoe
authors.initials: N
authors.lastname: Harafuji
authors.forename: J Chris
authors.initials: JC
authors.lastname: Detter
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.forename: Orsalem
authors.initials: O
authors.lastname: Kahsai
authors.forename: Sylvia
authors.initials: S
authors.lastname: Ahn
authors.forename: Cindy
authors.initials: C
authors.lastname: Zhang
authors.forename: Sharon A
authors.initials: SA
authors.lastname: Doyle
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Satoh
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Satou
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Saiga
authors.forename: Allen T
authors.initials: AT
authors.lastname: Christian
authors.forename: Dan S
authors.initials: DS
authors.lastname: Rokhsar
authors.forename: Trevor L
authors.initials: TL
authors.lastname: Hawkins
authors.forename: Mike
authors.initials: M
authors.lastname: Levine
authors.forename: Paul M
authors.initials: PM
authors.lastname: Richardson
mesh_terms: D000818:Animals; D022202:Chromosomes, Artificial, Bacterial; D002938:Ciona intestinalis / Q000235:genetics*; D004353:Drug Evaluation, Preclinical / Q000379:methods; D018274:Electroporation; D004817:Epidermis / Q000378:metabolism; D005801:Genes, Homeobox / Q000235:genetics*; D005822:Genetic Vectors; D007814:Larva / Q000235:genetics; D008722:Methods; D008969:Molecular Sequence Data; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014158:Transcription, Genetic; D015053:Zygote