title: Comparative genomics-based identification and analysis of cis-regulatory elements.
abstract: Identification of cis-regulatory elements, such as enhancers and promoters, is very important not only for analysis of gene regulatory networks but also as a tool for targeted gene expression experiments. In this chapter, we introduce an easy but reliable approach to predict enhancers of a gene of interest by comparing mammalian and Xenopus genome sequences, and to examine their activity using a co-transgenesis technique in Xenopus embryos. Since the bioinformatics analysis utilizes publically available web tools, bench biologists can easily perform it without any need for special computing capability. The co-transgenesis assay, which directly uses polymerase chain reaction products, quickly screens for the activity of the candidate elements in a cloning-free manner.
authors.affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan. ogino@bs.naist.jp
authors.forename: Hajime
authors.initials: H
authors.lastname: Ogino
authors.forename: Haruki
authors.initials: H
authors.lastname: Ochi
authors.forename: Chihiro
authors.initials: C
authors.lastname: Uchiyama
authors.forename: Sarah
authors.initials: S
authors.lastname: Louie
authors.forename: Robert M
authors.initials: RM
authors.lastname: Grainger
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D004742:Enhancer Elements, Genetic; D018014:Gene Transfer Techniques; D017930:Genes, Reporter; D016678:Genome; D023281:Genomics; D049452:Green Fluorescent Proteins / Q000096:biosynthesis / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D022661:RNA, Untranslated / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014981:Xenopus / Q000235:genetics*; D029867:Xenopus Proteins / Q000235:genetics
chemical_list: D022661:RNA, Untranslated; D029867:Xenopus Proteins; D049452:Green Fluorescent Proteins; D004247:DNA