Comparative Genomics-Based Identification and Analysis of Cis-Regulatory Elements

  • Hajime OginoEmail author
  • Haruki Ochi
  • Chihiro Uchiyama
  • Sarah Louie
  • Robert M. Grainger
Part of the Methods in Molecular Biology book series (MIMB, volume 917)


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.

Key words

Cis-regulatory elements Enhancer Comparative genomics Multiple alignment Phylogenetic footprinting Transcription factor-binding motif Xenopus transgenesis 



This work was supported by the Global COE Program in NAIST (Frontier Biosciences: strategies for survival and adaptation in a changing global environment), Grant-in-Aid for Scientific Research (C) (20579002 and 23570256) from JSPS and Grant-in-Aid for Scientific Research on Innovative Areas (21200064) from MEXT, Japan, to H. Ogino, by Grant-in-Aid for Young Scientists (B) (21770234) from JSPS and Research for Promoting Technological Seeds (A) (10-099) from JST, Japan, to H. Ochi, and by CREST (JST). This work was also supported by NIH grants EY00675, EY017400, EY018000, and RR013221 to R. Grainger.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Hajime Ogino
    • 1
    Email author
  • Haruki Ochi
    • 1
  • Chihiro Uchiyama
    • 1
  • Sarah Louie
    • 2
  • Robert M. Grainger
    • 2
  1. 1.Graduate School of Biological SciencesNara Institute of Science and Technology (NAIST)Takayama, IkomaJapan
  2. 2.Department of BiologyUniversity of VirginiaCharlottesvilleUSA

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