Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
???displayArticle.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.
Benko,
Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence.
2009, Pubmed
Benko,
Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence.
2009,
Pubmed Cañestro,
Evolutionary developmental biology and genomics.
2007,
Pubmed Fisher,
Conservation of RET regulatory function from human to zebrafish without sequence similarity.
2006,
Pubmed Hellsten,
The genome of the Western clawed frog Xenopus tropicalis.
2010,
Pubmed
,
Xenbase Kammandel,
Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity.
1999,
Pubmed Kasahara,
The medaka draft genome and insights into vertebrate genome evolution.
2007,
Pubmed Kleinjan,
Long-range downstream enhancers are essential for Pax6 expression.
2006,
Pubmed Kost,
The nucleotide sequence of the chick cytoplasmic beta-actin gene.
1983,
Pubmed Larkin,
Clustal W and Clustal X version 2.0.
2007,
Pubmed Lehman,
Illegitimate recombination in Xenopus: characterization of end-joined junctions.
1994,
Pubmed
,
Xenbase Lettice,
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly.
2003,
Pubmed Loots,
rVISTA 2.0: evolutionary analysis of transcription factor binding sites.
2004,
Pubmed Navratilova,
Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes.
2009,
Pubmed Noyes,
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.
2008,
Pubmed Ogino,
High-throughput transgenesis in Xenopus using I-SceI meganuclease.
2006,
Pubmed
,
Xenbase Ogino,
Resources and transgenesis techniques for functional genomics in Xenopus.
2009,
Pubmed
,
Xenbase Ogino,
Convergence of a head-field selector Otx2 and Notch signaling: a mechanism for lens specification.
2008,
Pubmed
,
Xenbase Ovcharenko,
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.
2004,
Pubmed Pennacchio,
In vivo enhancer analysis of human conserved non-coding sequences.
2006,
Pubmed Portales-Casamar,
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.
2010,
Pubmed Rada-Iglesias,
A unique chromatin signature uncovers early developmental enhancers in humans.
2011,
Pubmed
,
Xenbase Sagai,
Phylogenetic conservation of a limb-specific, cis-acting regulator of Sonic hedgehog ( Shh).
2004,
Pubmed Sandelin,
ConSite: web-based prediction of regulatory elements using cross-species comparison.
2004,
Pubmed Schwartz,
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.
2003,
Pubmed Stathopoulos,
Genomic regulatory networks and animal development.
2005,
Pubmed Visel,
ChIP-seq accurately predicts tissue-specific activity of enhancers.
2009,
Pubmed Wasserman,
Applied bioinformatics for the identification of regulatory elements.
2004,
Pubmed Waterhouse,
Jalview Version 2--a multiple sequence alignment editor and analysis workbench.
2009,
Pubmed Woolfe,
Highly conserved non-coding sequences are associated with vertebrate development.
2005,
Pubmed Xu,
Regulation of Pax6 expression is conserved between mice and flies.
1999,
Pubmed
