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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,
Convergence of a head-field selector Otx2 and Notch signaling: a mechanism for lens specification.
2008,
Pubmed
,
Xenbase
Ogino,
Resources and transgenesis techniques for functional genomics in Xenopus.
2009,
Pubmed
,
Xenbase
Ogino,
High-throughput transgenesis in Xenopus using I-SceI meganuclease.
2006,
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
