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Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning

Vokes, Steven A. and Ji, Hongkai and McCuine, Scott and Tenzen, Toyoaki and Giles, Shane and Zhong, Sheng and Longabaugh, William J. R. and Davidson, Eric H. and Wong, Wing H. and McMahon, Andrew P. (2007) Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development, 134 (10). 1977 -1989. ISSN 0950-1991. doi:10.1242/dev.001966. https://resolver.caltech.edu/CaltechAUTHORS:20091130-115929288

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Image (JPEG) (Fig. S1. Generation of epitope-tagged Gli1 knock-in construct.) - Supplemental Material
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Abstract

Sonic hedgehog (Shh) acts as a morphogen to mediate the specification of distinct cell identities in the ventral neural tube through a Gli-mediated (Gli1-3) transcriptional network. Identifying Gli targets in a systematic fashion is central to the understanding of the action of Shh. We examined this issue in differentiating neural progenitors in mouse. An epitope-tagged Gli-activator protein was used to directly isolate cis-regulatory sequences by chromatin immunoprecipitation (ChIP). ChIP products were then used to screen custom genomic tiling arrays of putative Hedgehog (Hh) targets predicted from transcriptional profiling studies, surveying 50-150 kb of non-transcribed sequence for each candidate. In addition to identifying expected Gli-target sites, the data predicted a number of unreported direct targets of Shh action. Transgenic analysis of binding regions in Nkx2.2, Nkx2.1 (Titf1) and Rab34 established these as direct Hh targets. These data also facilitated the generation of an algorithm that improved in silico predictions of Hh target genes. Together, these approaches provide significant new insights into both tissue-specific and general transcriptional targets in a crucial Shh-mediated patterning process.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1242/dev.001966DOIArticle
http://dev.biologists.org/cgi/content/abstract/134/10/1977PublisherArticle
Additional Information:© 2007 Company of Biologists Ltd. Accepted 5 March 2007. We thank Curis for providing Hh-Ag, Alex Joyner and David Rowitch for providing constructs, Zhenjuan Wang (Harvard Genome Manipulation Facility) for pronuclear injections, Jennifer Couget (GGR) for expert guidance on performing microarrays, Julia Zeitlinger for helpful advice on optimizing ChIP, and Renate Hellmiss-Peralte for advice and assistance on figures. We are indebted to Leo Brizuela, Brett Chevalier and Mel Kronick at Agilent Technologies for supporting this project. We thank Dr James Briscoe for discussion of unpublished material. The Pax6 antibody (developed by the Kawakami Laboratory), Nkx2.2 and FoxA2 antibodies (developed by the Jessell laboratory) were obtained from the Developmental Studies Hybridoma Bank. We acknowledge support from the NIH-NINDS #R37 NS033642 (A.P.M.), NIH #R01 GM67250 and HG3903-01 (W.W. and H.J.),Helen Hay Whitney Foundation (S.V.) and the Charles King Trust Fellowship (S.V.).
Funders:
Funding AgencyGrant Number
NIHR37 NS033642
NIHR01 GM67250
NIHHG3903-01
Helen Hay Whitney FoundationUNSPECIFIED
Charles King Trust FellowshipUNSPECIFIED
Subject Keywords:Chromatin immunoprecipitation; Gli; Neural patterning; Sonic hedgehog; Mouse
Issue or Number:10
DOI:10.1242/dev.001966
Record Number:CaltechAUTHORS:20091130-115929288
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20091130-115929288
Official Citation: * Steven A. Vokes, * Hongkai Ji, * Scott McCuine, * Toyoaki Tenzen, * Shane Giles, * Sheng Zhong, * William J. R. Longabaugh, * Eric H. Davidson, * Wing H. Wong, * and Andrew P. McMahon Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterningDevelopment 2007 134:1977-1989; published online before print April 18, 2007, doi:10.1242/dev.001966
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:16836
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:04 Jan 2010 18:40
Last Modified:08 Nov 2021 23:30

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