Identification of genes downstream of the Shh signalling in the developing chick wing and syn-expressed with Hoxd13 using microarray and 3D computational analysis

Fiona Bangs, Monique Welten, M G Davey, M Fisher, Y L Yin, H Downie, B Paton, R Baldock, D W Burt, Cheryll Tickle

Research output: Contribution to journalArticle

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Abstract

Sonic hedgehog (Shh) signalling by the polarizing region at the posterior margin of the chick wing bud is pivotal in patterning the digits but apart from a few key downstream genes, such as Hoxd13, which is expressed in the posterior region of the wing that gives rise to the digits, the genes that mediate the response to Shh signalling are not known. To find genes that are co-expressed with Hoxd13 in the posterior of chick wing buds and regulated in the same way, we used microarrays to compare gene expression between anterior and posterior thirds of wing buds from normal chick embryos and from polydactylous talpid(3) mutant chick embryos, which have defective Shh signalling due to lack of primary cilia. We identified 1070 differentially expressed gene transcripts, which were then clustered. Two clusters contained genes predominantly expressed in posterior thirds of normal wing buds; in one cluster, genes including Hoxd13, were expressed at high levels in anterior and posterior thirds in talpid3 wing buds, in the other cluster, genes including Ptc1, were expressed at low levels in anterior and posterior thirds in talpid3 wing buds. Expression patterns of genes in these two clusters were validated in normal and talpid3 mutant wing buds by in situ hybridisation and demonstrated to be responsive to application of Shh. Expression of several genes in the Hoxd13 cluster was also shown to be responsive to manipulation of protein kinase A (PKA) activity, thus demonstrating regulation by Gli repression. Genes in the Hoxd13 cluster were then sub-clustered by computational comparison of 3D expression patterns in normal wing buds to produce syn-expression groups. Hoxd13 and Sall1 are syn-expressed in the posterior region of early chick wing buds together with 6 novel genes which are likely to be functionally related and represent secondary targets of Shh signalling. Other groups of syn-expressed genes were also identified, including a group of genes involved in vascularisation.
LanguageEnglish
Pages428-441
Number of pages14
JournalMechanisms of Development
Volume127
Issue number9-12
DOIs
StatusPublished - Sep 2010

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Genes
Chick Embryo
Multigene Family
Gene Expression
Cilia
Cyclic AMP-Dependent Protein Kinases
In Situ Hybridization

Keywords

  • chicken
  • sonic hedgehog
  • Hoxd13
  • Talpid(3)
  • microarray
  • Ptc1
  • OPT
  • limb

Cite this

Identification of genes downstream of the Shh signalling in the developing chick wing and syn-expressed with Hoxd13 using microarray and 3D computational analysis. / Bangs, Fiona; Welten, Monique; Davey, M G; Fisher, M; Yin, Y L; Downie, H; Paton, B; Baldock, R; Burt, D W; Tickle, Cheryll.

In: Mechanisms of Development, Vol. 127, No. 9-12, 09.2010, p. 428-441.

Research output: Contribution to journalArticle

Bangs, Fiona ; Welten, Monique ; Davey, M G ; Fisher, M ; Yin, Y L ; Downie, H ; Paton, B ; Baldock, R ; Burt, D W ; Tickle, Cheryll. / Identification of genes downstream of the Shh signalling in the developing chick wing and syn-expressed with Hoxd13 using microarray and 3D computational analysis. In: Mechanisms of Development. 2010 ; Vol. 127, No. 9-12. pp. 428-441
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