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Genome-wide occupancy links Hoxa2 to Wnt-β-catenin signaling in mouse embryonic development.

Donaldson IJ, Amin S, Hensman JJ, Kutejova E, Rattray M, Lawrence N, Hayes A, Ward CM, Bobola N - Nucleic Acids Res. (2012)

Bottom Line: Examination of the binding targets of Hoxa2 faithfully captures the processes regulated by Hoxa2 during embryonic development; in addition, it uncovers a large cluster of potential targets involved in the Wnt-signaling pathway.In vivo examination of canonical Wnt-β-catenin signaling reveals activity specifically in Hoxa2 domain of expression, and this is undetectable in Hoxa2 mutant embryos.The comprehensive mapping of Hoxa2-binding sites provides a framework to study Hox regulatory networks in vertebrate developmental processes.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.

ABSTRACT
The regulation of gene expression is central to developmental programs and largely depends on the binding of sequence-specific transcription factors with cis-regulatory elements in the genome. Hox transcription factors specify the spatial coordinates of the body axis in all animals with bilateral symmetry, but a detailed knowledge of their molecular function in instructing cell fates is lacking. Here, we used chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) to identify Hoxa2 genomic locations in a time and space when it is actively instructing embryonic development in mouse. Our data reveals that Hoxa2 has large genome coverage and potentially regulates thousands of genes. Sequence analysis of Hoxa2-bound regions identifies high occurrence of two main classes of motifs, corresponding to Hox and Pbx-Hox recognition sequences. Examination of the binding targets of Hoxa2 faithfully captures the processes regulated by Hoxa2 during embryonic development; in addition, it uncovers a large cluster of potential targets involved in the Wnt-signaling pathway. In vivo examination of canonical Wnt-β-catenin signaling reveals activity specifically in Hoxa2 domain of expression, and this is undetectable in Hoxa2 mutant embryos. The comprehensive mapping of Hoxa2-binding sites provides a framework to study Hox regulatory networks in vertebrate developmental processes.

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Functional annotation of Hoxa2-bound regions. (A) Top over-represented categories in the Gene Ontology (GO) (blue), Mouse phenotypes (green) and Mouse expression (red). GO describes the biological processes associated with gene function; mouse phenotypes ontology contains data about mouse genotype–phenotype associations; Mouse Genome Informatics (MGI) expression contains information on tissue- and developmental-stage-specific expression in mouse. The number of genes contained in each category is indicated in brackets. The length of the bars corresponds to values on the x-axis, which are binomial raw (uncorrected) P- values. TS: Theiler Stage. (B) Top overrepresented categories in the Gene Ontology (GO) in Hoxa2-bound regions containing Hox (red), Hox-Pbx (purple), Hox and Hox-Pbx (blue), and no motif (turquoise). The proportion of peaks containing the different motifs with respect to the total of Hoxa2-bound regions is shown in the pie chart (together with percentage values for each fraction); for each class, the top five categories with P < 10−6 are shown.
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gkr1240-F3: Functional annotation of Hoxa2-bound regions. (A) Top over-represented categories in the Gene Ontology (GO) (blue), Mouse phenotypes (green) and Mouse expression (red). GO describes the biological processes associated with gene function; mouse phenotypes ontology contains data about mouse genotype–phenotype associations; Mouse Genome Informatics (MGI) expression contains information on tissue- and developmental-stage-specific expression in mouse. The number of genes contained in each category is indicated in brackets. The length of the bars corresponds to values on the x-axis, which are binomial raw (uncorrected) P- values. TS: Theiler Stage. (B) Top overrepresented categories in the Gene Ontology (GO) in Hoxa2-bound regions containing Hox (red), Hox-Pbx (purple), Hox and Hox-Pbx (blue), and no motif (turquoise). The proportion of peaks containing the different motifs with respect to the total of Hoxa2-bound regions is shown in the pie chart (together with percentage values for each fraction); for each class, the top five categories with P < 10−6 are shown.

Mentions: We used the web tool Genomic Regions Enrichment of Annotations Tool (GREAT) (23) to identify terms enriched in genes associated with Hoxa2-bound regions. Consistent with a functional significance of Hoxa2-binding events, GREAT analysis specifically identified enrichment of Hoxa2-bound regions near genes involved in biological processes regulated by Hoxa2 in embryonic development (Figure 3A). Hoxa2 loss-of-function affects formation of the middle ear, and ectopic expression disrupts development of the cranial skeleton (8–10,12,38–40). Middle ear morphogenesis and embryonic skeletal morphogenesis were identified in the top enriched biological processes. GREAT detected over-representation of genes expressed in the branchial arch in the gene-expression ontology, and genes whose mutations generate phenotypes such as middle ear abnormalities, delayed bone ossification and palatal development, another process controlled by Hoxa2 (41).Figure 3.


Genome-wide occupancy links Hoxa2 to Wnt-β-catenin signaling in mouse embryonic development.

Donaldson IJ, Amin S, Hensman JJ, Kutejova E, Rattray M, Lawrence N, Hayes A, Ward CM, Bobola N - Nucleic Acids Res. (2012)

Functional annotation of Hoxa2-bound regions. (A) Top over-represented categories in the Gene Ontology (GO) (blue), Mouse phenotypes (green) and Mouse expression (red). GO describes the biological processes associated with gene function; mouse phenotypes ontology contains data about mouse genotype–phenotype associations; Mouse Genome Informatics (MGI) expression contains information on tissue- and developmental-stage-specific expression in mouse. The number of genes contained in each category is indicated in brackets. The length of the bars corresponds to values on the x-axis, which are binomial raw (uncorrected) P- values. TS: Theiler Stage. (B) Top overrepresented categories in the Gene Ontology (GO) in Hoxa2-bound regions containing Hox (red), Hox-Pbx (purple), Hox and Hox-Pbx (blue), and no motif (turquoise). The proportion of peaks containing the different motifs with respect to the total of Hoxa2-bound regions is shown in the pie chart (together with percentage values for each fraction); for each class, the top five categories with P < 10−6 are shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351182&req=5

gkr1240-F3: Functional annotation of Hoxa2-bound regions. (A) Top over-represented categories in the Gene Ontology (GO) (blue), Mouse phenotypes (green) and Mouse expression (red). GO describes the biological processes associated with gene function; mouse phenotypes ontology contains data about mouse genotype–phenotype associations; Mouse Genome Informatics (MGI) expression contains information on tissue- and developmental-stage-specific expression in mouse. The number of genes contained in each category is indicated in brackets. The length of the bars corresponds to values on the x-axis, which are binomial raw (uncorrected) P- values. TS: Theiler Stage. (B) Top overrepresented categories in the Gene Ontology (GO) in Hoxa2-bound regions containing Hox (red), Hox-Pbx (purple), Hox and Hox-Pbx (blue), and no motif (turquoise). The proportion of peaks containing the different motifs with respect to the total of Hoxa2-bound regions is shown in the pie chart (together with percentage values for each fraction); for each class, the top five categories with P < 10−6 are shown.
Mentions: We used the web tool Genomic Regions Enrichment of Annotations Tool (GREAT) (23) to identify terms enriched in genes associated with Hoxa2-bound regions. Consistent with a functional significance of Hoxa2-binding events, GREAT analysis specifically identified enrichment of Hoxa2-bound regions near genes involved in biological processes regulated by Hoxa2 in embryonic development (Figure 3A). Hoxa2 loss-of-function affects formation of the middle ear, and ectopic expression disrupts development of the cranial skeleton (8–10,12,38–40). Middle ear morphogenesis and embryonic skeletal morphogenesis were identified in the top enriched biological processes. GREAT detected over-representation of genes expressed in the branchial arch in the gene-expression ontology, and genes whose mutations generate phenotypes such as middle ear abnormalities, delayed bone ossification and palatal development, another process controlled by Hoxa2 (41).Figure 3.

Bottom Line: Examination of the binding targets of Hoxa2 faithfully captures the processes regulated by Hoxa2 during embryonic development; in addition, it uncovers a large cluster of potential targets involved in the Wnt-signaling pathway.In vivo examination of canonical Wnt-β-catenin signaling reveals activity specifically in Hoxa2 domain of expression, and this is undetectable in Hoxa2 mutant embryos.The comprehensive mapping of Hoxa2-binding sites provides a framework to study Hox regulatory networks in vertebrate developmental processes.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.

ABSTRACT
The regulation of gene expression is central to developmental programs and largely depends on the binding of sequence-specific transcription factors with cis-regulatory elements in the genome. Hox transcription factors specify the spatial coordinates of the body axis in all animals with bilateral symmetry, but a detailed knowledge of their molecular function in instructing cell fates is lacking. Here, we used chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) to identify Hoxa2 genomic locations in a time and space when it is actively instructing embryonic development in mouse. Our data reveals that Hoxa2 has large genome coverage and potentially regulates thousands of genes. Sequence analysis of Hoxa2-bound regions identifies high occurrence of two main classes of motifs, corresponding to Hox and Pbx-Hox recognition sequences. Examination of the binding targets of Hoxa2 faithfully captures the processes regulated by Hoxa2 during embryonic development; in addition, it uncovers a large cluster of potential targets involved in the Wnt-signaling pathway. In vivo examination of canonical Wnt-β-catenin signaling reveals activity specifically in Hoxa2 domain of expression, and this is undetectable in Hoxa2 mutant embryos. The comprehensive mapping of Hoxa2-binding sites provides a framework to study Hox regulatory networks in vertebrate developmental processes.

Show MeSH