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The mRNA-Seq data of Zic3 overexpression in chicken limbs

ABSTRACT: The mRNA-Seq data of Zic3 overexpression in chicken limbs

PROVIDER: PRJNA1186557 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31361585_1.fastq.gz	Fastqsanger.gz
	SRR31361585_2.fastq.gz	Fastqsanger.gz
	SRR31361586_1.fastq.gz	Fastqsanger.gz
	SRR31361586_2.fastq.gz	Fastqsanger.gz
	SRR31361587_1.fastq.gz	Fastqsanger.gz

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Project description:We observed Zic3 highly expressed in the anterior regions of limb buds in all investigated tetrapods. To investigate the function of the Zic3 in limbs, we overexpressed the human-Zic3 gene in the lateral plate mesoderm (LPM) of developing chicken hindlimbs at HH10 using the RCAS avian retrovirus. Subsequently, the embryos were allowed to incubate until HH30. Autopod and zeugopod regions were dissected and subjected to transcriptome sequencing (mRNA-Seq), with the corresponding positions from individuals injected with the empty RCAS vector serving as controls. The results of the differential analysis and enrichment analysis revealed the regulatory network of Zic3 and various regulatory pathways that may be affected.

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Project description:Birds exhibit a remarkable diversity in limb morphology. Zic3, a transcription factor highly expressed in the anterior of the limb, has differential expression among bird species. To study how it regulates digit morphogenesis in birds, we overexpressed the chicken-Zic3 gene in the lateral plate mesoderm (LPM) of developing chicken hindlimbs at Hamburger Hamilton (HH) stage 10 using the RCAS avian retrovirus. At HH30, the autopod was dissected and subjected to transcriptome sequencing (mRNA-Seq), with the corresponding positions of individuals injected with the empty RCAS vector serving as controls. Enrichment analysis of differential genes and GSEA analysis suggest that the Zic3 gene inhibits multiple pathways related to skeletal development, resulting in a delay in digit development.

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Project description:Zic3 regulates early embryonic patterning in vertebrates. Its loss-of-function disrupts gastrulation, left-right patterning, and neurogenesis. We use the zebrafish as a model to study the developmental role of Zic3 in vivo. Using a combination of two genomics approaches – ChIP-seq and microarray, we identified Zic3 targets, which include genes from the Nodal and Wnt pathways, and show for the first time cis-regulation of these genes by Zic3 using in vivo enhancer assay. We uncovered a previously unrecognized link between Zic3 and the non-canonical Wnt pathway in gastrulation and left-right patterning, and identified neural pre-pattern genes as Zic3 targets during the early steps of neural induction. Zic3 preferably binds to distal intergenic regions, some of which contain evolutionarily conserved functional enhancers. Our study establishes the zebrafish as an excellent model for genome-wide study of a transcription factor in vivo.

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