Zic3 interacts with distant regulatory elements to regulate zebrafish developmental genes
Case Control
10.1371/journal.pgen.1003852
GSE41458
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.
True
cwinata
May 16, 2016, 8:07 a.m.
Nov. 7, 2018, 2:49 a.m.
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Controlled By | anatomical_term | Treatment | Hours Post Fertilization | Mutation Description |
|---|---|---|---|---|---|---|---|---|---|---|
| DCD006320BS | DCD000171SR | whole organism | Mathavan Lab, NTU Medical School | AB | 75%-epiboly | — | — | 8 | — |
| Applied Assay ID | Biosample Replicate | Assay | Controlled By |
|---|---|---|---|
| DCD000988AA | DCD012444BR | ChIP-seq_Mathavan_Lab_Zic3_0001AS | DCD000983AA |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|---|
| DCD000846SQ | DCD000985TR | Mathavan Lab, NTU Medical School | Illumina | HiSeq 2000 | — | ✘ | — | — | 01/01/2012 |
| Applied Assay ID | Biosample Replicate | Assay | Controlled By |
|---|---|---|---|
| DCD000983AA | DCD012446BR | ChIP-seq_Mathavan_Lab_input_control_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD000841SQ | DCD000980TR | Mathavan Lab, NTU Medical School | Illumina | HiSeq 2000 | 01/01/2012 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006321BS | DCD000171SR | tissue | Mathavan Lab, NTU Medical School | AB | 26+ somites | 24 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD000990AA | DCD012443BR | ChIP-seq_Mathavan_Lab_Zic3_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD000848SQ | DCD000987TR | Mathavan Lab, NTU Medical School | Illumina | HiSeq 2000 | 01/01/2012 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD000985AA | DCD012445BR | ChIP-seq_Mathavan_Lab_input_control_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Sequencing Date |
|---|---|---|---|---|---|
| DCD000843SQ | DCD000982TR | Mathavan Lab, NTU Medical School | Illumina | HiSeq 2000 | 01/01/2012 |