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| Status |
Public on Dec 02, 2013 |
| Title |
A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis |
| Organism |
Danio rerio |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Deletion of caudal/cdx genes alters hox gene expression and causes defects in posterior tissues and hematopoiesis. Yet, the defects in hox gene expression only partially explain these phenotypes. To gain deeper insight into Cdx4 function, we performed ChIP-seq combined with gene expression profiling in zebrafish, and identified the transcription factor spalt-like 4 (sall4) as a Cdx4 target. ChIP-seq revealed that Sall4 bound to its own gene locus and the cdx4 locus. Expression profiling showed that Cdx4 and Sall4 co-regulate genes such as hox, scl, and lmo2 that initiate hematopoiesis. Combined cdx4/sall4 gene knock-down impairs erythropoiesis, and overexpression of the Cdx4 and Sall4 target genes scl and lmo2 together rescued the erythroid program. These findings suggest that auto- and cross- regulation of Cdx4 and Sall4 establish a stable molecular circuit in mesoderm that facilitates the activation of the blood-specific program as development proceeds.
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| Overall design |
ChIP-seq was performed against Cdx4, Sall4, H3K27ac, and H3K4me3 in bud-stage zebrafish embryos. Input material was sequenced as controls.
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| Contributor(s) |
Paik EJ, Mahony S, White RM, Price EN, Dorjsuren B, DiBiase A, Mosimann C, Davidson AJ, Gifford DK, Zon LI |
| Citation(s) |
24286030 |
| Submission date |
Jun 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shaun Mahony |
| E-mail(s) |
mahony@psu.edu
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| Phone |
814-865-3008
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| Organization name |
Penn State University
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| Department |
Biochemistry & Molecular Biology
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| Lab |
Shaun Mahony
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| Street address |
404 South Frear Bldg
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platforms (2) |
| GPL9319 |
Illumina Genome Analyzer II (Danio rerio) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (7)
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| GSM1173379 |
ChIP-seq myc-tagged Cdx4 in bud-stage embryo |
| GSM1173380 |
ChIP-seq myc-tagged Sall4 in bud-stage embryo |
| GSM1173381 |
ChIP-seq H3K27ac in bud-stage embryo |
| GSM1173382 |
ChIP-seq H3K4me3 in bud-stage embryo |
| GSM1173383 |
Input sequencing in bud-stage embryo rep 1 |
| GSM1173384 |
Input sequencing in bud-stage embryo rep 2 |
| GSM1173385 |
Input sequencing in bud-stage embryo rep 3 |
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| Relations |
| BioProject |
PRJNA209381 |
| SRA |
SRP026282 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE48254_RAW.tar |
827.7 Mb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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