E-GEOD-48254 - A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis

Status
Released on 2 December 2013, last updated on 3 June 2014
Organism
Danio rerio
Samples (7)
Protocols (3)
Description
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. ChIP-seq was performed against Cdx4, Sall4, H3K27ac, and H3K4me3 in bud-stage zebrafish embryos. Input material was sequenced as controls.
Experiment type
ChIP-seq 
Contacts
Shaun Mahony <mahony@psu.edu>, Alan J Davidson, Anthony DiBiase, Bilguujin Dorjsuren, Christian Mosimann, David K Gifford, Elizabeth J Paik, Emily N Price, Leonard I Zon, Richard M White
Citation
A Cdx4-Sall4 Regulatory Module Controls the Transition from Mesoderm Formation to Embryonic Hematopoiesis. Paik EJ, Mahony S, White RM, Price EN, Dibiase A, Dorjsuren B, Mosimann C, Davidson AJ, Gifford D, Zon LI. , Europe PMC 24286030
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-48254.idf.txt
Sample and data relationshipE-GEOD-48254.sdrf.txt
Processed data (2)E-GEOD-48254.processed.1.zip, E-GEOD-48254.processed.2.zip
Links