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Cell type specific ATACseq (Crosslinked and TF-Sorted ATAC-seq (CaTS-ATAC)) reveals two distinct cis regulatory strategies for Shh interpretation in the mouse ventral neural tube

ABSTRACT: In many developing tissues the spatial and temporal pattern of gene expression is organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. The morphogen Sonic hedgehog (Shh) acts in a graded manner to direct neural progenitor specification in the neural tube. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. A common set of CREs are used to control gene activity in the majority of ventral neural progenitors. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for Foxa2-mediated cell specification across tissues.

ORGANISM(S): Mus musculus

PROVIDER: GSE204690 | GEO | 2022/06/06

REPOSITORIES: GEO

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Cell type specific RNAseq from crosslinked and and TF-Sorted ventral neural tube cell types

Project description:In many developing tissues the spatial and temporal pattern of gene expression is organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. The morphogen Sonic hedgehog (Shh) acts in a graded manner to direct neural progenitor specification in the neural tube. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. A common set of CREs are used to control gene activity in the majority of ventral neural progenitors. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for Foxa2-mediated cell specification across tissues.

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Project description:In studies investigating Sonic hedgehog (Shh) mediated patterning of the ventral neural tube, a process where Shh acts as a morphogen, we have investigated the transcriptional network underlying neural tube specification. Adopting an ES-cell based Shh neuronal specification assay (embryoid body; EBs) and a FLAG-tagged Gli protein (a transcriptional effector of the Shh pathway), we identified a number of direct targets of Gli action using Chromatin Immunoprecipitation (ChIP). These results will provide a first survey of the genome level response to this critical signaling input in vertebrate patterning Keywords: ChIP-chip, Gli transcription factors, Gli1, neural specification, mouse

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Project description:This experiment was specifically designed to measure neural targets of Shh signaling, we sought to profile the genes upregulated by Hh signaling in the ventral neural tube to obtain a valid dataset. To obtain ventral-specific markers, we generated retinoic acid-treated EBs grown in the presence or absence of HH-Ag. We did not observe induction of ventral Hh markers in RA-treated constitutive Gli1FLAG EBs and used these for the control, baseline set. The presence of FoxA2, Nkx2.9 and Nkx6.1 amongst the top 10 genes based on expression levels suggests that profiling significantly enriches for Hh-dependent cell types. As expected, the benchmark standard Gli1 was not up-regulated in our array, since it is constitutively expressed in the control as well. Keywords: neural progenitors, embryoid bodies, differentiation, Hedgehog, retinoic acid

2007-04-20 | GSE4936 | GEO

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