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CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE146752 | GEO | 2021/01/18

REPOSITORIES: GEO

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CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [RNA-seq]

Project description:CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. RNA-sequencing of CNSs of CTCF[0] mutants that completely lack CTCF identified putative targets that are expressed in altered patterns. We find that CTCF recruits Centrosomal protein 190 kDa (Cp190) to CTCF's binding sites to co-regulate a substantial fraction of common genes that we find are also altered in CNSs of Cp190[KO] mutants carrying a CRISPR/Cas9-mediated deletion of the Cp190 open reading frame.

2021-01-18 | GSE146751 | GEO

CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [Hi-C]

2021-01-18 | GSE146750 | GEO

CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [ChIP-seq]

Project description:CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. Chromatin immunoprecipitation (ChIP)-sequencing of CTCF and its partner protein Centrosomal protein 190 kDa (Cp190) in CNSs of wildtype (WT), CTCF[0] mutants completely lacking CTCF and Cp190[KO] mutants with a CRISPR/Cas9-mediated deletion of the Cp190 open reading frame identified CTCF and Cp190 peaks defined as enriched in WT relative to each respective mutant control. These experiments also revealed that CTCF recruits Cp190 to CTCF's binding sites, but Cp190 is dispensable for CTCF binding to most of CTCF's sites.

2021-01-18 | GSE146749 | GEO

CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system

Project description:CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system

| PRJNA611806 | ENA

CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [Hi-C]

Project description:CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [Hi-C]

| PRJNA611808 | ENA

CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [ChIP-seq]

Project description:CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [ChIP-seq]

| PRJNA611809 | ENA

CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [RNA-seq]

Project description:CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [RNA-seq]

| PRJNA611807 | ENA

Genes required for Drosophila nervous system development identified by RNA interference.

Project description:RNA interference was used to screen 3,314 Drosophila double-stranded RNAs, corresponding to approximately 25% of Drosophila genes, for genes that affect the development of the embryonic nervous system. RNA-interference-mediated gene silencing in Drosophila embryos resulted in loss-of-function mutant phenotypes for 43 genes, which is 1.3% of the genes that were screened. We found 18 genes that were not known previously to affect the development of the nervous system. The functions of some of the genes are unknown. Other genes encode protein kinases, transcription factors, and signaling proteins, as well as proteins with other functions.

| S-EPMC528945 | biostudies-literature

Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries.

Project description:BackgroundTopologically associating domains (TADs) are genomic regions of self-interaction. Additionally, it is known that TAD boundaries are enriched in CTCF binding sites. In turn, CTCF sites are known to be asymmetric, whereby the convergent configuration of a pair of CTCF sites leads to the formation of a chromatin loop in vivo. However, to date, it has been unclear how to reconcile TAD structure with CTCF-based chromatin loops.ResultsWe approach this problem by analysing CTCF binding site strengths and classifying clusters of CTCF sites along the genome on the basis of their relative orientation. Analysis of CTCF site orientation classes as a function of their spatial distribution along the human genome reveals that convergent CTCF site clusters are depleted while divergent CTCF clusters are enriched in the 5- to 100-kb range. We then analyse the distribution of CTCF binding sites as a function of TAD boundary conservation across seven primary human blood cell types. This reveals divergent CTCF site enrichment at TAD boundaries. Furthermore, convergent arrays of CTCF sites separate the left and right sections of TADs that harbour internal CTCF sites, resulting in unequal TAD 'halves'.ConclusionsThe orientation-based CTCF binding site cluster classification that we present reconciles TAD boundaries and CTCF site clusters in a mechanistically elegant fashion. This model suggests that the emergent structure of nuclear chromatin in the form of TADs relies on the obligate alternation of divergent and convergent CTCF site clusters that occur at different length scales along the genome.

| S-EPMC7422557 | biostudies-literature

Project description:Patched-related (Ptr), classified primarily as a neuroectodermal gene, encodes a protein with predicted topology and domain organization closely related to those of Patched (Ptc), the canonical receptor of the Hedgehog (Hh) pathway. To investigate the physiological function of Ptr in the developing nervous system, Ptr null mutant embryos were immunolabeled and imaged under confocal microscopy. These embryos displayed severe alterations in the morphology of the primary axonal tracts, reduced number, and altered distribution of the Repo-positive glia as well as peripheral nervous system defects. Most of these alterations were recapitulated by downregulating Ptr expression, specifically in embryonic nerve cells. Because similar nervous system phenotypes have been observed in hh and ptc mutant embryos, we evaluated the Ptr participation in the Hh pathway by performing cell-based reporter assays. Clone-8 cells were transfected with Ptr-specific dsRNA or a Ptr DNA construct and assayed for changes in Hh-mediated induction of a luciferase reporter. The results obtained suggest that Ptr could act as a negative regulator of Hh signaling. Furthermore, co-immunoprecipitation assays from cell culture extracts premixed with a conditioned medium revealed a direct interaction between Ptr and Hh. Moreover, in vivo Ptr overexpression in the domain of the imaginal wing disc where Engrailed and Ptc coexist produced wing phenotypes at the A/P border. Thus, these results strongly suggest that Ptr plays a crucial role in nervous system development and appears to be a negative regulator of the Hh pathway.

| S-EPMC9446084 | biostudies-literature

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