Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq]

ABSTRACT: While Drosophila has widespread contact domains, most domain boundaries are formed independently of CTCF by unclear mechanisms. We genetically ablate the ubiquitous boundary-associated factor Cp190 and examine impacts on genome folding and developmental gene regulation in Drosophila embryos. We find that Cp190 is widely required to form fly domain boundaries that are distal from transcribed gene promoters, while promoter proximal boundaries are unaffected by Cp190 loss.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE180374 | GEO | 2022/05/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [HiC]

Project description:While Drosophila has widespread contact domains, most domain boundaries are formed independently of CTCF by unclear mechanisms. We genetically ablate the ubiquitous boundary-associated factor Cp190 and examine impacts on genome folding and developmental gene regulation in Drosophila embryos. We find that Cp190 is widely required to form fly domain boundaries that are distal from transcribed gene promoters, while promoter proximal boundaries are unaffected by Cp190 loss.

2022-05-12 | GSE180375 | GEO

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C]

2022-05-12 | GSE193530 | GEO

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila

Project description:Animal genomes fold into contact domains defined by enhanced internal contact frequencies with debated functions in establishing independent gene regulatory domains. A large fraction of contact domains in mammals are formed by stalling of chromosomal loop-extruding cohesin by CTCF at domain boundaries. 90% of domain boundaries in Drosophila form CTCF-independently, and other proteins were proposed to form chromosomal loops with dual functions of segregating promoters from inappropriate regulatory elements and connecting distal regulatory elements to their correct targets. Here, we genetically ablate the ubiquitous boundary-associated factor Cp190 and assess impacts on genome folding and transcriptional regulation in embryos. Our results reveal that Cp190 is a major factor required for contact domain boundary formation and gene insulation in Drosophila.

2022-05-30 | PXD027795 | Pride

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila

Project description:Essential role of Cp190 in physical and regulatory boundary formation in Drosophila

| PRJNA748025 | ENA

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [HiC]

Project description:Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [HiC]

| PRJNA748170 | ENA

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq]

Project description:Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq]

| PRJNA748171 | ENA

Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C]

Project description:Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C]

| PRJNA796548 | ENA

Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties

Project description:The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary region with two attP sites. The attP sites were then used to generate four boundary replacements: λ DNA, nhomie forward (WT orientation), nhomie reverse (opposite of WT), and homie forward (same as WT homie). The nhomie forward replacement restores the WT physical and regulatory landscape: In MicroC experiments, the eve TAD is a volcano triangle topped by a plume, and the eve gene and its regulatory elements are sequestered from interactions with neighbors. The λ DNA replacement lacks boundary function: the endpoint of the “new” eve TAD on the nhomie side is ill-defined, and eve stripe enhancers activate a nearby gene, eIF3j. While nhomie reverse and homie forward restore the eve TAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, the eve TAD interacts with its neighbors, and the plume at the top of the eve volcano triangle is replaced by a cloud of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, the eve enhancers weakly activate genes in the neighboring TADs. Conversely, eve function is partially disrupted.

2024-04-04 | GSE263270 | GEO

Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster

Project description:The architectural protein Pita is critical for Drosophila embryogenesis and predominantly binds to gene promoters and insulators. In particular, Pita is involved in the organization of boundaries between regulatory domains, controlled by the expression of three hox genes in the Bithorax complex (BX-C). The best-characterized partner for Pita is the BTB/POZ-domain containing protein CP190. Here, we precisely mapped two unstructured regions of Pita that interact with the BTB domain of CP190. The deletion of the CP190-interacting regions did not significantly affect the binding of the mutant Pita protein to most chromatin sites. The expression of the mutant protein completely complemented the null pita mutation. However, the mutant Pita protein does not support the ability of multimerized Pita sites to prevent cross-talk between the iab-6 and iab-7 regulatory domains that activate the expression of Abdominal-B (Abd-B), one of the genes in the BX-C. The recruitment of the Pita region and the interaction with CP190 and the polytene chromosomes of larvae induces the formation of a new interband, which is a consequence of the formation of open chromatin in this region. These results suggested that the interaction with CP190 is required for the primary Pita activities, but other architectural proteins may also recruit CP190 in flies expressing only the mutant Pita protein.

2020-11-30 | GSE160007 | GEO

The transcription factor M1BP targets CP190 to chromatin to regulate transcription and chromatin insulator activity (ChIP-Seq)

Project description:Chromatin insulators are DNA-protein complexes that establish distinct higher order transcriptional domains. In Drosophila, CP190 is the only common factor for all the DNA-binding insulator protein complex. Insulators harbour two properties: they can block communication between an enhancer and a promoter, and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy insulator complex contains three core components; Su(Hw), CP190 and Mod(mdg4)67.2. In our studies, using mass-spec analysis and of immunopurified complexes from Drosophila embryonic nuclear extracts, we identified the transcription factor Motif 1 Binding Protein (M1BP) associated with CP190 and verified this interaction by coimmunoprecipitation. Furthermore, depletion of M1BP results in loss of both enhancer-blocking and barrier activities, also disrupts the nuclear localization of CP190-marked insulator bodies within the developing fly. ChIP-seq analysis of both factors in Kc167 cultured hemocytes revealed extensive overlap of the two factors, particularly at Motif 1 containing promoters. Depletion of M1BP results in extensive loss of CP190 chromatin association, and depletion of CP190 also greatly affects M1BP chromatin association. Moreover, EU-seq analysis after depletion of either CP190 or M1BP suggests they regulate gene expression in similar fashion. Further analysis using reporter assays verifies that CP190-dependent gene expression changes are dependent on the presence of Motif 1. Our results suggest a novel mechanistic relationship between CP190 and M1BP function with respect to transcriptional regulation and higher order chromatin organization.

2020-10-27 | GSE142531 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data