The Variable CTCF Site from Drosophila melanogaster Ubx Gene is ...
Abstract CTCF is the most thoroughly studied chromatin architectural protein and it is found in both Drosophila and mammals. CTCF preferentially binds to promoters and insulators and is thought to facilitate formation of chromatin loops. In a subset of sites, CTCF binding depends on the epigenetic status of the surrounding chromatin. One such variable CTCF site (vCTCF) was found in the intron ...
CTCF, BEAF-32, and CP190 are not required for the ... - Science
For example, a complete deletion of CTCF (removing both the maternal and zygotic supply) in vivo revealed that CTCF is not required for Drosophila embryogenesis (38) or for the maintenance of TAD structure in the larval nervous system (29), but it is required for boundary insulation and correct gene expression at a small subset of loci (29, 38).
The N-terminal dimerization domains of human and Drosophila CTCF have ...
Here we used the CTCFattP(mCh) platform to introduce desired changes in the Drosophila CTCF gene and generated a series of transgenic lines expressing dCTCF with different variants of the N-terminal domain. Our findings revealed that the functionality of dCTCF is significantly affected by the deletion of the N-terminal DD.
Adaptive evolution and the birth of CTCF binding sites in the ...
At least 89 new CTCF binding sites have originated in the Drosophila melanogaster genome since the most recent common ancestor with Drosophila simulans. Comparing these data to genome sequence data from 37 different strains of Drosophila melanogaster, we detected signatures of selection in both newly gained and evolutionarily conserved binding ...
The CCCTC-Binding Factor (CTCF) of Drosophila Contributes to the ...
In support of this hypothesis, we show that the Drosophila nucleolus contains CTCF, which is bound to transposable element sequences within the rDNA. Reduction in CTCF gene activity results in nucleolar fragmentation and reduced rDNA silencing, as does disruption of poly-ADP-ribosylation thought to be necessary for CTCF nucleolar localization.
CTCF loss has limited effects on global genome architecture in ...
We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system.
CTCF variants in 39 individuals with a variable neurodevelopmental ...
By utilizing Drosophila melanogaster we could demonstrate that Ctcf is crucial for learning and memory in a dosage-sensitive manner, thus confirming loss of function or haploinsufficiency as the ...
Integrating genetic variation with deep learning provides context for ...
The model can also predict measured allelic imbalance for strong effect variants, providing a mechanistic interpretation for how the variant impacts binding. This reveals unexpected relationships between TFs, including potential cooperative pairs, and mechanisms of tissue-specific recruitment of the ubiquitous factor CTCF.
Adaptive Evolution and the Birth of CTCF Binding Sites in the
Between species, binding divergence increased linearly with evolutionary distance, and CTCF binding profiles are diverging rapidly at the rate of 2.22% per million years (Myr). At least 89 new CTCF binding sites have originated in the Drosophila melanogaster genome since the most recent common ancestor with Drosophila simulans.
CTCF variants in 39 individuals with a variable neurodevelopmental ...
Methods Through international collaboration we collected data from 39 subjects with variants in CTCF. We performed transcriptome analysis on RNA from blood samples and utilized Drosophila melanogaster to investigate the impact of Ctcf dosage alteration on nervous system development and function.
The CCCTC-Binding Factor (CTCF) of Drosophila Contributes to the ...
We directly addressed whether CTCF is also found in the nucleolus of Drosophila, binds to the rDNA, regulates its expression, and influences the stability of the nucleolus. In the course of our work, we discovered that CTCF is not solely a marker for terminal differentiation since it is nucleolar in many non-differentiated cell types.
Drosophila architectural protein CTCF is not essential for fly survival ...
CTCF is the most likely ancestor of proteins that contain large clusters of C2H2 zinc finger domains (C2H2) and is conserved among most bilateral organisms. In mammals, CTCF functions as the main architectural protein involved in the organization of topology-associated domains (TADs). In vertebrates and Drosophila, CTCF is involved in the regulation of homeotic genes. Previously, it was found ...
An updated catalog of CTCF variants associated with neurodevelopmental ...
3. Results 3.1. Generation of CTCF variant dataset 3.1.1. Systematic review did not yield any new CTCF variants To provide a comprehensive catalog of CTCF variants associated with NDD phenotypes, a systematic review was first conducted to identify all CTCF variants discovered in probands with diagnosed NDDs. The literature search yielded 1,286 article records (Figure 1). After records were ...
Chromatin loops are an ancestral hallmark of the animal regulatory ...
In fact, a variety of architectural proteins other than CTCF have been described in Drosophila, many of which are zf-C2H2 proteins with restricted phylogenetic distributions such as the insect ...
The N-terminal dimerization domains of human and Drosophila CTCF have ...
Here we used the CTCF attP (mCh) platform to introduce desired changes in the Drosophila CTCF gene and generated a series of transgenic lines expressing dCTCF with different variants of the N-terminal domain. Our findings revealed that the functionality of dCTCF is significantly affected by the deletion of the N-terminal DD.
CTCF variants in 39 individuals with a variable neurodevelopmental ...
Methods: Through international collaboration we collected data from 39 subjects with variants in CTCF. We performed transcriptome analysis on RNA from blood samples and utilized Drosophila melanogaster to investigate the impact of Ctcf dosage alteration on nervous system development and function.
(PDF) CTCF variants in 39 individuals with a variable ...
from 39 subjects with variants in CTCF. We performed tran- scriptome analysis on RNA from blood samples and utilized Drosophila melanogaster to investigate the impact of Ctcf dosage
Determining the functional relationship between epigenetic and physical ...
The tight correlation between topologically associating domains (TADs) and epigenetic domains in Drosophila suggests that the epigenome contributes to define TADs. However, it is still unknown whether histone modifications are essential for TAD formation and structure. By either deleting or shifting key regulatory elements needed to establish the epigenetic signature of Polycomb TADs, we show ...
CTCF loss has limited effects on global genome architecture in ...
While Drosophila has widespread contact domains and CTCF, it is currently unclear whether CTCF-dependent domains exist in flies. We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system.