CCCTC-binding factor (CTCF) is an insulator protein that binds to a highly conserved DNA motif and facilitates regulation of three-dimensional (3D) nuclear architecture and transcription. CTCF binding sites (CTCF-BSs) reside in non-coding DNA and are frequently mutated in cancer. Our previous ...
for the glucocorticoid receptor (GR), differences as small as one nucleotide base among the endogenous GR binding sites can have a dramatic impact on GR conformation and activity [15]. Thus, binding sites play an important role in determining function. Using genome-wide location analysis, a majo...
CTCF-binding sites that are conserved among these species but were previously undetected. In particular, this program identified CTCF-binding sites that are located close to the Dlk1, Magel2 and Cdkn1c imprinted genes. Individual ChIP experi- ments confirmed the in vivo binding of the YY1 and ...
We have comprehensively characterized these three classes of CTCF sites with respect to several evolutionary, genomic, epigenomic, transcriptomic and functional features. We find that the low- occupancy sites tend to be cell type specific. Furthermore, while the high-occupancy sites associate with ...
(Supplementary Fig.12). We would expect mutations at these hotspots to be associated with expression change of the altered allele. However, allele-specific expression analysis is challenging to evaluate across distant sites. Indeed, for all three candidate CBS hotspots, we could not unambiguously ...
To filter the GRanges object and keep high-confidence CTCF sites, use: #Check length before filteringprint(paste("Number of CTCF motifs at the default 1e-4 threshold:", length(CTCF_hg38)))#> [1] "Number of CTCF motifs at the default 1e-4 threshold: 887980"#Filter and check length ...
The CTCF-binding Sites in Herpes Simplex Virus-II Display Promoter-blocking Activity CTCF-binding motifs are located in the LAT downstream and intron, and display promoter-blocking activity that may play an important part in HSV-2 latency... H Yang 被引量: 0发表: 0年 A Chromatin Insulator-...
To directly test this, we used CRISPR/Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal, convergent CTCF sites were disrupted or de...
Summary The role of CTCF in stabilizing long-range interactions between chromatin sites essential for maintaining nuclear architecture is well established. Most of these interactions involve recruitment of the cohesin complex to chromatin via CTCF. We find that CTCF also interacts with the centromeric pr...
17q21 asthma-risk SNPs switch CTCF-binding sites We performed anin silicoanalysis to identify the transcription factors whose binding to thecis-regulatory regions described above is perturbed by asthma-risk SNPs. Our evaluation pointed to perturbation of two CTCF-binding motifs as well as motifs of...