We find that CTCF loops are formed and disassembled at different stages of the differentiation process by either recruitment of CTCF to new anchor sites or use of pre-existing sites not previously involved in loop formation. Recruitment of CTCF to new sites in the genome involves demethylation of...
To understand the function of CTCF PTMs, potential PTMs should be mapped from the N to the C terminal with an unbiased method41. Hence, we mapped CTCF PTMs unbiasedly and a schematic overview is shown in Fig.1a. In brief, CTCF was purified from the lysates of WT mESCs and separated ...
(eRNAs). A species of bidirectional, unstable non-coding RNAs produced at enhancers. Considered a hallmark of active enhancers and sometimes used for enhancer annotation. CTCF A transcription factor that acts primarily in chromatin 3D architecture regulation, through anchoring long-range chromatin loops...
The latter finding is consistent with the role that convergently bound CTCF proteins play in loop formation. This study clarifies the relative and combined contribution of CTCF and CTCFL to chromosome organization and transcription, with direct implications for understanding how their co-expression ...
(CTCF), cAMP responsive element-binding protein (CREB), signal transducer and activator of transcription 3 (STAT3), and E2F interact directly with their binding sites and upregulate FOXM1 expression [9,30,31,32,33,34]. In human colorectal cancer (CRC), Gli1 regulates FOXM1 by directly ...
The epithelial-mesenchymal transition (EMT) is a vital driver of tumor progression. It is a well-known and complex trans-differentiation process in which epithelial cells undergo morphogenetic changes with loss of apical-basal polarity, but acquire spind
tRNA genes connected by DNA loops, which are proximal to CTCF binding sites and expressed at elevated levels compared to non-loop tDNAs, change coordinately with tDNAs and protein-coding genes at distal ends of interactions mapped by in situ Hi-C. We find that downregulated tRNA genes are ...
Types of 3D chromatin architecture Topologically associating domain (TAD) Topologically associating domains (TADs) are self-interacting regions characterised by increased intra-domain interactions [13,14]. The key player in defining the boundary of TADs is CTCF, a highly conserved zinc-finger DNA-bindi...
Functional role of extranucleosomal DNA and the entry site of the nucleosome in chromatin remodeling by ISW2. Mol. Cell. Biol. 24, 10047–10057 (2004). Article CAS PubMed PubMed Central Google Scholar Strohner, R. et al. A 'loop recapture' mechanism for ACF-dependent nucleosome ...
et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381–385 (2012). Article CAS PubMed PubMed Central Google Scholar Handoko, L. et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat. Genet. 43, 630–638 (2011). ...