接下来，作者研究CBS的变化是否会影响“环挤出模型”以及其绝缘性能。作者通过转基因鼠模型发现，在全基因组水平，特定CBSs形成染色质环并不依赖于模体（motif）定向，而是很可能依赖于环结构变化。作者还发现，CBSs的序列多样性以及其定向与绝缘性能关系不大。再下来，作者研究CTCF结合与EP边界功能之间的关系。作者发现...
转录抑制子CCCTC-结合因子(简称CTCF)存在于大部分边界区域之中【4】,其缺失会导致全基因组缺失TADs【8-10】。在TAD边界区域,CTCF结合位点(CTCF binding site,简称CBSs)在脊椎动物进化中高度保守。染色质环的形成通常与TAD边界密切相关,且常常形成于CBSs对之间。这一偏好性可以用“环挤出模型(loop extrusion model)”...
BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters ...
3、 Jpx RNA拮抗CTCF对靶标基因的结合 从头基序分析(De novo motif analysis)鉴定出18种Jpx结合基序,其中数个与已知的转录因子结合基序显示出相似性,特别是CTCF的结合位点。此前研究发现Jpx可以将CTCF从Xist启动子上驱逐下去【5】,于是作者使用ChIP...
The first genome-wide analysis of CTCF binding using ChIP-chip identified 13,804 sites in human fibroblasts (32), mostly outside promoters. More than 75% of these binding sites contained the consensus CTCF-binding motif (CCGCGNGGNGGCAG) (18). A landmark ChIP-seq study by Barski et al....
while a conserved base at position 9 of the 19 bp CTCF binding motif was the most commonly mutated position at CBSs in general, the CBS hotspot mutations had the highest enrichment in the 4 bp sequence flanking the 5′ end of the CTCF motif. Furthermore, C>T changes, which are rel...
The first CTCF-binding motif was altered by an asthma-risk SNP (rs4065275) in the ORMDL3 intronic region causing an A-to-G change in the motif, which is predicted to enhance the binding of CTCF (Fig. 4a and Supplementary Data set 5). We experimentally confirmed that CTCF binding in ...
Experiments using chromatin immunoprecipitation exonuclease (ChIP-exo) uncovered a broad CTCF-binding motif that contains a 12–15 bp consensus sequence, 5′-NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)-3′ (Nakahashi et al., 2013, Rhee and Pugh, 2011) (Figure 1A). This consensus is ...
CTCF与CTCF-s结合峰的差异(左)和结合motif的变化(右) “兄弟阋墙”,“小弟”屈居下风 CTCF和CTCF-s“兄弟俩”具有相似的DNA结合模式,在体外实验中竞争性结合DNA,细胞内情况会更复杂一些。利用CTCF N末端特异性抗体进行的ChIP-seq数据显示,在过表达CTCF-s(带FLAG标签)的细胞中,多数CTCF结合位点(下图Cluster 2)未...
优势二 数据高标准交付优势三 组织样本使用illumina原厂Tn5酶优势四 积累5年超过5000多例项目的冷冻组织提核实践，涉及干细胞、软骨，神经元、胎盘，各种昆虫等高难度样本类型。优势五 ATAC-seq motif分析，ATAC-seq与RNA-seq联合分析一网打尽，应有尽有。3嘉因生物-ATAC-seq客户文章 ...