Hyle Judith, Qi Wenjie, Djekidel Mohamed Nadhir, Rosikiewicz Wojciech, Xu Beisi, Li Chunliang
Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Genome Biol. 2025 May 12;26(1):126. doi: 10.1186/s13059-025-03582-x.
CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies report that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq.
Here, we investigate RNA's role in CTCF's transcription factor function through its chromatin occupancy. To systematically explore whether RNAs affect CTCF's ability to bind DNA, we perturb CTCF-RNA interactions by three independent approaches and examine CTCF genome occupancy by ChIP-seq. Although RNase A and triptolide treatment each affect a certain number of CTCF-binding peaks, few peaks overlap between treatment groups indicating the effect of RNA in regulating CTCF's DNA binding affinity is variable between loci. In addition, limited transcriptional or chromatin accessibility changes occur between cells expressing wild-type CTCF or CTCF lacking the RNA binding region.
Our data provide a complementary approach and in silico evidence to consider the significance of RNA affecting CTCF's DNA binding affinity globally.
CTCF是一种经过大量研究的转录因子，对维持染色质相互作用至关重要。多项独立研究报告称，CTCF在体外和细胞中均与RNA相互作用。然而，由于可用的研究技术有限，如CLIP-seq，关于CTCF的RNA结合亲和力的真实性及其生物学作用的争论仍在很大程度上存在。
在这里，我们通过CTCF的染色质占据情况来研究RNA在其转录因子功能中的作用。为了系统地探究RNA是否影响CTCF结合DNA的能力，我们通过三种独立方法干扰CTCF与RNA的相互作用，并通过ChIP-seq检测CTCF在基因组中的占据情况。虽然核糖核酸酶A和雷公藤内酯醇处理各自影响一定数量的CTCF结合峰，但处理组之间几乎没有重叠峰，这表明RNA在调节CTCF的DNA结合亲和力方面的作用在不同位点之间是可变的。此外，在表达野生型CTCF或缺乏RNA结合区域的CTCF的细胞之间，转录或染色质可及性变化有限。
我们的数据提供了一种补充方法和计算机模拟证据，以考虑RNA在全球范围内影响CTCF的DNA结合亲和力的重要性。
