Transcription processes compete with loop extrusion to homogenize promoter and enhancer dynamics

The spatiotemporal configuration of genes with distal regulatory elements is believed to be crucial for transcriptional control, but full mechanistic understanding is lacking. We combine simultaneous live tracking of pairs of genomic loci and nascent transcripts with molecular dynamics simulations to assess the Sox2 gene and its enhancer. We find that both loci exhibit more constrained mobility than control sequences due to stalled cohesin at CTCF sites. Strikingly, enhancer mobility becomes constrained on transcriptional firing, homogenizing its dynamics with the gene promoter, suggestive of their co-transcriptional sharing of a nuclear microenvironment. Furthermore, we find transcription and loop extrusion to be antagonistic processes constraining regulatory loci. These findings indicate that modulating chromatin mobility can be an additional, underestimated means for effective gene regulation. Allele-specific 4C-seq, with the Sox2 SCR as bait, for ESC lines, in duplicate (except for days 1, 2 and 3 of differentiation, which have one replicate)

人们普遍认为，带有远端调控元件的基因的时空构象对于转录调控至关重要，但目前仍缺乏完整的机制层面认知。我们将成对基因组位点与新生转录本的实时同步追踪技术与分子动力学模拟相结合，以解析Sox2基因及其增强子的调控特征。研究发现，由于黏连蛋白（cohesin）在CTCF结合位点处发生停滞，这两个基因组位点的运动相较于对照序列更为受限。值得注意的是，当转录激活时，增强子的运动亦会受到限制，使其动力学特征与基因启动子趋于一致，这表明二者可在转录过程中共用核微环境。此外，我们发现转录与环挤出是两种相互拮抗的过程，共同对调控位点的运动施加限制。上述研究结果表明，调控染色质运动性可作为一种此前被低估的有效基因调控手段。本研究针对胚胎干细胞（ESC）系开展了以Sox2 SCR为诱饵探针的等位基因特异性4C-seq实验，除分化第1、2、3天仅设置1次重复外，其余组别均设置2次生物学重复。