Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
Proc Natl Acad Sci U S A. 2021 Nov 16;118(46). doi: 10.1073/pnas.2113579118.
Using a tamoxifen-inducible time-course ChIP-sequencing (ChIP-seq) approach, we show that the ubiquitous transcription factor SP1 has different binding dynamics at its target sites in the human genome. SP1 very rapidly reaches maximal binding levels at some sites, but binding kinetics at other sites is biphasic, with rapid half-maximal binding followed by a considerably slower increase to maximal binding. While ∼70% of SP1 binding sites are located at promoter regions, loci with slow SP1 binding kinetics are enriched in enhancer and Polycomb-repressed regions. Unexpectedly, SP1 sites with fast binding kinetics tend to have higher quality and more copies of the SP1 sequence motif. Different cobinding factors associate near SP1 binding sites depending on their binding kinetics and on their location at promoters or enhancers. For example, NFY and FOS are preferentially associated near promoter-bound SP1 sites with fast binding kinetics, whereas DNA motifs of ETS and homeodomain proteins are preferentially observed at sites with slow binding kinetics. At promoters but not enhancers, proteins involved in sumoylation and PML bodies associate more strongly with slow SP1 binding sites than with the fast binding sites. The speed of SP1 binding is not associated with nucleosome occupancy, and it is not necessarily coupled to higher transcriptional activity. These results with SP1 are in contrast to those of human TBP, indicating that there is no common mechanism affecting transcription factor binding kinetics. The biphasic kinetics at some SP1 target sites suggest the existence of distinct chromatin states at these loci in different cells within the overall population.
使用他莫昔芬诱导的时程 ChIP-seq（ChIP-seq）方法，我们表明，普遍存在的转录因子 SP1 在人类基因组中的靶位点具有不同的结合动力学。SP1 在一些位点迅速达到最大结合水平，但在其他位点的结合动力学呈双相，快速达到半最大结合，然后缓慢增加到最大结合。虽然约 70%的 SP1 结合位点位于启动子区域，但结合动力学较慢的位点富含增强子和 Polycomb 抑制区域。出乎意料的是，结合动力学较快的 SP1 位点往往具有更高的质量和更多的 SP1 序列基序副本。不同的共结合因子根据其结合动力学及其位于启动子或增强子的位置，在 SP1 结合位点附近聚集。例如，NFY 和 FOS 优先与具有快速结合动力学的启动子结合的 SP1 位点结合，而 ETS 和同源域蛋白的 DNA 基序则优先在结合动力学较慢的位点观察到。在启动子上而不是增强子上，与 sumoylation 和 PML 体相关的蛋白质与结合动力学较慢的 SP1 结合位点的结合更强，而不是与结合动力学较快的位点。SP1 的结合速度与核小体占有率无关，并且不一定与更高的转录活性相关。这些 SP1 的结果与人类 TBP 的结果形成对比，表明没有影响转录因子结合动力学的共同机制。一些 SP1 靶位点的双相动力学表明，在总体人群的不同细胞中，这些基因座存在不同的染色质状态。
