Access of transcription factors (TFs) to their target sequences is governed by nucleosome occupancy, but the effect of local chromatin state on the ability of individual TFs to bind to their targets remains unclear. In this work, Dirk Schübeler and colleagues apply a reductionist approach to determine the in vivo occupancy of over 100 individual TF-binding motifs within different chromatin contexts using single-molecule footprinting. They find that a set of TFs, including the pioneer factors OCT4 and SOX2, are able to engage with their targets in a sequence with unphased nucleosome positioning, but these factors are unable to bind when their endogenous site is occupied by a nucleosome. By contrast, other TFs, such as BANP, REST or CTCF, can displace nucleosomes and thus bind regardless of nucleosome positioning. Interestingly, longer motif length, rather than type of DNA-binding domain, appears to be an important factor in obtaining a TF footprint. Together, these findings challenge the view of a binary distinction of TFs into pioneer and non-pioneer factors, and also emphasize the importance of chromatin context for shaping specific TF-binding patterns in the genome.

Original reference: Mol. Cell 84, 3455–3468.e6 (2024)

转录因子 （TF） 对其靶序列的访问受核小体占有率控制，但局部染色质状态对单个 TF 与其靶标结合能力的影响仍不清楚。在这项工作中，Dirk Schübeler 及其同事应用还原论方法，使用单分子足迹确定不同染色质环境中 100 多个单个 TF 结合基序的体内占有率。他们发现一组 TFs，包括先锋因子 OCT4 和 SOX2，能够以无相位核小体定位的序列与其靶标结合，但当它们的内源位点被核小体占据时，这些因子无法结合。相比之下，其他 TFs，如 BANP、REST 或 CTCF，可以取代核小体，因此无论核小体定位如何，都可以结合。有趣的是，较长的基序长度，而不是 DNA 结合结构域的类型，似乎是获得 TF 足迹的重要因素。总之，这些发现挑战了将 TF 二元区分为先锋因子和非先锋因子的观点，也强调了染色质环境对于塑造基因组中特定 TF 结合模式的重要性。

原始参考：Mol. Cell84， 3455–3468.e6 （2024）