Polycomb repressive complex 1 regulates the nucleosome landscape but not accessibility at target genes [RNA-seq]

Polycomb repressive complexes 1 and 2 (PRC1/2) act to limit transcriptional activity at gene promoters. One of the mechanisms by which they are proposed to achieve this is through the compaction of nucleosomal chromatin. However, this model is based largely upon in vitro studies and has yet to be explored sufficiently in living cells. We therefore characterised the chromatin accessibility of Polycomb-occupied gene promoters using assay for transposase accessible chromatin (ATAC-seq). Although Polycomb-occupied promoters exist in a less accessible state compared to Polycomb-free promoters, we were surprised to observe that deletion of either PRC1, PRC2 or both PRC1/2 did not result in any increases in chromatin accessibility. This was in contrast to widespread increases in the transcriptional activity of Polycomb target genes. Together with experiments examining chromatin accessibility in the context of RNA polymerase II inhibition, we therefore demonstrate an apparent uncoupling of the chromatin accessibility and transcriptional activity of gene promoters.

多梳抑制复合体1和2（Polycomb Repressive Complexes 1/2, PRC1/2）可抑制基因启动子区域的转录活性。目前学界提出其实现该调控的机制之一是通过压缩核小体染色质。然而，该模型主要基于体外实验研究，尚未在活细胞中得到充分探究。为此，我们利用转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing, ATAC-seq）技术，对结合多梳蛋白的基因启动子的染色质可及性进行了表征。尽管与未结合多梳蛋白的启动子相比，结合多梳蛋白的启动子所处的染色质可及性更低，但我们意外观察到，单独敲除PRC1、PRC2或同时敲除两者，均未使染色质可及性出现任何升高。这一结果与多梳靶基因转录活性显著上调的现象形成鲜明对比。结合RNA聚合酶II（RNA polymerase II）抑制条件下的染色质可及性相关实验，我们最终证实了基因启动子的染色质可及性与转录活性之间存在明显的解偶联现象。