Fujimori Taihei, Rios-Martinez Carolina, Thurm Abby R, Hinks Michaela M, Doughty Benjamin R, Sinha Joydeb, Le Derek, Hafner Antonina, Greenleaf William J, Boettiger Alistair N, Bintu Lacramioara
Department of Bioengineering, Stanford University, Stanford, CA, USA.
Biophysics Program, Stanford University, Stanford, CA, USA.
bioRxiv. 2023 Oct 5:2023.10.03.560616. doi: 10.1101/2023.10.03.560616.
Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.
抑制性染色质修饰被认为会使染色质压缩从而沉默转录。然而，目前尚不清楚在沉默和表观遗传记忆形成过程中染色质结构是如何变化的。我们在报告基因处招募和释放阻遏物后，测量了单细胞中的基因表达和染色质结构。染色质结构是异质性的，在活跃和沉默状态下均存在开放和紧密构象。与表观遗传记忆相关的阻遏物的招募会导致跨越10 - 20千碱基的染色质压缩，而可逆性沉默在此尺度上不会引起压缩。染色质压缩是可遗传的，但随着时间的推移会在分子水平上从组蛋白甲基化（H3K9me3）转变为DNA甲基化。沉默结束时的压缩水平定量地预测了数周后的表观遗传记忆。同样，Nanog基因座处的染色质压缩预测了干细胞命运决定的程度。这些发现表明，基因本身之外的数十千碱基范围内的染色质状态对于表观遗传记忆的形成很重要。
