We present replication-aware single-molecule accessibility mapping (RASAM), a method to nondestructively measure replication status and protein-DNA interactions on chromatin genome-wide. Using RASAM, we uncover a genome-wide state of single-molecule “hyperaccessibility” post-replication that resolves over several hours. Combining RASAM with cellular models for rapid protein degradation, we demonstrate that histone chaperone CAF-1 reduces nascent chromatin accessibility by filling single-molecular “gaps” and generating closely spaced dinucleosomes on replicated DNA. At cis-regulatory elements, we observe unique modes by which nascent chromatin hyperaccessibility resolves: at CCCTC-binding factor (CTCF)-binding sites, CTCF and nucleosomes compete, reducing CTCF occupancy and motif accessibility post-replication; at active transcription start sites, high chromatin accessibility is maintained, implying rapid re-establishment of nucleosome-free regions. Our study introduces a new paradigm for studying replicated chromatin fiber organization. More broadly, we uncover a unique organization of newly replicated chromatin that must be reset by active processes, providing a substrate for epigenetic reprogramming.

中文翻译：

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新复制的哺乳动物染色质的单分子可及性景观


我们提出了复制感知单分子可及性映射 （RASAM），这是一种无损测量全基因组染色质上复制状态和蛋白质-DNA 相互作用的方法。使用 RASAM，我们发现了复制后单分子“超可访问性”的全基因组状态，该状态在几个小时内解决。将 RASAM 与用于快速蛋白质降解的细胞模型相结合，我们证明组蛋白伴侣 CAF-1 通过填充单分子“间隙”并在复制的 DNA 上产生紧密间隔的二核小体来降低新生染色质的可及性。在顺式调节元件处，我们观察到新生染色质超可及性解决的独特模式：在 CCCTC 结合因子 （CTCF） 结合位点，CTCF 和核小体竞争，降低 CTCF 占有率和复制后基序可及性;在活跃的转录起始位点，保持了高染色质可及性，这意味着快速重建无核小体区域。我们的研究引入了一种研究复制的染色质纤维组织的新范式。更广泛地说，我们发现了新复制的染色质的独特组织，该组织必须通过活性过程重置，从而为表观遗传重编程提供底物。