Primary architecture of chromatin fibers The organization of chromosomal DNA, including the positioning of nucleosomes and nucleosome-free regions harboring regulatory proteins along single chromatin fibers, is fundamental to genome function. However, most sequencing methods cannot elucidate this organization at the nucleotide level. Stergachis et al. present an approach, Fiber-seq, that maps chromatin fibers onto the underlying DNA template using methyltransferases to create a kind of stencil in fly and human cells. This method identifies chromatin structure at nearly a single-molecule level and can monitor the position of nucleosomes. Using Fiber-seq, the authors identify how regulatory DNA activation is related to nucleosome positioning and DNA variation. Science, this issue p. 1449 Fiber-seq translates single-molecule chromatin stencils into a readout of the primary architecture of chromatin. Gene regulation is chiefly determined at the level of individual linear chromatin molecules, yet our current understanding of cis-regulatory architectures derives from fragmented sampling of large numbers of disparate molecules. We developed an approach for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using nonspecific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing of chromatin stencils enabled nucleotide-resolution readout of the primary architecture of multikilobase chromatin fibers (Fiber-seq). Fiber-seq exposed widespread plasticity in the linear organization of individual chromatin fibers and illuminated principles guiding regulatory DNA actuation, the coordinated actuation of neighboring regulatory elements, single-molecule nucleosome positioning, and single-molecule transcription factor occupancy. Our approach and results open new vistas on the primary architecture of gene regulation.

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染色质纤维测序捕获的单分子调控结构

染色质纤维的主要结构 染色体 DNA 的组织，包括沿单个染色质纤维定位含有调节蛋白的核小体和无核小体区域，是基因组功能的基础。然而，大多数测序方法无法在核苷酸水平上阐明这种组织。Stergachis 等人。提出了一种方法，Fiber-seq，它使用甲基转移酶将染色质纤维映射到底层 DNA 模板上，从而在果蝇和人类细胞中创建一种模板。该方法在近乎单分子水平上识别染色质结构，并可监测核小体的位置。使用 Fiber-seq，作者确定了调节性 DNA 激活与核小体定位和 DNA 变异之间的关系。科学，这个问题 p。1449 Fiber-seq 将单分子染色质模板转化为染色质初级结构的读数。基因调控主要在单个线性染色质分子的水平上确定，但我们目前对顺式调控结构的理解来自大量不同分子的碎片化采样。我们开发了一种使用非特异性 DNA N6-腺嘌呤甲基转移酶将单个染色质纤维的结构精确模板化到其复合 DNA 模板上的方法。染色质模板的单分子长读长测序能够以核苷酸分辨率读出多千碱基染色质纤维 (Fiber-seq) 的初级结构。Fiber-seq 揭示了单个染色质纤维线性组织中的广泛可塑性，并阐明了指导调节 DNA 驱动、相邻调节元件的协调驱动、单分子核小体定位和单分子转录因子占据的指导原则。我们的方法和结果为基因调控的主要架构开辟了新的前景。