The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function^1,2,3. Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi^4,5,6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation⁷, are invisible with such approaches⁸. Here we developed immunoGAM, an extension of genome architecture mapping (GAM)^2,9, to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation^2,10. We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive ‘melting’ of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.

染色质的三维 (3D) 结构本质上与基因调控和细胞功能相关^1,2,3。基于染色质构象捕获的方法已经绘制了神经元系统中的染色质结构图，例如体外分化的神经元、通过荧光激活细胞分选从不同动物和分离的整个海马皮层组织中分离的神经元^4,5,6。然而，通过成像捕获的染色质组织的变化，例如激活后Bdnf远离核外围的重新定位⁷，用这种方法是看不见的⁸。在这里，我们开发了immunoGAM，它是基因组架构图谱(GAM) ^2,9的扩展，可在单个动物的特定脑细胞类型中绘制全基因组范围的3D染色质拓扑图，而无需破坏组织。GAM 是一种免连接技术，通过对薄（约 220 nm）核冷冻切片中的 DNA 内容进行测序来绘制基因组拓扑图。染色质相互作用是通过核切片集合中接触位点共分离概率的增加来识别的。ImmunoGAM 扩展了 GAM 的范围，能够在复杂组织内使用低细胞数量（大约 1,000 个细胞）选择特定细胞类型，并避免组织解离^2,10。我们报告了与基因表达模式相关的多个基因组尺度的细胞类型特异性 3D 染色质结构。我们发现，当长基因高度表达和/或具有高染色质可及性时，它们会发生广泛的“融化”。最特定的神经元亚型接触包含与特殊过程相关的基因，例如成瘾和突触可塑性，这些基因在可及的染色质区域内包含神经元转录因子的假定结合位点。此外，感觉受体基因优先发现于脑细胞的异染色质区室中，这些区室在数十兆碱基范围内建立了牢固的接触。我们的结果表明，脑细胞中高度特异性的染色质构象与基因调控机制和专门功能密切相关。