德国柏林洪堡大学Ana Pombo、Warren Winick-Ng等研究人员合作发现，细胞类型的特化由特定的染色质拓扑结构编码。2021年11月17日，国际知名学术期刊《自然》在线发表了这一成果。

研究人员开发了immunoGAM，这是基因组结构图谱（GAM）的延伸，用于绘制特定脑细胞类型的全基因组三维染色质拓扑结构图，无需破坏组织，且来自单一动物。GAM是一种无需连接的技术，通过对薄薄的（约220纳米）核冷冻切片中的DNA内容进行测序，绘制基因组拓扑结构图。染色质的相互作用是通过在核切片集合中接触位点的共同聚集的概率增加来确定的。immunoGAM扩大了GAM的范围，能够在复杂的组织内使用低细胞数（大约1000个细胞）选择特定的细胞类型，并避免组织解离。研究人员报告了与基因表达模式有关的多种基因组尺度的细胞类型专门的三维染色质结构。

研究人员发现，当长基因高度表达和/或具有高染色质可及性时，长基因的广泛"融化"。神经元亚型中最特殊的接触点包含与特化过程相关的基因，如成瘾和突触可塑性，这些基因在可接触的染色质区域内藏有神经元转录因子的推定结合点。此外，感觉受体基因优先发现于脑细胞的异染色体区，它建立了跨越几十兆的强联系。这些结果表明，脑细胞中高度特异的染色质构象与基因调控机制和专门功能密切相关。

据了解，染色质的三维（3D）结构与基因调控和细胞功能有着内在的联系。基于染色质构象捕获的方法绘制了神经元系统的染色质结构图，如体外分化的神经元、通过荧光激活细胞分选从不同动物的皮层组织中分离出来的神经元以及从离体的整个海马。然而，通过成像捕捉到的染色质组织的变化，如激活后Bdnf远离核外周的位置，在这种方法中是看不见的。

附：英文原文

Title: Cell-type specialization is encoded by specific chromatin topologies

Author: Winick-Ng, Warren, Kukalev, Alexander, Harabula, Izabela, Zea-Redondo, Luna, Szab, Dominik, Meijer, Mandy, Serebreni, Leonid, Zhang, Yingnan, Bianco, Simona, Chiariello, Andrea M., Irastorza-Azcarate, Ibai, Thieme, Christoph J., Sparks, Thomas M., Carvalho, Slvia, Fiorillo, Luca, Musella, Francesco, Irani, Ehsan, Triglia, Elena Torlai, Kolodziejczyk, Aleksandra A., Abentung, Andreas, Apostolova, Galina, Paul, Eleanor J., Franke, Vedran, Kempfer, Rieke, Akalin, Altuna, Teichmann, Sarah A., Dechant, Georg, Ungless, Mark A., Nicodemi, Mario, Welch, Lonnie, Castelo-Branco, Gonalo, Pombo, Ana

Issue&Volume: 2021-11-17

Abstract: The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1,2,3. 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 hippocampi4,5,6. 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 220nm) 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 1,000cells) within a complex tissue and avoids tissue dissociation2,10. 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.

DOI: 10.1038/s41586-021-04081-2

Source: https://www.nature.com/articles/s41586-021-04081-2