Spatial profiling of chromatin accessibility in mouse and human tissues.
Spatial profiling of chromatin accessibility in mouse and human tissues.
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DOI：
10.1038/s41586-022-05094-1
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发表时间：
2022-09
期刊：
影响因子：
64.8
通讯作者：
Fan, Rong
中科院分区：
文献类型：
--
作者：
Deng, Yanxiang;Bartosovic, Marek;Ma, Sai;Zhang, Di;Kukanja, Petra;Xiao, Yang;Su, Graham;Liu, Yang;Qin, Xiaoyu;Rosoklija, Gorazd B.;Dwork, Andrew J.;Mann, J. John;Xu, Mina L.;Halene, Stephanie;Craft, Joseph E.;Leong, Kam W.;Boldrini, Maura;Castelo-Branco, Goncalo;Fan, Rong
组织中的细胞功能依赖于局部环境，需要新的方法来绘制组织背景下的生物分子和细胞的空间图谱。空间转录学的出现使得基因组水平的基因表达图谱成为可能，但在细胞水平和基因组水平上捕捉组织的空间表观遗传信息的能力还很欠缺。在这里，我们描述了一种通过结合原位Tn5转座化学和微流控确定性条形码，使用下一代测序(SPACE-ATAC-SEQ)对组织切片进行空间分辨染色质可及性分析的方法。使用SPACE-ATAC-SEQ分析小鼠胚胎可以描绘特定组织区域的表观遗传环境，并确定参与中枢神经系统发育的基因调控因子。绘制小鼠和人类大脑中可访问的基因组图显示了大脑区域的复杂区域化。将SPACE-ATAC-SEQ应用于扁桃体组织，解决了淋巴滤泡和滤泡外带中免疫细胞类型和状态的空间差异组织。这项技术通过空间分辨染色质可及性分析来进步空间生物学，以提高我们对细胞身份、细胞状态和细胞命运决定的理解，这些决定与发育和疾病的表观遗传基础有关。Space-ATAC-Seq-使用下一代测序描绘的小鼠胚胎组织区域特定表观遗传景观，空间地解决了组织切片的染色质可及性剖析，并确定了参与中枢神经系统和淋巴组织发育的基因调节因子。
Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry and microfluidic deterministic barcoding. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease. Spatial-ATAC-seq—spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing—delineated tissue-region-specific epigenetic landscapes in mouse embryos and identified gene regulators involved in the development of the central nervous system and the lymphoid tissue.
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影响因子：
64.8
作者：
Cao, Junyue;Spielmann, Malte;Shendure, Jay
通讯作者：
Shendure, Jay
影响因子：
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作者：
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影响因子：
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作者：
Elsner, Rebecca A.;Ernst, David N.;Baumgarth, Nicole
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Baumgarth, Nicole
影响因子：
64.8
作者：
Gorkin, David U.;Barozzi, Iros;Ren, Bing
通讯作者：
Ren, Bing
单细胞染色质可及性揭示了调节变化的原理。
影响因子：
64.8
作者：
Buenrostro JD;Wu B;Litzenburger UM;Ruff D;Gonzales ML;Snyder MP;Chang HY;Greenleaf WJ
通讯作者：
Greenleaf WJ