Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Nat Methods. 2023 May;20(5):686-694. doi: 10.1038/s41592-023-01845-8. Epub 2023 Apr 27.
In biological systems, spatial organization and function are interconnected. Here we present photoselective sequencing, a new method for genomic and epigenomic profiling within morphologically distinct regions. Starting with an intact biological specimen, photoselective sequencing uses targeted illumination to selectively unblock a photocaged fragment library, restricting the sequencing-based readout to microscopically identified spatial regions. We validate photoselective sequencing by measuring the chromatin accessibility profiles of fluorescently labeled cell types within the mouse brain and comparing with published data. Furthermore, by combining photoselective sequencing with a computational strategy for decomposing bulk accessibility profiles, we find that the oligodendrocyte-lineage-cell population is relatively enriched for oligodendrocyte-progenitor cells in the cortex versus the corpus callosum. Finally, we leverage photoselective sequencing at the subcellular scale to identify features of chromatin that are correlated with positioning at the nuclear periphery. These results collectively demonstrate that photoselective sequencing is a flexible and generalizable platform for exploring the interplay of spatial structures with genomic and epigenomic properties.
在生物系统中，空间组织和功能是相互关联的。在这里，我们提出了光选择性测序，这是一种在形态上不同的区域内进行基因组和表观基因组分析的新方法。从完整的生物样本开始，光选择性测序使用靶向照明来选择性地解开光笼片段文库，将基于测序的读出限制在显微镜识别的空间区域。我们通过测量在小鼠大脑中荧光标记的细胞类型的染色质可及性图谱并与已发表的数据进行比较，验证了光选择性测序。此外，通过将光选择性测序与用于分解批量可及性图谱的计算策略相结合，我们发现皮质中的少突胶质细胞谱系细胞群体相对于胼胝体更富集少突胶质前体细胞。最后，我们利用亚细胞尺度的光选择性测序来识别与核周定位相关的染色质特征。这些结果共同表明，光选择性测序是一个灵活且可推广的平台，可用于探索空间结构与基因组和表观基因组特性的相互作用。
