Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.
Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.
复制标题
多重样本和单细胞中基因调控元件的扩展表征亚硫酸盐测序。
DOI：
10.1038/s41587-021-00910-x
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发表时间：
2021-09
影响因子：
46.9
通讯作者：
Bernstein BE
中科院分区：
文献类型：
--
作者：
Shareef SJ;Bevill SM;Raman AT;Aryee MJ;van Galen P;Hovestadt V;Bernstein BE
DNA甲基化的生物学作用已经通过基于全基因组或减少代表性亚硫酸氢盐测序的分析方法阐明，但这些方法不能有效地调查哺乳动物基因组中大量的非编码调控元件。在这里，我们提出了一个扩展的代表性亚硫酸氢盐测序（XRBS）的DNA甲基化的靶向分析方法。我们的设计在扩大调控元件的覆盖范围和可重复地富集启动子、增强子和CTCF结合位点中的信息性CpG二核苷酸之间取得了平衡。在亚硫酸氢盐转化之前合并条形码化的DNA片段，允许在低输入样品中进行多重处理和技术一致性。将XRBS应用于单个白血病细胞使我们能够评估单个细胞的遗传拷贝数变异和甲基化变异。我们的分析突出了异染色质H3K9me3区域在其甲基化中具有最高的细胞间变异性，这可能反映了这些晚期复制区域固有的表观遗传不稳定性，并且由于采样细胞之间细胞周期阶段的差异而加剧。
The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of noncoding regulatory elements in mammalian genomes. Here we present a extended representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design strikes a balance between expanding coverage of regulatory elements and reproducibly enriching informative CpG dinucleotides in promoters, enhancers, and CTCF binding sites. Barcoded DNA fragments are pooled prior to bisulfite conversion, allowing multiplex processing and technical consistency in low input samples. Application of XRBS to single leukemia cells enabled us to evaluate genetic copy-number variations and methylation variability across individual cells. Our analysis highlights heterochromatic H3K9me3 regions as having the highest cell-to-cell variability in their methylation, likely reflecting inherent epigenetic instability of these late replicating regions, compounded by differences in cell cycle stages among sampled cells.
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影响因子：
64.8
作者：
Ghandi, Mahmoud;Huang, Franklin W.;Sellers, William R.
通讯作者：
Sellers, William R.
影响因子：
64.8
作者：
Hark, AT;Schoenherr, CJ;Tilghman, SM
通讯作者：
Tilghman, SM
影响因子：
30.8
作者：
Corces, M. Ryan;Buenrostro, Jason D.;Wu, Beijing;Greenside, Peyton G.;Chan, Steven M.;Koenig, Julie L.;Snyder, Michael P.;Pritchard, Jonathan K.;Kundaje, Anshul;Gkeenleaf, William J.;Majeti, Ravindra;Chang, Howard Y.
通讯作者：
Chang, Howard Y.
影响因子：
1.2
作者：
Garrett-Bakelman, Francine E.;Sheridan, Caroline K.;Melnick, Ari M.
通讯作者：
Melnick, Ari M.
影响因子：
64.8
作者：
Bell, AC;Felsenfeld, G
通讯作者：
Felsenfeld, G