Genome-wide maps of nuclear lamina interactions (DamID on microarray; LaminB1, KBM7 cells, haploid). Homo sapiens

Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, single-cell gene expression and chromatin accessibility analysis shows that loci with consistent NL contacts are expressed at lower levels and are more consistently inaccessible than loci with lower contact frequencies. These results highlight fundamental principles of single cell chromatin organization. Overall design: LaminB1-chromatin interactions were assayed in human KBM7 by viral transductions with Dam-Lamn B1 and Dam-only constructs. There were 2 biological replicates, hybridized in a dye-swap design

哺乳动物间期染色体通过数百个大型核纤层结合结构域（Lamina Associated Domains, LADs）与核纤层（nuclear lamina, NL）发生相互作用。本研究报道一种可在单个人类细胞中全基因组范围内定位核纤层接触位点的方法。对约400张单细胞核纤层接触图谱的分析显示，其核心染色质架构为：与核纤层发生接触的基因贫乏型LADs具有较高的细胞间一致性，而散布其间的另一类LADs与核纤层的相互作用变异性更强。相较于保守型接触位点，这类变异性接触位点对基因组倍性改变的敏感性更高。单细胞核纤层接触图谱表明，核纤层接触涉及数百千碱基范围内的多价相互作用。此外，本研究还观察到广泛的染色体内核纤层接触协同现象，即使在数十兆碱基的跨度内也存在此类协同调控。这类协同作用的基因座在Hi-C检测中表现出偏好性相互作用。最后，单细胞基因表达与染色质可及性分析显示，与核纤层接触保守的基因座，其表达水平更低，且相较于接触频率较低的基因座，这类基因座的染色质可及性也更为稳定地处于较低水平。本研究结果揭示了单细胞水平染色质组织的基本调控原则。

总体实验设计：通过病毒转导Dam-Lamn B1与仅含Dam的构建体，在人类KBM7细胞系中检测核纤层蛋白B1-染色质相互作用。本实验包含2组生物学重复，并采用染料互换设计完成杂交。