Mikkelsen Tarjei S, Ku Manching, Jaffe David B, Issac Biju, Lieberman Erez, Giannoukos Georgia, Alvarez Pablo, Brockman William, Kim Tae-Kyung, Koche Richard P, Lee William, Mendenhall Eric, O'Donovan Aisling, Presser Aviva, Russ Carsten, Xie Xiaohui, Meissner Alexander, Wernig Marius, Jaenisch Rudolf, Nusbaum Chad, Lander Eric S, Bernstein Bradley E
Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
Nature. 2007 Aug 2;448(7153):553-60. doi: 10.1038/nature06008. Epub 2007 Jul 1.
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
我们报告了基于单分子的测序技术在哺乳动物细胞组蛋白修饰高通量分析中的应用。通过从染色质免疫沉淀的DNA中获得超过40亿个碱基的序列，我们生成了小鼠胚胎干细胞、神经祖细胞和胚胎成纤维细胞的全基因组染色质状态图谱。我们发现，赖氨酸4和赖氨酸27的三甲基化能有效区分表达的基因、准备表达的基因或稳定抑制的基因，因此反映了细胞状态和谱系潜能。赖氨酸36的三甲基化标记主要的编码和非编码转录本，有助于基因注释。在卫星序列、端粒和活跃的长末端重复序列中检测到赖氨酸9和赖氨酸20的三甲基化，并且其可扩散到近端的单一序列中。赖氨酸4和赖氨酸9的三甲基化标记印记控制区域。最后，我们表明利用单核苷酸多态性可以以等位基因特异性的方式读取染色质状态。这项研究为应用全面的染色质分析来表征不同的哺乳动物细胞群体提供了一个框架。
