Zhao Hainan, Zhang Wenli, Zhang Tao, Lin Yuan, Hu Yaodong, Fang Chao, Jiang Jiming
Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
Genome Biol. 2020 Feb 3;21(1):24. doi: 10.1186/s13059-020-1927-5.
Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species.
We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains.
MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
转录调控依赖于顺式调控元件（CRE）与调控蛋白之间的相互作用。活跃的CRE嵌入对核酸酶可及的开放染色质中。包括基于核酸酶DNase I的DNase-seq和基于转座酶Tn5的ATAC-seq在内的多种技术已被广泛用于鉴定与开放染色质相关的基因组区域。这些技术在剖析动植物物种基因表达的调控网络中发挥了关键作用。
我们开发了一种名为微球菌核酸酶超敏测序（MH-seq）的技术，用于鉴定拟南芥中与开放染色质相关的基因组区域。富含MH-seq读数的基因组区域被称为微球菌核酸酶超敏位点（MHS）。MHS与先前通过DNase-seq和ATAC-seq鉴定的大多数（约90%）开放染色质重叠。令人惊讶的是，22%的MHS未被DNase-seq或ATAC-seq读数覆盖，这些被称为“特异性MHS”（sMHS）。sMHS倾向于远离启动子定位，并且相当一部分sMHS源自转座元件。最有趣的是，包含sMHS的基因组区域富含表观遗传标记，包括H3K27me3和DNA甲基化。此外，sMHS表现出许多独特的特征，包括与转录抑制因子的关联。因此，sMHS跨越了DNase I或Tn5可能无法触及的不同类别的开放染色质。我们推测，相对于DNase I或Tn5，微球菌核酸酶的小尺寸使其能够进入相对更紧密的染色质结构域。
微球菌核酸酶可用于鉴定DNase I或Tn5无法触及的开放染色质区域。因此，MH-seq为鉴定和编目植物中所有类别的开放染色质提供了一个重要工具。
