PMID- 32014062 OWN - NLM STAT- MEDLINE VI - 21 IP - 1 TI - Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. PG - 24 LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Genome Biol JT - Genome biology JID - 100960660 IS - 1474-760X (Electronic) LID - 10.1186/s13059-020-1927-5 [doi] FAU - Zhao, Hainan AU - Zhao H AD - Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. AD - Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA. FAU - Zhang, Wenli AU - Zhang W AD - Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA. wzhang25@njau.edu.cn. AD - State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, China. wzhang25@njau.edu.cn. FAU - Zhang, Tao AU - Zhang T AD - Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA. AD - Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China. FAU - Lin, Yuan AU - Lin Y AD - Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. AD - Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA. FAU - Hu, Yaodong AU - Hu Y AD - Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA. FAU - Fang, Chao AU - Fang C AD - Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. AD - Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA. FAU - Jiang, Jiming AU - Jiang J AUID- ORCID: 0000-0002-6435-6140 AD - Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. jiangjm@msu.edu. AD - Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA. jiangjm@msu.edu. AD - Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA. jiangjm@msu.edu. AD - Michigan State University AgBioResearch, East Lansing, MI, 48824, USA. jiangjm@msu.edu. IS - 1474-7596 (Linking) RN - 0 (Chromatin) RN - 0 (Histones) SB - IM MH - Arabidopsis MH - Chromatin/chemistry/*genetics MH - *DNA Methylation MH - Gene Expression Regulation, Plant MH - *Histone Code MH - Histones/chemistry/metabolism MH - Sequence Analysis, DNA/*methods OTO - NOTNLM OT - *ATAC-seq OT - *Arabidopsis thaliana OT - *DNA methylation OT - *DNase-seq OT - *Histone modification OT - *Open chromatin OT - *cis-regulatory elements PMC - PMC6996174 DCOM- 20210104 LR - 20210104 DP - 20200203 DEP - 20200203 AB - BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.