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| Status |
Public on Aug 27, 2023 |
| Title |
Characterization of distinct types of open chromatin and their impacts on gene transcription in maize [MNase-seq] |
| Organisms |
Arabidopsis thaliana; Zea mays |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Open chromatin plays key roles in regulating gene expression in eukaryotic genomes. However, functional implications of fragile nucleosome overlapping open chromatin are still largely unknown, especially in plants. Here, through simultaneous measurement of MHSs and nucleosomes, we detected two distinct types of open chromatin, one with nucleosome-free (type-I MHSs) and the other with fragile nucleosomes (type-II MHSs) in maize and Arabidopsis. Both types of MHSs can function as cis-regulatory elements and have similar TF binding motifs. Furthermore, fragile nucleosomes with MHSs have unique DNA sequence features with less AT and more GC dinucleotides, whereas other fragile nucleosomes without overlapping MHSs have more AT and less GC dinucleotides. In particular, we observed distinct fragile nucleosome positioning patterns occurred around the summit of type-I and type-II MHSs, phased fragile nucleosome arrays and only two well-phased fragile nucleosomes surrounding the summit of type-I and type-II MHSs, respectively. We finally found that type-II MHS-related genes with BCTSS or SCTSS express more than type-I-related genes with the corresponding CTSS, which is mediated by combined actions of MHSs with TFs, fragile nucleosomes, Pol II and epigenetic marks.
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| Overall design |
Low-MNase-seq, High-MNase-seq.
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| Contributor(s) |
Lin K, Gao J, Zhang W |
| Citation missing |
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| Submission date |
Aug 30, 2020 |
| Last update date |
Aug 27, 2023 |
| Contact name |
Wenli Zhang |
| E-mail(s) |
wzhang25@njau.edu.cn
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| Organization name |
Nanjing Agricultural University
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| Street address |
No.1, Weigang Street, Xuanwu District, Nanjing
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| City |
Nanjing City |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platforms (2) |
| GPL25410 |
Illumina NovaSeq 6000 (Zea mays) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE157152 |
Characterization of distinct types of open chromatin and their impacts on gene transcription in maize |
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| Relations |
| BioProject |
PRJNA660276 |
| SRA |
SRP279371 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE157150_RAW.tar |
897.0 Mb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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