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Series GSE152046 Query DataSets for GSE152046
Status Public on Aug 22, 2020
Title Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.
Overall design ATAC–seq maize B73 root tissue, duplicate samples.
Contributor(s) Schmitz RJ
Citation(s) 32879011
Submission date Jun 08, 2020
Last update date Nov 21, 2020
Contact name Robert J Schmitz
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
Platforms (1)
GPL20156 Illumina NextSeq 500 (Zea mays)
Samples (2)
GSM4600940 Maize_B73_ATAC_root_rep1
GSM4600941 Maize_B73_ATAC_root_rep2
BioProject PRJNA638148
SRA SRP266484

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE152046_ATAC_bed_column_header_descriptions.txt.gz 122 b (ftp)(http) TXT
GSE152046_RAW.tar 607.0 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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