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Series GSE128434 Query DataSets for GSE128434
Status Public on Sep 19, 2019
Title The prevalence, evolution and chromatin signatures of plant regulatory elements
Organisms Populus trichocarpa; Arabidopsis thaliana; Glycine max; Phaseolus vulgaris; Hordeum vulgare; Oryza sativa; Setaria viridis; Sorghum bicolor; Zea mays; Asparagus officinalis; Brachypodium distachyon; Spirodela polyrhiza; Eutrema salsugineum
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin accessibility and modification is a hallmark of regulatory DNA, which has led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants especially in species with large and complex genomes. The majority of distal CREs have been moved away from their target genes by transposable element (TE) proliferation, but a significant number of distal CREs also appear to be created by TEs. Finally, plant distal CREs are associated with three major types of chromatin signatures that are distinct from metazoans. Taken together, these results suggest that CREs are prevalent in plants, highly dynamic during evolution, and function with distinct chromatin pathways to regulate gene expression.  
 
Overall design Examination of Chromatin accessibilities, different histone modifications, and expressions in 13 plant species.
 
Contributor(s) Schmitz RJ
Citation(s) 31740772, 32879011, 34568920
Submission date Mar 18, 2019
Last update date Oct 06, 2021
Contact name Robert J Schmitz
E-mail(s) schmitz@uga.edu
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 (13)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL20156 Illumina NextSeq 500 (Zea mays)
GPL20690 Illumina NextSeq 500 (Sorghum bicolor)
Samples (170)
GSM3674582 RNA_Asparagus_10days_leaf_rep1
GSM3674583 RNA_Arabidopsis_7days_leaf_rep1
GSM3674584 RNA_Brachypodium_7days_leaf_rep1
Relations
BioProject PRJNA527732
SRA SRP188687

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

Supplementary file Size Download File type/resource
GSE128434_BED_files.tar.gz 3.3 Mb (ftp)(http) TAR
GSE128434_RAW.tar 22.3 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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