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Series GSE175662 Query DataSets for GSE175662
Status Public on May 01, 2022
Title Chromatin Accessibility Analysis Reveals Distinct Functions for HDAC and EZH2 Activities in Early Regeneration
Organism Xenopus tropicalis
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Xenopus tropicalis tadpoles have the capability to scarlessly regenerate appendages including the limb and tail. Following injury, complex genetic processes must be activated and inactivated with high spatial and temporal resolution to result in a properly patterned appendage. Functional studies have established that histone modifying enzymes that act to close chromatin are required for regeneration, but the genomic regions sensitive to these activities are not established. Here we show that early inhibition of HDAC or Ezh2 activity results in incomplete regeneration. To identify the impact that each of these perturbations has on chromatin accessibility, we applied an assay for transposase accessible chromatin (ATAC-seq) to HDAC or Ezh2 inhibited regenerating tadpoles. We find that neither perturbation results in a global increase in chromatin accessibility, but that both inhibitors have targeted effects on chromatin accessibility and gene expression. Upon HDAC inhibition, promoter regions and regulatory regions neighboring genes associated with neuronal regeneration are precociously accessible, whereas following EZH2 inhibition we find gene bodies and regulatory regions associated with regulation of the immune response and apoptosis are preferentially accessible. Together this suggests distinct roles for EZH2 activity and HDAC activity in appendage regeneration.
 
Overall design ATAC-seq timecourse analysis of chromatin dynamics of HDAC inhibited or EZH2 inhibited regenerated tadpole tails and their vehicle controls. Samples in duplicate.
 
Contributor(s) Arbach HE, Harland-Dunaway M, Braden C, Chitsazan AD, Pickering E, Patel JH, Wills AE
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Submission date May 27, 2021
Last update date May 02, 2022
Contact name Anneke Dixie Kakebeen
E-mail(s) akakebee@uw.edu
Organization name University of Washington
Department Biochemistry
Lab Andrea Wills
Street address 5611 9th Ave NW
City Seattle
State/province WA
ZIP/Postal code 98107
Country USA
 
Platforms (1)
GPL24884 Illumina NextSeq 500 (Xenopus tropicalis)
Samples (35)
GSM5343547 G001_SG_Wills_08_WhT41_S1_R
GSM5343548 G002_SG_Wills_08_0HPA_S2_R
GSM5343549 G003_SG_Wills_08_Veh3HPA_S3_R
Relations
BioProject PRJNA733163
SRA SRP321625

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

Supplementary file Size Download File type/resource
GSE175662_RAW.tar 14.1 Mb (http)(custom) TAR (of BED)
GSE175662_all.summits.window.merged.saf.txt.gz 2.5 Mb (ftp)(http) TXT
GSE175662_summit_window_merged_counts_geo.txt.gz 10.5 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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