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Series GSE260822 Query DataSets for GSE260822
Status Public on Jun 17, 2024
Title Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals-tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, revealing that chemically-induced epigenome changes can have long-term consequences on imprinted gene expression.
 
Overall design RNAseq, WGBS and CUT&Tag datasets were obtained from INTACT purified endosperm nuclei from Col × Ler (L) reciprocal crosses at 4 days after pollination (DAP).
WGBS and CUT&Tag were generated in duplicates using the INTACT line (referred as C) or TEmob (T3, referred as Cm) genetic background in recirpocal crosses with Ler (L).
RNAseq libraries were generated in triplicates from TEmob (Cm) x Ler (L) reciprocal crosses.
Web link https://academic.oup.com/nar/article/52/15/8833/7706484#479489403
 
Citation(s) 38967011
Submission date Mar 04, 2024
Last update date Sep 16, 2024
Contact name Juan C Santos-González
E-mail(s) juan.santos@slu.se
Organization name SLU
Department Department of Plant Biology and Forest Genetics
Lab Köhler's lab
Street address Almas Allé 5
City Uppsala
State/province Uppsala
ZIP/Postal code 75007
Country Sweden
 
Platforms (3)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL26208 Illumina NovaSeq 6000 (Arabidopsis thaliana)
GPL34120 NextSeq 1000 (Arabidopsis thaliana)
Samples (40)
GSM8125020 at-endosperm-H3K9m2_replicate1_col_C_x_ler
GSM8125021 at-endosperm-H3_replicate1_col_C_x_ler
GSM8125022 at-endosperm-H3K27m3_replicate1_col_C_x_ler
This SuperSeries is composed of the following SubSeries:
GSE260818 Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm (CUT&Tag)
GSE260819 Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis
GSE260820 Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm (WGBS aerial)
Relations
BioProject PRJNA1083570

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
GSE260822_RAW.tar 1.9 Gb (http)(custom) TAR (of TXT)
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