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Series GSE120519 Query DataSets for GSE120519
Status Public on May 29, 2019
Title Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Transposable elements (TEs) are largely inactive. Interestingly, a subset of TEs are naturally expressed in the vegetative cell (VC) of the male gametophyte, pollen in Arabidopsis. However, the extent and mechanism of such TE activation were unknown. Through RNA-seq, we identified pollen-activated TEs and annotated the transcriptional start sites (TSSs) and transcriptional termination sites (TTSs) using a program called Mikado. We have previously shown that H1 is expressed in sperm but not in VC, which prompted us to ectopically express H1 in VC for studying TE regulation through RNA-seq and bisulfite-seq. Our RNA-seq data shows that H1 expression in VC represses some of pollen-activated TEs. Furthermore, bisulfite-seq data from the pollen nuclei isolated via fluorescence-activated cell sorting (FACS) shows that H1 expression in VC increases DNA methylation of some of H1-repressed TEs around their TSSs, while leaving other H1-repressed TEs unchanged in DNA methylation. Our results indicate that H1 represses TE expression through both DNA methylation-dependent and -independent mechanisms and that natural depletion of H1 in VC allows TEs to be activated.
Overall design To identify pollen-activated TEs, we did RNA-seq using pollen grains from WT and four replicates were included. To find out if H1 expression in VC can repress TE expression, we performed RNA-seq using pollen grains from WT or pVC::H1 with three replicates being done for each genotype. Bisulfite-seq was performed using sperm nuclei (SN) and vegetative nuclei (VN) from WT as well as VN from pVC::H1. By comparing WT SN with WT VN, we want to show if pollen-activated TEs are regulated by DEMETER-mediated DNA demethylation and if H1 represses TE expression through DNA methylation regulation.
Contributor(s) He S, Vickers M, Zhang J, Feng X
Citation(s) 31135340
Submission date Sep 26, 2018
Last update date May 31, 2019
Contact name Xiaoqi Feng
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Xiaoqi Feng
Street address Norwich Research Park
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
Platforms (4)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (16)
GSM3402473 WT SN BS-seq
GSM3402474 WT VN BS-seq
GSM3402475 pVC::H1 VN BS-seq
BioProject PRJNA493255
SRA SRP162679

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
GSE120519_RAW.tar 1.0 Gb (http)(custom) TAR (of GFF, TSV)
GSE120519_TAIR10_gene_plus_mikado_TE_transcripts.gff.gz 444.8 Kb (ftp)(http) GFF
GSE120519_mikado-permissive.superloci.gff.gz 367.0 Kb (ftp)(http) GFF
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Raw data are available in SRA
Processed data provided as supplementary file

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