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Series GSE122394 Query DataSets for GSE122394
Status Public on Nov 20, 2019
Title DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcripts
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 DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. In plants and animals with mosaic genomic methylation, functionally mysterious methylation is also common within constitutively active housekeeping genes. Here we show that H1 is enriched in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally alters nucleosome organization, and activates H1-bound genes, but only weakly de-represses transposable elements. However, H1 loss strongly activates transposable elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation of genes also activates antisense transcription, which is enhanced by H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain transcriptional homeostasis by silencing transposable elements and aberrant intragenic transcripts. Such functionality plausibly explains why DNA methylation, a well-known mutagen, has been maintained within coding sequences of crucial plant and animal genes.
Overall design Bisulfite and RNA sequencing was performed using wt, h1, met1, h1met1, h1;met1 +/- plants (5-6 replicates, one sample for h1;met1 +/-) to examine the effect of DNA methylation and histone H1 loss on RNA expression. Decap-seq was performed using wt, met1, h1met1, and h1;met1+/- plants (2-3 replicates, one sample for h1;met1+/-). H1 ChAP and H3K9me2 ChIP sequencing: pH1-H1-BLRP transgenic plants were generated in wt and met1 plants to monitor H1 distribution change. Antibody against H3K9me2 (Abcam, cat. No. AB1220) was used to enrich chromatin bound to modified histones in wt and met1 plants.

Contributor(s) Choi J, Lyons DB, Kim MY
Citation Jaemyung Choi, David Bruce Lyons, Yvonne Kim, Jonathan David Moore, Daniel Zilberman. DNA methylation and histone H1 cooperatively repress transposable elements and aberrant intragenic transcripts. bioRxiv 527523; doi:10.1101/527523
Submission date Nov 09, 2018
Last update date Nov 24, 2019
Contact name Jaemyung Choi
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Daniel Zilberman
Street address Norwich Research Park
City Norwich
ZIP/Postal code NR4 7UH
Country United Kingdom
Platforms (3)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (132)
GSM3465878 wt_bisulfite_rep1
GSM3465879 wt_bisulfite_rep2
GSM3465880 wt_bisulfite_rep3
BioProject PRJNA504886
SRA SRP168382

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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
GSE122394_RAW.tar 1.1 Gb (http)(custom) TAR (of BW, GFF)
GSE122394_col.bisulfite.CG.w50.gff.gz 17.7 Mb (ftp)(http) GFF
GSE122394_col.bisulfite.CHG.w50.gff.gz 17.8 Mb (ftp)(http) GFF
GSE122394_col.bisulfite.CHH.w50.gff.gz 21.4 Mb (ftp)(http) GFF 33.1 Mb (ftp)(http) BW 63.3 Mb (ftp)(http) BW 59.0 Mb (ftp)(http) BW 85.6 Mb (ftp)(http) BW 73.4 Mb (ftp)(http) BW 61.9 Mb (ftp)(http) BW 62.0 Mb (ftp)(http) BW 67.0 Mb (ftp)(http) BW 73.3 Mb (ftp)(http) BW 83.4 Mb (ftp)(http) BW 94.1 Mb (ftp)(http) BW 73.2 Mb (ftp)(http) BW 83.5 Mb (ftp)(http) BW 33.3 Mb (ftp)(http) BW 95.7 Mb (ftp)(http) BW 85.1 Mb (ftp)(http) BW 42.6 Mb (ftp)(http) BW 72.1 Mb (ftp)(http) BW
GSE122394_h1met1.bisulfite.CG.w50.gff.gz 15.8 Mb (ftp)(http) GFF
GSE122394_h1met1.bisulfite.CHG.w50.gff.gz 17.5 Mb (ftp)(http) GFF
GSE122394_h1met1.bisulfite.CHH.w50.gff.gz 19.9 Mb (ftp)(http) GFF 33.3 Mb (ftp)(http) BW
GSE122394_met1.bisulfite.CG.w50.gff.gz 15.8 Mb (ftp)(http) GFF
GSE122394_met1.bisulfite.CHG.w50.gff.gz 17.6 Mb (ftp)(http) GFF
GSE122394_met1.bisulfite.CHH.w50.gff.gz 20.3 Mb (ftp)(http) GFF 33.3 Mb (ftp)(http) BW 100.2 Mb (ftp)(http) BW 89.6 Mb (ftp)(http) BW 75.0 Mb (ftp)(http) BW 68.1 Mb (ftp)(http) BW 78.8 Mb (ftp)(http) BW 69.9 Mb (ftp)(http) BW
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Processed data provided as supplementary file

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