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Series GSE165877 Query DataSets for GSE165877
Status Public on Aug 11, 2021
Title Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability
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
Genome variation profiling by high throughput sequencing
Summary The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeller DDM1 causes hundreds of genomic regions to switch from CMT2-dependency to RdDM-dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). Furthermore, we found that blocking the pathway switch by disrupting both DDM1 and RdDM causes strong reactivation of TEs and a burst of TE transposition in the first generation of mutant plants, indicating that the pathway conversion is critical to maintaining TE repression and protecting genomic stability. Our findings reveal the existence of a novel pathway conversion-based backup mechanism to guarantee the maintenance of DNA methylation and genome integrity.
Overall design To investigate potential genetic interactions between the CMT2 and RdDM pathways, we generated single-base resolution maps of the DNA methylomes of the nrpd1, nrpe1, cmt2, ddm1, ddm1nrpd1, ddm1nrpe1, and ddm1cmt2 mutants, RNA sequencing in ddm1, ddm1nrpd1, ddm1nrpe1, and ddm1cmt2 mutants, resequencing in ddm1, nrpd1 and ddmcmt2.
Contributor(s) He L, Zhao C, Zhang Q, Zinta G, Wang D, Lozano-Durán R, Zhu J
Citation(s) 34453006
BioProject PRJNA697952
Submission date Feb 01, 2021
Last update date Aug 30, 2021
Contact name Cheng Zhao
Organization name Karolinska institute
Department Clinical Science
Lab Petropoulos lab
Street address H9 Klinisk vetenskap,171 77 Stockholm
City Stockholm
State/province Stockholm
ZIP/Postal code 171 77
Country Sweden
Platforms (2)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL23157 HiSeq X Ten (Arabidopsis thaliana)
Samples (42)
GSM5051937 DNAseq of Arabidopsis: Col-0_rep1
GSM5051938 DNAseq of Arabidopsis: Col-0_rep2
GSM5051939 DNAseq of Arabidopsis: ddm1-1_nrpd1_rep1
SRA SRP303860

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Supplementary file Size Download File type/resource
GSE165877_RAW.tar 804.6 Mb (http)(custom) TAR (of BW, TDF, WIG)
GSE165877_RNASeq_sample_rawcounts_CPM.tsv.gz 2.6 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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