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Series GSE201838 Query DataSets for GSE201838
Status Public on Aug 09, 2022
Title Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [DRIP-seq]
Organism Arabidopsis thaliana
Experiment type Other
Summary Nodulin homeobox (NDX) is a nuclear protein described as the regulator of specific euchromatic genes that controls multiple aspects of Arabidopsis development. At the molecular level, NDX was shown to i) interact with the Polycomb repressive complex 1 (PRC1) to promote deposition of repressive histone marks at abscisic acid-responsive gene loci, and (ii) stabilize an R-loop structure within the Flowering Locus C (FLC) to control its expression. Herein, we aimed to understand the global role of NDX in chromatin-based gene regulation and comprehensively characterized its genomic binding sites and transcriptional relationships involving sRNA profiling, DNA methylation, and 3D chromatin structure. Using quantitative microscopic and genomics approaches we show that NDX is a highly immobile heterochromatic protein that localizes primarily to centromeres and pericentromeric regions. Most NDX binding sites coincide with heterochromatic sRNA loci that are known to mediate transcriptional gene silencing via the RNA-dependent DNA methylation (RdDM) pathway. NDX localization was antagonistic with R-loop structures that were prevalent in euchromatic chromosomal arms. Functional analysis revealed that the absence of NDX led to differential hypo- and hyper-methylation in the CG / CHG / CHH sequence context, of which hypo-CHH / CHG sites were co-localized with NDX chromatin binding sites. The identified hypo-CHH/CHGs were associated with increased heterochromatic sRNA production (predominantly 24nt sRNAs) and parallel transcriptional activation of pericentric transposons. Chromosome conformation capture (Hi-C) revealed significant chromatin structural changes in the ndx mutant, with decreased intra-chromosomal interactions (chromatin decompaction) at pericentromeric regions where NDX is enriched in wild type plants, and increased inter-chromosomal contacts between KNOT-forming regions. KNOT interactions involved de novo interchromosomal contacts similar to genome structural changes observed in DNA methylation mutants. We conclude that the main role of NDX is the functional regulation of heterochromatin, which is mechanistically coupled to the effector phase of the RdDM pathway.
Overall design DRIP-seq
Contributor(s) Karányi Z, Mosolygó-L Á, Feró O, Horváth A, Boros-Oláh B, Nagy É, Hetey S, Holb I, Vecsernyés M, Szaker H, Miskei M, Csorba T, Székvölgyi L
Citation(s) 36030240
Submission date Apr 28, 2022
Last update date May 10, 2023
Contact name Márton Miskei
Organization name University of Debrecen
Department Department of Biochemistry and Molecular Biology
Street address Nagyerdei Krt. 48.
City Debrecen
ZIP/Postal code 4032
Country Hungary
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (8)
GSM6077003 DRIP_col0_input
GSM6077004 DRIP_col0_ip_rep1
GSM6077005 DRIP_col0_ip_rep2
This SubSeries is part of SuperSeries:
GSE201841 Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis
BioProject PRJNA833204

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
GSE201838_at_drip_col0.bed.gz 163.6 Kb (ftp)(http) BED 45.9 Mb (ftp)(http) BW 45.8 Mb (ftp)(http) BW 44.2 Mb (ftp)(http) BW
GSE201838_at_drip_ndx1-4.bed.gz 155.2 Kb (ftp)(http) BED 46.0 Mb (ftp)(http) BW 45.9 Mb (ftp)(http) BW 44.7 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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