Journal
NATURE COMMUNICATIONS
Volume 13, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-022-32709-y
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Funding
- National Research, Development and Innovation Fund of Hungary [TKP2021-EGA-18]
- Bolyai Janos fellowship of the Hungarian Academy of Sciences
- National Research, Development and Innovation Fund [UNKP-21-5-DE-11, UNKP-22-5-DE-3]
- [HAS-Lendulet-LP2015-9/2015]
- [NKFIH-NNE-130913]
- [GINOP-2.3.2-15-2016-00024]
- [NKFIH-K137678]
- [NKFIH-K129283]
- [K137722]
- [K136513]
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Arabidopsis NODULIN HOMEOBOX (NDX) is a key regulator of heterochromatin that controls siRNA production and non-CG DNA methylation at pericentromeric regions. Inactivation of NDX leads to differential siRNA accumulation and DNA methylation. Hi-C analysis shows significant chromatin structural changes in the ndx mutant, with decreased intrachromosomal interactions at pericentromeres and increased interchromosomal contacts between KNOT-forming regions.
Arabidopsis NODULIN HOMEOBOX (NDX) is a nuclear protein described as a regulator of specific euchromatic genes within transcriptionally active chromosome arms. Here we show that NDX is primarily a heterochromatin regulator that functions in pericentromeric regions to control siRNA production and non-CG methylation. Most NDX binding sites coincide with pericentromeric het-siRNA loci that mediate transposon silencing, and are antagonistic with R-loop structures that are prevalent in euchromatic chromosomal arms. Inactivation of NDX leads to differential siRNA accumulation and DNA methylation, of which CHH/CHG hypomethylation colocalizes with NDX binding sites. Hi-C analysis shows significant chromatin structural changes in the ndx mutant, with decreased intrachromosomal interactions at pericentromeres where NDX is enriched in wild-type plants, and increased interchromosomal contacts between KNOT-forming regions, similar to those observed in DNA methylation mutants. We conclude that NDX is a key regulator of heterochromatin that is functionally coupled to het-siRNA loci and non-CG DNA methylation pathways. Arabidopsis NDX was previously reported as a regulator of euchromatic gene expression. Here the authors show that NDX functions at pericentromeric regions and regulates heterochromatin homeostasis by controlling siRNA production and non-CG methylation.
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