Biology subjects

Edera, A.

Publications and source records attributed to Edera, A..

4 recordsLinked to original sources

bioRxiv2026

GH1-HMGA proteins restrict RNA-directed DNA methylation and antagonize linker histone H1 at euchromatic transposable elements

In plant genomes, transposable elements (TEs) are silenced by CG and non-CG DNA methylation, with non-CG methylation maintained by CMT chromomethylases and the RNA-directed DNA methylation (RdDM) pathway. In Arabidopsis, linker histone H1 differentially influences these pathways, as loss of H1 causes non-CG hypermethylation at pericentromeric TEs but hypomethylation at euchromatic TEs in gene-rich regions. The molecular basis of this antagonism has remained unclear. Here, we show that GH1-HMGAs, a family of H1-related High Mobility Group proteins, bind AT-rich sequences at euchromatic TEs and prevent RdDM-dependent non-CG methylation by limiting siRNA accumulation. Furthermore, GH1-HMGA and H1 compete for chromatin association at these TEs, as loss of GH1-HMGA triggers ectopic H1 redistribution, while loss of H1 increases GH1-HMGA enrichment, providing a mechanistic explanation for the non-CG hypomethylation observed in h1 mutants. Collectively, these findings reveal how GH1-HMGA proteins specifically restrain RdDM activity at euchromatic TEs and elucidate how the H1/GH1-HMGA balance spatially partitions distinct DNA methylation pathways across the genome.

genetics↗

bioRxiv2026

Centromeric origin of Arabidopsis interstitial telomeric repeat domains

The mechanisms underlying the emergence of new DNA repeat classes remain poorly understood. One such example is the formation of interstitial telomeric repeat (ITR) domains commonly viewed as telomere-fossil byproducts of chromosome rearrangements. Here, we report that in Arabidopsis thaliana, ITRs arise from centromeres as centromeric-telomeric mosaic satellites that expand into higher-order structures via in situ amplification. Long-read sequencing of mutation accumulation lines and forward simulations of mutational processes confirmed the propensity of centromeres to form telomeric motifs. During establishment, ITRs adopt an atypical chromatin state that excludes CENH3 incorporation, thereby enabling escape from the functional constraints of centromere identity. Accordingly, a pangenomic survey of natural accessions showed that ITRs vary abruptly and independently of telomere length, notably through transposon-associated block duplications. These findings identify centromeres as major sources of telomeric sequences and an original route for the emergence of new DNA satellite types.

genomics↗

bioRxiv2023

Simultaneous Profiling of Chromatin Accessibility and DNA Methylation in Complete Plant Genomes Using Long-Read Sequencing

Epigenetic regulations, including chromatin accessibility, nucleosome positioning, and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. We uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also detects DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains with antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms.

genomics↗

bioRxiv2023

Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide

The mobilization of retrotransposons yields major-effect mutations. Here, we report an adaptive retrotransposon insertion within the first intron of the Arabidopsis floral-repressor locus FLOWERING LOCUS C (FLC). The insertion-mutation augments the environmental sensitivity of FLC by affecting the balance between coding and non-coding transcript isoforms in response to environmental threads. We show that this balance is modulated epigenetically by DNA methylation and orchestrated by IBM2, a factor involved in the processing of intronic heterochromatin. The stress-sensitive allele of FLC has recently spread across populations subjected to recurrent chemical weeding, and we demonstrate that retrotransposon-driven acceleration of life cycle represents a rapid response to herbicide. Our findings illustrate how retrotransposition can create environmentally-sensitive alleles that facilitate adaptation to anthropogenic disturbances of the environment.

plant biology↗