Biology subjects

Wlodzimierz, P.

Publications and source records attributed to Wlodzimierz, P..

7 recordsLinked to original sources

bioRxiv2026

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Centromeres evolved at the root of eukaryotes to segregate chromosomes during cell division. Despite their ancient origin, centromeric DNA sequences evolve rapidly and adopt diverse architectures, including point centromeres, satellite arrays, transposon clusters, and holocentrics. To analyse centromere evolution at a broad scale, we characterised architectures across 325 diverse Darwin Tree of Life genome assemblies. Centromere architecture is evolutionarily labile, and similar configurations arise independently across divergent lineages. In plants and animals, we modelled centromere evolution as a recurrent cycle, in which satellite- and transposon-based architectures interconvert, with independent origins of holocentricity. We curated >23 million satellite repeats comprising 263 families from 165 species. Despite sequence divergence between satellite families, higher order repeats are prevalent, indicating constraint on repeat architecture rather than primary sequence. Satellite arrays are heavily invaded by diverse transposon families, consistent with convergent adaptation to the centromeric niche. In 89 species, transposons themselves constitute the primary centromere structure. We observed centrophilic transposons forming tandem arrays, suggesting mechanisms for satellite regeneration. Our sample includes five independent origins of holocentricity in plants and animals, which vary in association with periodic satellite arrays. We propose that genetic instability, centrophilic transposition, and transmission distortion promote recurrent centromere architectural interconversions during evolution.

genomics↗

bioRxiv2026

CRISPR-mediated centromere fission generates neo-chromosomes with distorted meiotic inheritance in Arabidopsis

Centromeres are essential for chromosome segregation and are epigenetically defined by CENH3/CENP-A nucleosomes. Centromere position along chromosomes varies within and between species, ranging from telocentric to metacentric architectures. Yet, how centromere position influences chromosome inheritance and karyotype evolution remains poorly understood. To reposition the centromere, we used CRISPR-Cas9 to break the centromeric satellite array of Arabidopsis thaliana chromosome 3. Fission chromosomes rapidly acquired telomeres, converting a metacentric into two stable telocentric neo-chromosomes. Neo-centromere formation involved genetic restructuring and de novo satellite higher-order repeat formation, together with epigenetic remodeling of CENH3 and DNA methylation. Crossing the six-chromosome fission line to five-chromosome wild type produced a meiosis-specific trivalent that mis-segregated and generated aneuploidy. Trivalent recombination doubled through two obligate crossovers, which were shifted towards the telomeres. Inheritance was strongly distorted in favor of the wild type centromere, as telocentrics segregated into inviable monosomic gametes. The reciprocal trisomic gametes were associated with centromere-proximal recombination, demonstrating that crossover position governs trivalent segregation. Distortion further increased when CENH3 was over-expressed, implicating centromere strength in the outcomes of trivalent meiosis. Our results reveal rapid centromere remodeling following karyotype change, and how trivalent centromere architecture distorts inheritance, with implications for hybrid incompatibility and synthetic chromosome design.

genetics↗

bioRxiv2026

Pangenome analysis reveals the evolutionary dynamics of repeat-based holocentromeres

Centromeres are essential for chromosome segregation, yet their organisation and evolution remain poorly understood in holocentric species, where kinetochore activity is distributed along entire chromosomes1,2. While monocentric centromeres are often structured by megabase-sized satellite arrays3-5, the role of repetitive DNA in holocentric systems remains enigmatic. Here, we analyse the dynamics of centromeric Tyba satellite DNA repeats and transposable elements across a chromosome-scale pangenome comprising 56 long-read haplotype assemblies from 20 Rhynchospora species6,7, a plant genus with repeat-based holocentromeres8,9. We identify over 4.6 million monomers of the Tyba satellite repeat, arranged into 43,400 discrete arrays that span all chromosomes. CENH3 ChIP-seq reveals that, unexpectedly, the same Tyba satellite defines holocentromere across the entire genus, demonstrating deep conservation of centromeric DNA over over 40 million years despite extensive karyotype evolution and centromere array turnover. We show that Tyba arrays function as modular centromeric units whose number and spacing, but not size, scale with chromosome length. Tyba sequence diversity recapitulates species phylogeny, while higher-order repeat formation and antagonism with transposable elements shape array turnover. A novel synteny-aware algorithm reveals rapid gain, loss, and rearrangement of arrays across homologous chromosomes. Using cytogenetics and polymer simulations, we demonstrate that inter-array spacing governs chromatin loop length and chromatid thickness, linking repeat-based holocentromere organisation directly to chromosome mechanics. Our findings uncover a scalable, modular logic for holocentromere function and establish a framework for understanding the plasticity of repeat-based centromere evolution and genome architecture in eukaryotes.

genomics↗

bioRxiv2025

CRISPR targeting of H3K4me3 activates gene expression and unlocks centromeric crossover recombination in Arabidopsis

H3K4me3 is a fundamental and highly conserved chromatin mark across eukaryotes, playing a central role in many genome-related processes, including transcription, maintenance of cell identity, DNA damage repair, and meiotic recombination. However, identifying the causal function of H3K4me3 in these diverse pathways remains a challenge, and we lack the tools to manipulate it for agricultural benefit. Here we use the CRISPR-based SunTag system to direct H3K4me3 methyltransferases in the model plant, Arabidopsis thaliana. Targeting of SunTag-SDG2 activates the expression of the endogenous reporter gene, FWA. We show that SunTag-SDG2 can be employed to increase pathogen resistance by targeting the H3K4me3-dependent disease resistance gene, SNC1. Meiotic crossover recombination rates impose a limit on the speed with which new traits can be transferred to elite crop varieties. We demonstrate that targeting of SunTag-SDG2 to low recombining centromeric regions can significantly stimulate proximal crossover formation. Finally, we reveal that the effect is not specific to SDG2 and is likely dependent on the H3K4me3 mark itself, as the orthogonal mammalian-derived H3K4me3 methyltransferase, PRDM9, produces a similar effect on gene expression with reduced off-target potential. Overall, our study supports an instructive role for H3K4me3 in transcription and meiotic recombination and opens the door to precise modulation of important agricultural traits.

plant biology↗

bioRxiv2023

Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis

BackgroundCentromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly divergent within and between species. Despite variability in DNA sequence, centromeres are also universally suppressed for meiotic crossover recombination, across eukaryotes. However, the genetic and epigenetic factors responsible for suppression of centromeric crossovers remain to be completely defined. ResultsTo explore the centromere-proximal recombination landscape, we mapped 14,397 crossovers against fully assembled Arabidopsis thaliana genomes. A. thaliana centromeres comprise megabase-scale satellite repeat arrays that load nucleosomes containing the CENH3 histone variant. Each chromosome possesses a structurally polymorphic 3-4 megabase region where crossovers were absent, that includes the satellite arrays, flanked by 1-2 megabase low-recombination zones. The recombination-suppressed regions are enriched for Gypsy/Ty3 retrotransposons, and additionally contain expressed genes with high genetic diversity that initiate meiotic recombination, yet do not crossover. We mapped crossovers at high-resolution in proximity to CEN3, which resolved punctate centromere-proximal hotspots that overlapped gene islands embedded in heterochromatin. Centromeres are densely DNA methylated and the recombination landscape was remodelled in DNA methylation mutants. We observed that the centromeric low-recombining zones decreased and increased crossovers in CG (met1) and non-CG (cmt3) mutants, respectively, whereas the core non recombining zones remained suppressed. ConclusionOur work relates the genetic and epigenetic organisation of the A. thaliana centromeres and flanking pericentromeric heterochromatin to the zones of crossover suppression that surround the CENH3-occupied satellite repeat arrays.

genomics↗

bioRxiv2021

The genetic and epigenetic landscape of the Arabidopsis centromeres

Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used ultra-long-read sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support high CENH3 occupancy and are densely DNA methylated, with satellite variants private to each chromosome. CENH3 preferentially occupies satellites with least divergence and greatest higher-order repetition. The centromeres are invaded by ATHILA retrotransposons, which disrupt genetic and epigenetic organization of the centromeres. Crossover recombination is suppressed within the centromeres, yet low levels of meiotic DSBs occur that are regulated by DNA methylation. We propose that Arabidopsis centromeres are evolving via cycles of satellite homogenization and retrotransposon-driven diversification. One-sentence summaryLong read sequencing and assembly of the Arabidopsis centromeres reveals their genetic and epigenetic topography.

genomics↗

bioRxiv2019

NuA4-dependent H4 acetylation is adopted to specifically control photosynthesis-related genes

NuA4, an essential histone acetyltransferase complex, is required for efficient transcription in eukaryotes. Using genome editing, genomic approaches and biochemical assays, we characterized plant homologues of two key components of this complex, EPL1 and EAF1 in Arabidopsis thaliana. Surprisingly, we found that loss of AtEPL1, which is necessary for enzymatic activity of NuA4, is not lethal. Contrary to yeast, mutants lacking AtEAF1, responsible for complex targeting, display severe pleiotropic phenotype which copies that of Atepl1. Atepl1 and Ateaf1 mutants grow slowly, contain reduced chlorophyll levels and small chloroplasts. We provide evidence that these alterations are not caused by disturbance of GLK transcription factors, the major regulators of chloroplast development. Using ChIP-seq we show that H4 acetylation levels are dramatically reduced in the chromatin of the Atepl1 mutant, while H3 acetylation remains mostly unchanged. We use our data to define NuA4-dependent genes and show that chloroplast-related genes are significantly overrepresented in this group, consistent with the pale-green phenotypes of the mutants. We propose that NuA4 was adopted in plants to control nuclear-encoded photosynthesis genes. SignificancePhotosynthesis depends on chloroplast proteins, most of which are nucleus-encoded and thus subject to control mechanisms common across eukaryotes. Here we show that NuA4, an evolutionary conserved transcriptional coactivator, is necessary for proper development of photosynthetic apparatus. Surprisingly, in contrast to yeast and metazoans, plants engineered to lack core NuA4 subunits are capable of vegetative development despite dramatic genome-wide loss of NuA4-dependent H4K5 acetylation. This chromatin perturbation seems to directly affect 350 genes which, in addition to reduced H4K5ac levels, display decreased transcript levels but no loss of transcription-related H3K9ac. A significant proportion of these genes are related to chloroplast function, particularly to translation, an intriguing parallel to the yeast NuA4s role in transcription of ribosome biogenesis-related genes.

molecular biology↗