Biology subjects

Yelina, N. E.

Publications and source records attributed to Yelina, N. E..

4 recordsLinked to original sources

bioRxiv2026

Distinct and Cooperative Roles of DNA Methylation and Meiotic Chromosome Architecture in Crossover Control

During meiosis, homologous chromosomes exchange segments in a process termed crossover recombination. Crossovers are non-randomly distributed along chromosomes, and in many eukaryotes, including plants, meiotic chromosome architecture and chromatin states control recombination landscapes. Whether these two components genetically interact has remained underexplored. To address this question, we combined Arabidopsis thaliana, hereinafter, Arabidopsis, mutations that disrupt meiotic chromosome architecture by depleting the meiotic chromosome axis (asy1/+) or synaptonemal complex (zyp1) with mutations in the DNA methyltransferases MET1 and CMT3 (met1/+ and cmt3), which lead to a loss of cytosine DNA methylation, the hallmark of heterochromatin, in the CG and CHG contexts, respectively. We quantified crossovers in telomere- and centromere-proximal chromosome intervals using fluorescent seed-based reporters and found that DNA methylation and meiotic chromosome architecture proteins can have distinct or cooperative roles in crossover control depending on the chromosome interval and DNA methylation context. We demonstrate that axis and synaptonemal complex act together with CG DNA methylation to control crossovers, while CHG DNA hypomethylation cannot fully restore a loss of centromere-proximal recombination caused by the depletion of ASY1 or ZYP1. Remarkably, increasing ASY1 dosage promotes crossovers within the pericentromere, representing a new non-epigenetic route to upregulate pericentromeric recombination. Author summaryMeiotic crossovers reshuffle genetic variation and are essential for evolution and crop breeding. However, crossovers occur unevenly along chromosomes, limiting genetic exchange in pericentromeric regions. Here, we investigate the genetic interactions between cytosine DNA methylation and meiotic chromosome architecture and show that, although heterochromatin depletion can permit pericentromeric crossovers, the structural integrity of the meiotic chromosome axis and the synaptonemal complex are essential to drive recombination. Remarkably, modulating the dosage of a chromosome axis protein provides a non-epigenetic strategy to increase pericentromeric crossovers, revealing new opportunities to reshape recombination landscapes in model and crop plants.

plant biology↗

bioRxiv2023

Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha

Photosynthesis in eukaryotic cells takes place in chloroplasts that develop from undifferentiated plastids in response to light. In angiosperms, after perception of light de-repression allows Elongated Hypocotyl 5 (HY5) transcription factor to initiate photomorphogenesis, and two families of transcription factors known as Golden2-like (GLK) and GATA are considered master regulators of chloroplast development. The MIR171-targeted SCARECROW-LIKE (SCL) GRAS transcription factors also impact on chlorophyll biosynthesis. The extent to which these proteins carry out conserved roles in non-seed plants is not known. Here we report in the model liverwort Marchantia polymorpha that GLK controls chloroplast biogenesis and HY5 shows a small conditional effect on chlorophyll content. In contrast, GATA and SCL have no detectable roles in this fundamental process. ChIP-SEQ and RNA-SEQ revealed that MpGLK regulates many photosynthetic and chloroplast development-related genes, but also has a broader set of targets than previously reported in angiosperms. This implies GLK carries out a conserved role relating to chloroplast biogenesis in land plants but also supports extensive divergence between its targets in M. polymorpha and flowering plants. The data support the hypothesis that regulation of chloroplast biogenesis in M. polymorpha is streamlined compared with angiosperms and allows us to present a core regulatory network for chloroplast biogenesis in land plants.

plant biology↗

bioRxiv2021

CRISPR targeting of MEIOTIC-TOPOISOMERASE VIB-dCas9 to a recombination hotspot is insufficient to increase crossover frequency in Arabidopsis

During meiosis, homologous chromosomes pair and recombine, which can result in reciprocal crossovers that increase genetic diversity. Crossovers are unevenly distributed along eukaryote chromosomes and show repression in heterochromatin and the centromeres. Within the chromosome arms crossovers are often concentrated in hotspots, which are typically in the kilobase range. The uneven distribution of crossovers along chromosomes, together with their low number per meiosis, creates a limitation during crop breeding, where recombination can be beneficial. Therefore, targeting crossovers to specific genome locations has the potential to accelerate crop improvement. In plants, meiotic crossovers are initiated by DNA double strand breaks (DSBs) that are catalysed by SPO11 complexes, which consist of two catalytic (SPO11-1 and SPO11-2) and two non-catalytic subunits (MTOPVIB). We used the model plant Arabidopsis thaliana to target a dCas9-MTOPVIB fusion protein to the 3a crossover hotspot via CRISPR. We observed that this was insufficient to significantly change meiotic crossover frequency or pattern within 3a. We discuss the implications of our findings for targeting meiotic recombination within plant genomes.

plant biology↗

bioRxiv2017

Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions

Meiotic recombination initiates via DNA double strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Recombination frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis SPO11-1-oligonucleotides. DSB hotspots occurred in gene promoters, terminators and introns, driven by AT-sequence richness, which excludes nucleosomes and allows SPO11-1 access. A strong positive relationship was observed between SPO11-1 DSBs and final crossover levels. Euchromatic marks promote recombination in fungi and mammals, and consistently we observe H3K4me3 enrichment in proximity to DSB hotspots at gene 5-ends. Repetitive transposons are thought to be recombination-silenced during meiosis, in order to prevent non-allelic interactions and genome instability. Unexpectedly, we found strong DSB hotspots in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. Hotspot transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination-enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin on the DSB landscape. Epigenetic activation of transposon meiotic DSBs occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription and H3K4me3. Increased met1 SPO11-1 DSBs occurred most strongly within centromeres and Gypsy and CACTA/EnSpm coldspot transposons. Together, our work reveals complex interactions between chromatin and meiotic DSBs within genes and transposons, with significance for the diversity and evolution of plant genomes.

genomics↗