Biology subjects

Gy, I.

Publications and source records attributed to Gy, I..

3 recordsLinked to original sources

bioRxiv2025

The Arabidopsis GyraseB3 contributes to transposon silencing by promoting histone deacetylation

DNA methylation and histone modifications are key epigenetic marks controlling chromatin structure, gene expression and transposable element (TE) activity. In plants, the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1) prevents heterochromatic silencing marks from accumulating on actively transcribed genes. Through a genetic screen of mutants defective in IBM1 production, we identified suppressor mutations in genes essential for maintaining balanced genome-wide epigenetic states. The gyrb3 mutation partly reversed DNA hypermethylation in IBM1-deficient plants, revealing a novel role for GyrB3, a nuclear protein combining domains from cyanobacterial gyrases and ELM2/SANT proteins involved in histone acetylation. In gyrb3 mutants, TEs exhibit transcriptional activity, showing reduced DNA methylation and increased histone H3 acetylation, both of which are epigenetic marks associated with expression activation. GyrB3 physically interacts with histone deacetylases like HISTONE DEACETYLASE6 (HDA6), likely mediating their activities at TEs. The functional overlap between HDA6 and GyrB3 is further supported by the observation that, similar to gyrb3, a mutation in hda6 suppresses the Ibm2 phenotype. Our findings reinforce that histone deacetylation is essential for TE silencing and that loss of IBM1 in plants abolished the frontiers between genes and TEs, emphasizing its importance in maintaining epigenomic stability. Key PointsO_LIIBM1 is a histone demethylase that safeguards actively transcribed genes from inappropriate heterochromatic silencing, thereby preserving their function and epigenomic integrity. A gyrb3 mutant suppresses the developmental abnormalities observed in ibm1 or ibm2 mutants. C_LIO_LIGyrB3, though misannotated as a plant gyrase, appears to have evolved away from its conventional role and instead functions in epigenetic regulation. C_LIO_LIGyrB3 is a nuclear protein that interacts with histone deacetylases such as HDA6 to repress transposon activity; mutating GYRB3 results in elevated transposon expression, driven by reduced DNA methylation and increased histone acetylation. C_LI

plant biology↗

bioRxiv2020

The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in Arabidopsis thaliana

Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudo-functionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. While such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions which included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently co-exist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.

evolutionary biology↗

bioRxiv2019

Transcriptional natural variation at FLM induces synergistic pleiotropy in Arabidopsis thaliana

Investigating the evolution of complex phenotypes and the underlying molecular bases of their variation is critical to understand how organisms adapt to the environment. We used leaf growth as a model trait as it is highly integrative of internal and external cues and relies on functions at different levels of the plant organization. Applying classical quantitative genetics on a recombinant inbred line population derived from a Can-0 x Col-0 cross, we identified the MADS-box transcription factor FLOWERING LOCUS M (FLM) as a player of the phenotypic variation for leaf growth and colour. Interestingly, we showed that allelic variation at FLM modulates plant growth strategy along the leaf economics spectrum, a trade-off between resource acquisition and resource conservation observable across thousands of plant species. We demonstrated that the functional differences at FLM relies on a single intronic substitution, disturbing transcript splicing and leading to a low expression of the active FLM transcript. Using phenotypic and climatic data across Arabidopsis natural populations, our work shows how noncoding genetic variation of a single gene may be adaptive through synergistic pleiotropy.

plant biology↗