Biology subjects

Saze, H.

Publications and source records attributed to Saze, H..

8 recordsLinked to original sources

bioRxiv2026

Molding the Rice Methylome for Disease Resistance

In Arabidopsis thaliana, epigenetic changes in the DNA methylome can prime transcriptional responses to biotic and abiotic stress, resulting in enhanced resistance. Epigenetic recombinant inbred lines have further enabled the identification of trans-generationally stable epialleles controlling stress resistance without adverse effects on plant growth, highlighting their potential for crop improvement. Unfortunately, extending these approaches to crops has remained largely unsuccessful due to differences in genome architecture. The rice (Oryza sativa) genome consists for [~]40% of transposable elements and other epigenetically regulated repeat sequences. Therefore, perturbation of DNA methylation typically leads to severe developmental defects, sterility or lethality, which precludes the use of methylome engineering strategies for epiallele mapping and crop improvement. Here, we exploit an inducible system to introduce for the first time widespread epigenetic variation in rice without detrimental phenotypic consequences. We combined the A. thaliana DNA demethylase AtROS1 with the {beta}-estradiol-activated XVE cassette (XVE:AtROS1-YFP) to enable transient DNA demethylation during early development. Induction of the construct in transgenic Nipponbare seedlings yielded genome-wide changes in the DNA methylome which persisted for at least one generation. Strikingly, these methylome changes did not cause developmental defects or reduced seed yield, but instead correlated with enhanced resistance against Xanthomonas oryzae, the causal agent of bacterial leaf blight in rice. Our study demonstrates that controlled, transient DNA demethylation can uncouple epigenetic variation from deleterious phenotypes in rice. This approach provides a practical framework for generating epigenetic mapping populations and opens new avenues for harnessing epigenetic variation in crop improvement.

plant biology↗

bioRxiv2025

Transcriptome and epigenome dynamics underpin cold stress priming in Arabidopsis

Stress priming is a critical adaptive mechanism that enables plants to enhance responses to recurring environmental stresses. While transcriptomic changes associated with cold stress priming have been reported, the underlying epigenetic mechanisms remain largely unknown. Here, we investigated transcriptomic and DNA methylation dynamics during cold priming in Arabidopsis thaliana. Cold stress induces distinct gene expression patterns between primed and non-primed plants, accompanied by DNA methylation changes across all cytosine contexts in both protein-coding genes and transposable elements (TEs). Furthermore, DNA methylation mutants exhibit altered cold stress memory, highlighting a role for DNA methylation in preventing spurious gene activation and maintaining priming specificity. Notably, met1, deficient in CG methylation, shows reduced methylation at the CBF gene cluster, which correlates with its overexpression and enhanced activation of downstream cold-responsive genes. Our findings demonstrate that DNA methylation modulates cold stress memory by shaping chromatin states and ensuring transcriptional precision.

plant biology↗

bioRxiv2025

Nuclear envelope dysfunction drives premature aging and modulates heterochromatic methylome drift in Arabidopsis

Aging involves progressive functional decline accompanied by molecular and epigenomic drift. Although nuclear-envelope (NE) defects cause premature aging in animals, the contribution of nuclear architecture to aging in plants remains unclear. Here we show that NE integrity is essential for maintaining epigenetic stability in Arabidopsis thaliana. Under short-day conditions, loss of KAKU4 or CRWN proteins uncovers a photoperiod-sensitive, progeroid-like trajectory with premature senescence, transcriptional drift, and disruption of heterochromatin maintenance. Multi-omics analyses reveal that KAKU4 occupancy is confined to euchromatin and contracts with age, while CHH and CHG methylation erosion occurs within H3K9me2-enriched, transposon-dense heterochromatin. Wild-type plants normally exhibit age-associated CHH hypermethylation at transposable elements, a process abolished in NE mutants. Thus, nuclear-envelope integrity couples chromatin organization to the direction and rate of epigenomic drift, positioning perinuclear architecture as a conserved determinant of heterochromatin stability and aging trajectory across eukaryotes.

plant biology↗

bioRxiv2025

De novo genome assembly of an interspecific hybrid grapevine 'Maeve'

The grapevine is one of the most ancient and economically important horticultural crops in the world. The grapevine species Vitis vinifera is cultivated globally; however, due to its susceptibility to pathogens and environmental stresses, wild Vitis species and their hybrids are often used as rootstocks in vineyards. Here, we report the genome analysis of a Vitis strain named Maeve, which was identified in a vineyard in Japan, though its genetic origin remains unclear. We performed haplotype-resolved de novo assembly of the Maeve genome using PacBio HiFi sequencing and Hi-C assembly. Our genome analysis revealed that Maeve has originated from an interspecific hybridization between an unknown V. vinifera cultivar and the V. riparia Gloire cultivar, likely arising through breeding or natural pollination. This novel cultivar has a potential to expand wine grape production across a wider range of environmental conditions where conventional cultivars are unsuitable for viticulture.

plant biology↗

bioRxiv2024

RNA quality control by CCR4 safeguards chromatin integrity and centromere function in Arabidopsis

The centromere is a pivotal chromatin domain that ensures accurate chromosome segregation during cell division. However, the epigenome regulation of the centromere and its impact on centromere function remain largely elusive. Here in the model plant Arabidopsis, we show that CCR4, the catalytic subunit of the RNA deadenylation complex CCR4-NOT, is essential for maintenance of the centromere epigenome and chromosome integrity. We demonstrate that CCR4 is involved in shortening of the poly(A) tails of transcripts originated from centromeric transposons and repeats, thereby promoting the production of small interfering RNAs (siRNAs). The CCR4-dependent siRNAs guide non-CG DNA methylation at centromere repeats, and CCR4 cooperates with canonical DNA methylation pathways to enhance centromeric H3K9 methylation and ensure mitotic chromosome stability. Our study illustrates the crucial role of RNA quality control in RNA interference and reveals the elaborate mechanism that safeguards plant centromeres through epigenomic regulation.

plant biology↗

bioRxiv2024

RNA N6-adenine methylation dynamics impact Hyaloperonospora arabidopsidis resistance in Arabidopsis

In plants, epitranscriptomic mark N6-adenine methylation (m6A) is dynamically regulated by (a)biotic stressors. However, there is limited knowledge on m6A dynamics at single nucleotide resolution on specific RNA molecule under stresses, and their role in environmental adaptation. By using Oxford Nanopore Technology direct RNA sequencing (ONT-DRS) and a neural network model, here we show transcript-specific dynamics of m6A modification at single nucleotide resolution by biotic stress during Hyaloperonospera arabidopsidis (Hpa) infection in Arabidopsis. In wild-type seedlings, pathogen infection causes significant reduction of global m6A ratios, which correlates with activation of m6A-modified transcripts. Defect of m6A deposition in the m6A mutant hakai-1 mimics m6A reduction from Hpa infection at [~]70% of sites, resulting in constitutive overexpression of basal defence genes and enhanced resistance against the pathogen. Our results demonstrate that m6A dynamics impact defence response against pathogen, providing a promising target for future crop improvement strategies.

plant biology↗

bioRxiv2022

Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, "ParasiTE", we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides novel insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.

genetics↗

bioRxiv2020

CREB-binding protein gene, HAC701, negatively regulates WRKY45-dependent immunity in rice

CREB-binding protein (CBP) is a known transcriptional coactivator and an acetyltransferase that functions in several cellular processes by regulating gene expression. However, how it functions in plant immunity remains unexplored. By characterizing hac701, we demonstrate that HAC701 negatively regulates the immune responses in rice. hac701 shows enhanced disease resistance against a bacterial pathogen, Pseudomonas syringae pv. oryzae (Pso), which causes bacterial halo blight of rice. Our transcriptomic analysis revealed that rice WRKY45, one of the main regulators of rice immunity, is upregulated in hac701 and possibly conferring the resistance phenotype against Pso. The morphological phenotypes of hac701 single mutants were highly similar to WRKY45 overexpression transgenic lines reported in previous studies. In addition, we also compared the list of genes in these studies when WRKY45 is overexpressed and chemically induced transiently with the differentially expressed genes (DEGs) in hac701, and found that they largely overlap. When we investigated for cis-elements found 1kb upstream of WRKY45 gene and WRKY45-dependent DEGs, we found that WRKY45 promoter contains the CRE motif, a possible target of HAC701-mediated regulation. Genome-wide H3K9 acetylation profiling showed depletion of acetylation at large set of genes in hac701. However, consistent with the upregulation of WRKY45 gene expression, our ChIP-sequencing analysis demonstrated that regions of WRKY45 promoter are enriched in H3K9 acetylation in hac701 compared to the segregated wild type control in the mock condition. WRKY45 promoter might be on the receiving end for possible genome-wide compensatory effects when a global regulator like HAC701 is mutated. Finally, we show that HAC701 may have roles in systemic immune signaling. We therefore propose that wild type HAC701 negatively regulates WRKY45 gene expression, thereby suppressing immune responses. SIGNIFICANCEHAC701 is a member of CREB-binding protein (CBP) family that acts as transcriptional coactivator and acetyltransferase. However, little is known how it regulates innate immunity in plants. Herein we reported that rice HAC701 suppresses WRKY45-dependent defense pathway. Our study showed that HAC701 seemingly interacts genetically with WRKY45 in rice to modulate immune responses against pathogens.

plant biology↗