A5039766490- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Epigenetics and DNA Methylation
- Plant nutrient uptake and metabolism
- Genomics and Chromatin Dynamics
- Legume Nitrogen Fixing Symbiosis
- Plant tissue culture and regeneration
- Cancer-related gene regulation
- RNA modifications and cancer
- Plant Gene Expression Analysis
- Genetic Syndromes and Imprinting
- Plant responses to water stress
- Protist diversity and phylogeny
- Soybean genetics and cultivation
- Genetic Mapping and Diversity in Plants and Animals
- Plant Reproductive Biology
- Plant Virus Research Studies
- Ubiquitin and proteasome pathways
- Plant Parasitism and Resistance
- Photosynthetic Processes and Mechanisms
- Plant Genetic and Mutation Studies
Tel Aviv University
2015-2023
University of California, Berkeley
2009-2014
Weizmann Institute of Science
2002-2009
Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and extent biology conservation is unclear. We quantified DNA 17 eukaryotic genomes found that gene body conserved between plants animals, whereas selective transposons not. show plant CHG context extends to green algae exclusion histone H2A.Z from methylated we present evidence for RNA-directed fungal genes. Our data demonstrate extant systems are mosaics derived features, indicate an...
Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated DNA glycosylase DEMETER, but extent methylation changes not known. Here, we show that virtually entire demethylated, coupled with extensive local non-CG hypermethylation small interfering RNA-targeted sequences. Mutation DEMETER partially restores CG to levels found other tissues, indicating specific Endosperm accompanied CHH embryo...
Intergenerational Transposable Shutdown elements (TEs) are a potential threat, especially to the germline genome. In many eukaryotes, TEs shut down by DNA methylation and/or small-RNA–mediated silencing. Therefore, it seems counterintuitive that results obtained Ibarra et al. (p. 1360 ) on Arabidopsis showed in cells of this plant's sexual apparatus, small demethylated DEMETER (DME) glycosylase and become activated. But turns out activation triggers formation small-interfering RNAs, which...
Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), CHH, CHH targeted the RNAi pathway. Arabidopsis thaliana endosperm, placenta-like tissue that nourishes embryo, globally hypomethylated CG context while retaining high non-CG methylation. Global dynamics seeds cereal crops provide bulk human nutrition remain...
Cytosine methylation at CG sites ((m)CG) plays critical roles in development, epigenetic inheritance, and genome stability mammals plants. In the dicot model plant Arabidopsis thaliana, methyltransferase 1 (MET1), a principal methylase, functions to maintain (m)CG during DNA replication, with its null mutation resulting global hypomethylation pleiotropic developmental defects. Null of methylase has not been characterized whole-genome level other higher eukaryotes, leaving generality findings...
Abstract To properly regulate the genome, cytosine methylation is established by animal DNA methyltransferase 3 s (DNMT3s). While altered DNMT3 homologs, Domains rearranged methyltransferases ( DRMs ), have been shown to establish via RNA directed (RdDM) pathway, role of true-plant orthologs remains elusive. Here, we profile de novo (RPS transgene) and genomic in basal plant, Physcomitrella patens , mutated each its PpDNMTs . We show that PpDNMT3b mediates CG CHH methylation, independently...
Abstract Background DNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional developmental role such remains poorly understood. Here, we explore dynamic range honey bee, a model organism for methylation. Results Our data show that CG bodies globally fluctuates during bee development. However, these changes cause no expression alterations. Intriguingly, despite global alterations, tissue-specific...
Summary Cytosine methylation at symmetrical CpG and CpNpG sequences plays a key role in the epigenetic control of plant growth development; yet, way by which signal is interpreted into functional state has not been elucidated. In animals, recognized methyl‐CpG‐binding domain (MBD) proteins that specifically bind methylated dinucleotides. Arabidopsis thaliana , 12 putative MBD were identified classified seven subclasses. Here, we characterized six representing four subclasses (II, III, IV,...
Methyl-CpG binding domain (MBD) proteins in Arabidopsis thaliana bind vitro methylated CpG sites. Here, we aimed to characterize the properties of AtMBDs chromatin nuclei. By expressing wild-type cells fused green fluorescent protein (GFP), showed that AtMBD7 was evenly distributed at all chromocenters, whereas AtMBD5 and 6 preference for two perinucleolar chromocenters adjacent nucleolar organizing regions. AtMBD2, previously shown be incapable vitro-methylated CpG, dispersed within...
Significance While DNA methylation in plants occurs at CG, CHG, and CHH sequence contexts, their comparative roles genome regulation remain elusive. Here, we utilized Physcomitrella patens as a plant model suitable to study this question. By profiling transcriptomes series of context-specific mutants, found redundancy between asymmetric (CHH) symmetric silencing transposons, that regulates the expression CG/CHG-depleted transposons. Specific elimination CG had significantly smaller effect on...
Abstract Plants possess a single gene for the structurally related HETEROCHROMATIN PROTEIN1 (HP1), termed LIKE-HP1 (LHP1). We investigated subnuclear localization, binding properties, and dynamics of LHP1 proteins in Arabidopsis thaliana cells. Transient expression assays showed that tomato (Solanum lycopersicum) fused to green fluorescent protein (GFP; Sl LHP1-GFP) (At localized heterochromatic chromocenters punctuated distribution within nucleus; but not was also nucleolus. Mutations...
Cytosine methylome data is commonly generated through next-generation sequencing, with analyses averaging methylation states of individual reads. We propose an alternative method analysing single-read data. Using this method, we identify patterns relating to the mechanism two plant non-CG-methylating enzymes, CMT2 and DRM2. CMT2-methylated regions show higher stochasticity, while DRM2-methylated have variation among cells. Based on these patterns, develop a classifier that predicts enzyme...
Heterochromatin protein 1 (HP1) controls heterochromatin formation in animal cells, at least partly through interaction with lysine 9 (Lys-9)-methylated histone H3. We aimed to determine whether a structurally conserved human HP1 exhibits localization plant cells and studied its relation modified generated transgenic tobacco plants cycling expressing the HP1γ fused green fluorescent (GFP) followed association chromatin. Plants GFP-HP1γ showed no phenotypic perturbations. found that is...
The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation protein stability and transcription. In Arabidopsis thaliana, mutations in the exhibit number diverse pleiotropic phenotypes. Total or partial loss function leads to misregulation genes involved DNA methylation, suggesting that part phenotype due global effects on methylation.We determined analyzed methylomes transcriptomes both...
The Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 is disrupted by Evelknievel (EK) retroelement, inserted within exon 13, or contains frameshift mutations, resulting truncated, non-functional protein. In contrast to other transposable elements, no transcriptional activation of EK was observed under stress conditions (e.g., protoplasting). We wanted explore regulatory pathway responsible for silencing Ler ecotype and...
Abstract DNA methylation in plants occurs CG, CHG, and CHH sites. While depletion of CG transposons is associated with ample transcriptional activation, it was mainly studied species limited non-CG that linked to methylation. Here we profiled transcription the moss plant, Physcomitrella patens , has robust similar symmetrical CHG levels. Separated contextual mechanisms enabled generation numerous context-specific hypomethylated mutants. Our transcriptome data show specific elimination fully...