Project description:In vertebrates, DNA methylation predominantly occurs at CG dinucleotides however, widespread non-CG methylation (mCH) has been reported in mammalian embryonic stem cells and in the brain. In mammals, mCH is found at CAC trinucleotides in the nervous system, where it is associated with transcriptional repression, and at CAG trinucleotides in embryonic stem cells, where it positively correlates with transcription. Moreover, CAC methylation appears to be a conserved feature of adult vertebrate brains. Unlike any of those methylation signatures, here we describe a novel form of mCH that occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, remodelled during mid-blastula transition, and re-established during gastrulation in all embryonic layers. Moreover, we identify DNA methyltransferase 3ba (Dnmt3ba) as the primary enzyme responsible for the deposition of this mCH mark. Finally, we observe that TGCT-methylated repeats are specifically associated with H3K9me3-marked heterochromatin suggestive of a functional interplay between these two gene-regulatory marks. Altogether, this work provides insight into a novel form of vertebrate mCH and highlights the substrate diversity of vertebrate DNA methyltransferases.
Project description:Dnmt1/MET1 methyltransferases mediate the epigenetic inheritance of cytosine methylation within CG dinucleotides (mCG). These enzymes use a semiconservative mechanism previously expected to produce binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is quantitatively associated with transposon expression and is stably inherited across many generations. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamical balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that mCG epigenetic inheritance in plant heterochromatin is highly dynamic, with CG sites frequently switching methylation states.
Project description:CG Methylation of Col, Van and reciprocal hybrids using HpaII and MspI digestion followed by bioprime random labeling, and hybridization to AtTILE1 forward array. Study on constitutive and ploymorphic CG methylation between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of CG methylation in reciprocal hybrids. Keywords: genomic hybridization
Project description:Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information each generation by germline reprogramming. To assess the extent of germline reprogramming in plants, we sequenced the methylome of three haploid cell types from developing pollen: the sperm cell (SC), the vegetative cell, and their precursor the post-meiotic microspore. Whole genome bisulfite sequencing of FACS-purified sperm cells, vegetative nuclei and microspores
Project description:Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information each generation by germline reprogramming. To assess the extent of germline reprogramming in plants, we sequenced the methylome of three haploid cell types from developing pollen: the sperm cell (SC), the vegetative cell, and their precursor the post-meiotic microspore.
Project description:The DUX4 transcription factor is normally expressed in the cleavage stage embryo and regulates genes involved in zygotic genome activation. Mis-expression of DUX4 in skeletal muscle, however, is toxic and causes facioscapulohumeral muscular dystrophy (FSHD). We recently showed DUX4-induced toxicity is due, in part, to the accumulation of double-stranded RNAs (dsRNAs) with concomitant activation of the PKR viral response pathway. Here, using dsRNA immunoprecipitation coupled with next-generation sequencing, we determined that DUX4-induced dsRNAs originate from intergenic regions enriched for Alu and LINE-1 elements, endogenous retroviruses, and pericentric human satellite II (HSATII) repeats. DUX4-induced HSATII dsRNAs are formed via temporally controlled bidirectional expression with predominant transcription of one strand preceding the other. Whereas DUX4 activation of dsRNAs derived from intergenic regions such as HSATII contributes to toxicity in FSHD, in the early embryo these dsRNAs might facilitate heterochromatin formation, as has been proposed for cleavage stage expression of mouse major satellites.
Project description:This study investigated the mechanisms and novel engineering strategy of locus- specific transgenerational epigenetic inheritance by depositing centromere repeats