Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA174185 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.
| PRJNA260113 | ENA
Project description:This research uses consecutive generations of two independent mutation accumulation (MA) lines in model organism A. thaliana to understand transgenerational stability of epialleles via self-fertilization. With whole-genome bisulfite sequencing, regions of instability were identified and quantified. The vast majority of the methylated genome is stably inherited to offspring and the identified unstable regions do not change frequently between generations. Additionally, an epigenetic cross of two MA lines was created to understand inheritance patterns of epialleles via outcrossing in the absence of genetic variation. Whole-genome bisulfite sequencing was used to predict epigenotype of the offspring without single nucleotide polymorphisms. In regions of differential methylation between the parents, about half of regions show predictable inheritance.
2017-07-24 | GSE94298 | GEO
Project description:DNA methylation inheritance across generations
| PRJNA343778 | ENA
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
2012-08-31 | E-GEOD-40501 | biostudies-arrayexpress
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.
2012-08-31 | GSE40501 | GEO
Project description:We report the survey of two repressive epigenetic marks in hand-dissected mature Arabidopsis embryos. DNA from approximately 2500 embryos was extracted for each samples. DNA was treated with bisulfite and fractionated for whole genome bisulfite sequencing to reveal methylated cytosines. Chromatin was fractionnated and immuno-precipited with either anti-H3K9me2 or anti-H3 to test for histone methylation. Both profiles were compared in different mutant backgrounds to survey how small RNA influence reprogramming in the embryo.
2021-05-26 | GSE147245 | GEO
Project description:Pseudouridine (Ψ) is an isomer of uridine found in ribosomal, transfer and other structural RNAs as well as in some mRNAs and non-coding RNAs, but is difficult to detect in short RNA sequences. Using modified techniques we found Ψ in microRNAs (miRNAs) and their precursors from mammalian and plant cells, primarily at the 5ʹ terminus of the mature miRNA. Small RNAs targeting transposons in reproductive cells (piRNA in testis and easiRNA in pollen) were highly enriched for Ψ, indicating a potential role in epigenetic inheritance. In pollen, pseudouridylated small RNAs were produced by RNA polymerase IV and were localized to sperm cells, as were miRNAs with terminal Ψ. We show that pseudouridylated easiRNAs from pollen contribute to imprinting and the triploid block (chromosome dosage-dependent epigenetic lethality) via the activity of PAUSED/HEN5, the plant homolog of Exportin-t. Exportin-t is required for nuclear export of pseudouridylated tRNA, and we found that PSD is required for cell-cell transport of small RNA in the germline.
2023-08-07 | GSE229986 | GEO
Project description:Transitive silencing of mobile small RNAs in Arabidopsis Pollen
| PRJNA281937 | ENA
Project description:Small RNA diversity and function has been widely characterized in various tissues of the sporophytic generation of the angiosperm model Arabidopsis thaliana. In contrast, there is limited knowledge about small RNA diversity and their roles in developing male gametophytes. We thus carried out small RNA sequencing on RNA isolated from four stages of developing Arabidopsis thaliana pollen. Spores from 4 stages of pollen development (UNM: Uninucleate microspore M-bM-^@M-^S BCP: Bicellular pollen M-bM-^@M-^S TCP: Tricellular pollen M-bM-^@M-^S MP: Mature pollen) were isolated using a percoll gradient-based method (Honys and Twell, 2004) and the small RNA fraction for each sample was isolated and sequenced by Illumina technology. Reference: Honys, D. and Twell, D. (2004) Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol. 5/11/R85.
2014-07-01 | E-GEOD-34190 | biostudies-arrayexpress
Project description:Transgenerational epigenetic inheritance (TEI) describes the transmission of gene-regulatory information across generations without altering DNA sequences. TEI allows priming of offspring towards changing environmental conditions and plays a role in the maintenance of gene silencing of selfish genetic elements like transposons. Small regulatory RNAs are well known to act in TEI, and can be transmitted via the male. Such inheritance via sperm requires dedicated mechanisms, as much of the cellular content is extruded during spermatogenesis. We identify a phase separation-based mechanism, which couples the paternal inheritance of a specific small RNA-bound silencing factor via S-palmitoylation to the transport of membranous organelles. Our findings uncover a thus far unknown paternal TEI mechanism, and describe a novel mode of transport of phase-separated condensates.
2021-03-26 | PXD019099 | Pride