RNA-directed DNA Methylation Erdmann, Robert M; Picard, Colette L
PLoS genetics,
10/2020, Letnik:
16, Številka:
10
Journal Article
Recenzirano
Odprti dostop
RNA-directed DNA methylation (RdDM) is a biological process in which non-coding RNA molecules direct the addition of DNA methylation to specific DNA sequences. The RdDM pathway is unique to plants, ...although other mechanisms of RNA-directed chromatin modification have also been described in fungi and animals. To date, the RdDM pathway is best characterized within angiosperms (flowering plants), and particularly within the model plant Arabidopsis thaliana. However, conserved RdDM pathway components and associated small RNAs (sRNAs) have also been found in other groups of plants, such as gymnosperms and ferns. The RdDM pathway closely resembles other sRNA pathways, particularly the highly conserved RNAi pathway found in fungi, plants, and animals. Both the RdDM and RNAi pathways produce sRNAs and involve conserved Argonaute, Dicer and RNA-dependent RNA polymerase proteins. RdDM has been implicated in a number of regulatory processes in plants. The DNA methylation added by RdDM is generally associated with transcriptional repression of the genetic sequences targeted by the pathway. Since DNA methylation patterns in plants are heritable, these changes can often be stably transmitted to progeny. As a result, one prominent role of RdDM is the stable, transgenerational suppression of transposable element (TE) activity. RdDM has also been linked to pathogen defense, abiotic stress responses, and the regulation of several key developmental transitions. Although the RdDM pathway has a number of important functions, RdDM-defective mutants in Arabidopsis thaliana are viable and can reproduce, which has enabled detailed genetic studies of the pathway. However, RdDM mutants can have a range of defects in different plant species, including lethality, altered reproductive phenotypes, TE upregulation and genome instability, and increased pathogen sensitivity. Overall, RdDM is an important pathway in plants that regulates a number of processes by establishing and reinforcing specific DNA methylation patterns, which can lead to transgenerational epigenetic effects on gene expression and phenotype.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In today's knowledge intensive and post-factual world, student teachers' relationship towards knowledge is a vital element in learning to teach. Student teachers must have a sense of epistemic agency ...to see themselves as productive participants in knowledge-laden activities. However, little attention has been paid to the role of agency in the interconnections between research and teaching in higher education. This study aims to identify how epistemic agency is manifested in student teachers' expressions when they are provided with tools for knowledge production (educational research skills). Epistemic agency was examined as a narrative practice in student teachers' texts (N = 73), and a data-driven analysis was conducted. The results explore the four dimensions of professional practice towards which the students directed their epistemic agency: 'the self', 'the class', 'the research literature', and 'the everyday life'. The study makes visible the variety of how engagement with research skills can promote epistemic agency.
In order to interpret cosmic ray observations, detailed modeling of propagation effects invoking all important messengers is necessary. We introduce a new photon production and propagation code as an ...inherent part of the CRPropa 3 software framework. By implementing additional photon production channels, which are important for energies below ∼ 1018 eV, this code can be used for multi-messenger studies connecting the TeV and sub EeV energy regime and for interpreting models of ultra-high energy cosmic ray sources. We discuss the importance of the individual production channels and propagation effects and present example applications.
We describe a method of reconstructing air showers induced by cosmic rays using deep learning techniques. We simulate an observatory consisting of ground-based particle detectors with fixed locations ...on a regular grid. The detector’s responses to traversing shower particles are signal amplitudes as a function of time, which provide information on transverse and longitudinal shower properties. In order to take advantage of convolutional network techniques specialized in local pattern recognition, we convert all information to the image-like grid of the detectors. In this way, multiple features, such as arrival times of the first particles and optimized characterizations of time traces, are processed by the network. The reconstruction quality of the cosmic ray arrival direction turns out to be competitive with an analytic reconstruction algorithm. The reconstructed shower direction, energy and shower depth show the expected improvement in resolution for higher cosmic ray energy.
We present a two-stage neural network architecture that enables a fully autonomous and comprehensive characterization of collision events by exclusively exploiting the four-momenta of final-state ...particles. We refer to the first stage of the architecture as Lorentz Boost Network (LBN). The LBN allows the creation of particle combinations representing rest frames. The LBN also enables the formation of further composite particles, which are then transformed into said rest frames by Lorentz transformation. The properties of the composite, transformed particles are compiled in the form of characteristic variables that serve as input for a subsequent network. This second network has to be configured for a specific analysis task such as the separation of signal and background events. Using the example of the classification of t tH and t +b events, we compare the separation power of the LBN approach with that of domain-unspecific deep neural networks (DNN). We observe leading performance with the LBN, even though we provide the DNNs with extensive additional input information beyond the particle four-momenta. Furthermore, we demonstrate that the LBN forms physically meaningful particle combinations and autonomously generates suitable characteristic variables.
Teachers' agency has recently been vastly studied from a sociocultural perspective, emphasising that teachers' action is shaped by the structures within which teachers work. However, this study ...provides a different perspective, introducing relational sociology to the research on teachers' agency. Here, agency is seen as embedded in interdependencies and relationships, either personal or impersonal. Finnish newly qualified teachers were interviewed concerning their teacher training and work to explore how they negotiated agency in their narratives. The analysis shows the entanglement of master- and counter-narratives in agency negotiation as the teachers drew on prevailing societal master-narratives and simultaneously provided opposing categories through counter-narratives. The results reveal three aspects of relationships through which the agency was negotiated: political, cultural, and epistemic. The study contributes to the understanding of teachers' agency, paying attention to language and the plurality of relationships in agency negotiation and formation.
Imprinted gene expression occurs during seed development in plants and is associated with differential DNA methylation of parental alleles, particularly at proximal transposable elements (TEs). ...Imprinting variability could contribute to observed parent-of-origin effects on seed development. We investigated intraspecific variation in imprinting, coupled with analysis of DNA methylation and small RNAs, among three Arabidopsis strains with diverse seed phenotypes. The majority of imprinted genes were parentally biased in the same manner among all strains. However, we identified several examples of allele-specific imprinting correlated with intraspecific epigenetic variation at a TE. We successfully predicted imprinting in additional strains based on methylation variability. We conclude that there is standing variation in imprinting even in recently diverged genotypes due to intraspecific epiallelic variation. Our data demonstrate that epiallelic variation and genomic imprinting intersect to produce novel gene expression patterns in seeds.
Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, ...reflecting genomic DNA content. Here, we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24-nt small RNAs are reduced in transposable elements and enriched in genes compared with the embryo. We find an inverse relationship between the parent of origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs. Disruption of the Pol IV sRNA pathway causes a shift toward maternal allele mRNA expression for many genes. Furthermore, paternal inheritance of an RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. Thus, RNA Pol IV mediates the transcriptional balance between maternally and paternally inherited genomes in endosperm.
Display omitted
•Genic 24-nt small RNAs (sRNAs) enriched in endosperm compared with other tissues•Inverse relationship between allelic bias of mRNAs and sRNAs•Maternal:paternal transcript ratio is actively regulated by RNA Pol IV pathway•Mutations in Pol IV suppress negative effects of extra paternal genome dosage
The endosperm is a triploid seed tissue critical for seed viability. Imprinted expression occurs there, but whether active regulation of maternal:paternal transcript ratios occurs on a broader scale is unknown. Erdmann et al. show that the RNA Pol IV small RNA pathway mediates dosage interactions between maternal and paternal genomes.
Abstract
The reconstruction of cosmic ray-induced air showers from measurements of radio waves constitutes a major challenge. In this work, we focus on recovering the full three-dimensional ...electromagnetic field from two recorded signal traces of an antenna station covering two horizontal polarization directions. The simulated field is folded by a direction and frequency-dependent characteristic antenna response pattern, resulting in voltage signal traces as a function of time. Both signal traces are contaminated by simulated background noise. We use conditional Invertible Neural Networks (cINNs) to learn posterior distributions, from which the most likely electromagnetic field given a measured signal trace can be inferred. To improve robustness, we extend the method with an autoencoder by reducing the parameter phase space and decoupling the cINN from specific data shapes. Thereby, each signal trace is condensed into a small number of abstract parameters in the latent space on which the cINN operates. The presented method shows promising results and can be transferred to other unfolding problems where the recovery of the pre-measurement state is of interest.
We present a new approach for the identification of ultra-high energy cosmic rays from sources using dynamic graph convolutional neural networks. These networks are designed to handle sparsely ...arranged objects and to exploit their short- and long-range correlations. Our method searches for patterns in the arrival directions of cosmic rays, which are expected to result from coherent deflections in cosmic magnetic fields. The network discriminates astrophysical scenarios with source signatures from those with only isotropically distributed cosmic rays and allows for the identification of cosmic rays that belong to a deflection pattern. We use simulated astrophysical scenarios where the source density is the only free parameter to show how density limits can be derived. We apply this method to a public data set from the AGASA Observatory.