RNA-directed DNA Methylation Erdmann, Robert M; Picard, Colette L
PLoS genetics,
10/2020, Letnik:
16, Številka:
10
Journal Article
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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.
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.
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•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.
Content coverage is frequently identified by faculty as a barrier to the implementation of student-centered instructional strategies. This need to cover content may be a personal belief faculty hold ...and/or an external requirement imposed (or perceived to be) on them (
e.g.
, by their department, institution, accreditors,
etc.
). Studies have shown improved learning outcomes for instructors that adhere to depth (as opposed to breadth) approaches. This study sought to characterize chemistry assistant professors' perspectives on content coverage and the reasoning supporting these perspectives. Nine chemistry assistant professors were interviewed, and constant comparative analysis was used to reveal patterns in faculty thinking. Most of the faculty participants appeared to lean to one side in "the debate" of content coverage and generally expressed that they were acting in the best interests of their students. For some their personal beliefs mainly drove their preference while for others, contextual factors contributed to their choice.
Classroom observation protocols can provide an exceedingly rich form of data. However, this is a double-edged sword, as researchers often struggle to take full advantage of the detailed data outputs. ...In this essay, we introduce a new approach to the analysis of classroom observation data, termed "classroom as genome" (CAG). We illustrate how real-time classroom observation data and genomic data can be viewed as quite analogous, both conceptually and in terms of downstream analysis. We provide both abstract and concrete examples of how the tools of genomics and bioinformatics can be applied to classroom observation outputs. We also show how this philosophy of analysis allows for the layering of information from multiple observation protocols onto the same classroom data. The CAG approach enables biology education researchers to explore detailed patterns within observed classrooms in a highly scalable manner.
The assessment of instructional quality has been and continues to be a desirable, yet difficult endeavor in higher education. The development of new teaching evaluation frameworks along with ...instruments to measure various aspects of teaching practices holds promise. The challenge rests in the implementation of these frameworks and measures in authentic settings. Part of this challenge is for instructors, researchers, and administrators to parse through and select a meaningful set of tools from the plethora of existing instruments. In this study, we aim to start clarifying the landscape of measures of instructional practice by exploring the complementarity of two existing instruments: the Classroom Observation Protocol for Undergraduate STEM (COPUS) and the Learner-Centered Teaching Rubrics (LCTR). We collected classroom observations and course artifacts from 28 science instructors from research-intensive institutions across the United States. Results show the need to use both instruments to capture nuanced and comprehensive description of a faculty member's instructional practice. This study highlights the messiness of measuring instructional quality and the need to explore the implementation of teaching evaluation frameworks and measures of instructional practices in authentic settings.
5-Hydroxymethylcytosine (5-hmC) is an intermediate in active demethylation in metazoans, as well as a potentially stable epigenetic mark. Previous reports investigating 5-hydroxymethylcytosine in ...plants have reached conflicting conclusions. We systematically investigated whether 5-hmC is present in plant DNA using a range of methods. Using the model organism Arabidopsis thaliana, in addition to other plant species, we assayed the amount or distribution of 5-hydroxymethylcytosine by thin-layer chromatography, immunoprecipitation-chip, ELISA, enzymatic radiolabeling, and mass spectrometry. The failure to observe 5-hydroxymethylcytosine by thin-layer chromatography established an upper bound for the possible fraction of the nucleotide in plant DNA. Antibody-based methods suggested that there were low levels of 5-hmC in plant DNA, but these experiments were potentially confounded by cross-reactivity with the abundant base 5-methylcytosine. Enzymatic radiolabeling and mass spectrometry, the most sensitive methods for detection that we used, failed to detect 5-hydroxymethylcytosine in A. thaliana genomic DNA isolated from a number of different tissue types and genetic backgrounds. Taken together, our results led us to conclude that 5-hmC is not present in biologically relevant quantities within plant genomic DNA.
Key message
Size limits on molecular movement among female gametes.
Cellular decisions can be influenced by information communicated from neighboring cells. Communication can occur via signaling or ...through the direct transfer of molecules. Movement of RNAs and proteins has frequently been observed among symplastically connected plant cells. In flowering plants, the female gametes, the egg cell and central cell, are closely apposed within the female gametophyte. Here we investigated the ability of fluorescently labeled dyes and small RNAs to move from the
Arabidopsis thaliana
central cell to the egg apparatus following microinjection. These results define a size limit of at least 20 kDa for symplastic movement between the two gametes, somewhat larger than that previously observed in
Torenia fournieri
. Our results indicate that symplastic connectivity in
Arabidopsis thaliana
changes after fertilization and suggest that prior to fertilization mechanisms are in place to facilitate small RNA movement from the central cell to the egg cell and synergids.
...because of the transposition, some p-values in Figure 1—source data 5 were calculated incorrectly (a side-by-side comparison is shown in Supplementary file 1, file held on figshare under ...http://dx.doi.org/10.6084/m9.figshare.1409445). The correction does not change any of the conclusions that we drew from these data, which were ‘Imprinting calls based on whole-genome mRNA-seq were validated by sequencing or performing CAPs digestion on RT-PCR amplicons of 29 genes from independently isolated embryo and endosperm RNA samples (Figure 1—figure supplement 2, Figure 1—source data 5); results were mostly consistent with the mRNA-seq data’.
Dilated cardiomyopathy (DCM) is a major cause of heart failure with a high familial recurrence risk. So far, the genetics of DCM remains largely unresolved. We conducted the first genome-wide ...association study (GWAS) to identify loci contributing to sporadic DCM.
One thousand one hundred and seventy-nine DCM patients and 1108 controls contributed to the discovery phase. Pools of DNA stratified on disease status, population, age, and gender were constituted and used for testing association of DCM with 517 382 single nucleotide polymorphisms (SNPs). Three DCM-associated SNPs were confirmed by individual genotyping (P < 5.0 10(-7)), and two of them, rs10927875 and rs2234962, were replicated in independent samples (1165 DCM patients and 1302 controls), with P-values of 0.002 and 0.009, respectively. rs10927875 maps to a region on chromosome 1p36.13 which encompasses several genes among which HSPB7 has been formerly suggested to be implicated in DCM. The second identified locus involves rs2234962, a non-synonymous SNP (c.T757C, p. C151R) located within the sequence of BAG3 on chromosome 10q26. To assess whether coding mutations of BAG3 might cause monogenic forms of the disease, we sequenced BAG3 exons in 168 independent index cases diagnosed with familial DCM and identified four truncating and two missense mutations. Each mutation was heterozygous, present in all genotyped relatives affected by the disease and absent in a control group of 347 healthy individuals, strongly suggesting that these mutations are causing the disease.
This GWAS identified two loci involved in sporadic DCM, one of them probably implicates BAG3. Our results show that rare mutations in BAG3 contribute to monogenic forms of the disease, while common variant(s) in the same gene are implicated in sporadic DCM.
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