Epigenetic inheritance in apomictic dandelions : stress-induced and heritable modifications in DNA methylation and small RNA

Epigenetic variation, such as changes in DNA methylations, regulatory small RNAs (sRNAs) and chromatin modifications can be induced by environmental stress. There is increasing information that such induced epigenetic modifications can be transmitted to offspring, potentially mediating adaptive transgenerational responses to environmental changes. However, it is unclear if this phenomenon is common and relevant for adaptation under natural conditions. My thesis study aimed to examine epigenetic inheritance in common and widespread apomictic dandelions (Taraxacum officinale Wig.). Due to their asexual reproduction mode by producing clonal seeds offspring from seeds are genetically uniform and thus suitable to investigate epigenetic effects that are not confounded with genetic variation. I exposed apomictic dandelion lineages to drought and salicylic acid (SA) stress, which induces plant defense responses following pathogen attack, and found effects on patterns of DNA methylation up to two stress-free offspring generations after exposure. However, a heritable stress signal was not present in all tests and was stress- and lineage-dependent. Drought stress triggered a weak and lineage-dependent signal that was lost again in the second offspring generation. SA treatment revealed a stress-related increased rate of DNA methylation changes in the two offspring generations, but no stress signal was found in the stressed generation itself. I also observed changes in small RNA production due the drought and SA stress experienced two generations ago. These transgenerational sRNA effects showed association with gene functions related to grandparental drought and SA stress, which suggests functional relevance of the transgenerational effects. I used a reciprocal transplantation field experiment to investigate whether exposing dandelions to natural field stresses also triggers DNA methylation changes. The experiment revealed evidence of adaptive divergence between the populations, suggesting that non-native habitats are experienced as more stressful. However, under these field conditions no induction-based DNA methylation changes were found that persisted into offspring. By using AFLP and MS-AFLP screening of natural apomictic dandelion populations across a north-south transect in Europe I examined if natural, heritable DNA methylation variation reflects underlying genetic variation, or if it shows patterns that are not predictable from underlying genetics. I found that a large part of heritable DNA methylation differentiation along the north-south transect was correlated with genetic differentiation. However, a fraction of differentiation in heritable DNA methylation was independent from genetic variation. This suggests a potential of epigenetics to play an evolutionary role independently, at least to some extent, from underlying genetics. Overall, I found indications of epigenetic inheritance in apomictic dandelions. Whether epigenetic variation would result in adaptive phenotypic variation in nature and whether it would persist long enough to play a relevant role in adaptation remains unclear and requires further study.</p

IVOA Recommendation: Vocabularies in the Virtual Observatory Version 1.19

This document specifies a standard format for vocabularies based on the W3C's Resource Description Framework (RDF) and Simple Knowledge Organization System (SKOS). By adopting a standard and simple format, the IVOA will permit different groups to create and maintain their own specialised vocabularies while letting the rest of the astronomical community access, use, and combine them. The use of current, open standards ensures that VO applications will be able to tap into resources of the growing semantic web. The document provides several examples of useful astronomical vocabularies

Variability of Hot Supergiant IRAS 19336-0400 in the Early Phase of its Planetary Nebula Ionization

We present photoelectric and spectral observations of a hot candidate proto-planetary nebula - early B-type supergiant with emission lines in spectrum - IRAS 19336-0400. The light and color curves display fast irregular brightness variations with maximum amplitudes Delta V=0.30 mag, Delta B=0.35 mag, Delta U=0.40 mag and color-brightness correlations. By the variability characteristics IRAS 19336-0400 appears similar to other hot proto-planetary nebulae. Based on low-resolution spectra in the range lambda 4000-7500 A we have derived absolute intensities of the emission lines H_alpha, H_beta, H_gamma, [SII], [NII], physical conditions in gaseous nebula: n_e=10^4 cm^{-3}, T_e=7000 \pm 1000 K. The emission line H_alpha, H_beta equivalent widths are found to be considerably variable and related to light changes. By UBV-photometry and spectroscopy the color excess has been estimated: E_{B-V}=0.50-0.54. Joint photometric and spectral data analysis allows us to assume that the star variability is caused by stellar wind variations.Comment: 11 pages, 6 figures, 2 tables, accepted for publication in Pis'ma Astron. Zh. (Astronomy Letters

Catalogue of far-infrared loops in the Galaxy

Aims: An all-sky survey of loop- and arc-like intensity enhancements has been performed in order to investigate the large-scale structure of the diffuse far-infrared emission. Methods: We used maps made of 60 and 100 micrometer processed IRAS data (Sky Survey Atlas and dust infrared emission maps) to identify large-scale structures: loops, arcs or cavities, in the far-infrared emission in the Galaxy. Distances were attributed to a subsample of loops using associated objects. Results: We identified 462 far-infrared loops, analyzed their individual FIR properties and their distribution. This data forms the Catalogue of Far-Infrared Loops in the Galaxy. We obtained observational estimates of f_in~30% and f_out~5% for the hot gas volume filling factor of the inward and outward Galactic neighbourhood of the Solar System. We obtained a slope of the power law size luminosity function {beta}=1.37 for low Galactic latitudes in the outer Milky Way. Conclusions: Deviations in the celestial distribution of far-infrared loops clearly indicate, that violent events frequently overwrite the structure of the interstellar matter in the inner Galaxy. Our objects trace out the spiral arm structure of the Galaxy in the neighbourhood of the Sun and their distribution clearly suggests that there is an efficient process that can generate loop-like features at high Galactic latitudes. Power law indices of size luminosity distributions suggest, that the structure of the ISM is ruled by supernovae and stellar winds at low Galactic latitudes while it is governed by supersonic turbulence above the Galactic plane.Comment: 11 pages - 10 figures (together with Appendix A), accepted for publication in Astronomy & Astrophysics. Appendix B, C and D are available at http://kisag.konkoly.hu/CFIRLG

“Stripe” Transcription Factors Provide Accessibility to Co-Binding Partners in Mammalian Genomes

Regulatory elements activate promoters by recruiting transcription factors (TFs) to specific motifs. Notably, TF-DNA interactions often depend on cooperativity with colocalized partners, suggesting an underlying cis-regulatory syntax. To explore TF cooperativity in mammals, we analyze ∼500 mouse and human primary cells by combining an atlas of TF motifs, footprints, ChIP-seq, transcriptomes, and accessibility. We uncover two TF groups that colocalize with most expressed factors, forming stripes in hierarchical clustering maps. The first group includes lineage-determining factors that occupy DNA elements broadly, consistent with their key role in tissue-specific transcription. The second one, dubbed universal stripe factors (USFs), comprises ∼30 SP, KLF, EGR, and ZBTB family members that recognize overlapping GC-rich sequences in all tissues analyzed. Knockouts and single-molecule tracking reveal that USFs impart accessibility to colocalized partners and increase their residence time. Mammalian cells have thus evolved a TF superfamily with overlapping DNA binding that facilitate chromatin accessibility

Mouse screen reveals multiple new genes underlying mouse and human hearing loss

Adult-onset hearing loss is very common, but we know little about the underlying molecular pathogenesis impeding the development of therapies. We took a genetic approach to identify new molecules involved in hearing loss by screening a large cohort of newly generated mouse mutants using a sensitive electrophysiological test, the auditory brainstem response (ABR). We review here the findings from this screen. Thirty-eight unexpected genes associated with raised thresholds were detected from our unbiased sample of 1,211 genes tested, suggesting extreme genetic heterogeneity. A wide range of auditory pathophysiologies was found, and some mutant lines showed normal development followed by deterioration of responses, revealing new molecular pathways involved in progressive hearing loss. Several of the genes were associated with the range of hearing thresholds in the human population and one, SPNS2, was involved in childhood deafness. The new pathways required for maintenance of hearing discovered by this screen present new therapeutic opportunities

Epigenetic variation in asexually reproducing organisms

The role that epigenetic inheritance can play in adaptation may differ between sexuals and asexuals because (1) the dynamics of adaptation differ under sexual and asexual reproduction and the opportunities offered by epigenetic inheritance may affect these dynamics differently; and (2) in asexual reproduction epigenetic reprogramming mechanisms that are associated with meiosis can be bypassed, which could promote the buildup of epigenetic variation in asexuals. Here, we evaluate current evidence for an epigenetic contribution to adaptation in asexuals. We argue that two aspects of epigenetic variation should have particular relevance for asexuals, namely epigenetics-mediated phenotypic plasticity within and between generations, and heritable variation via stochastic epimutations. An evaluation of epigenetic reprogramming mechanisms suggests that some, but not all, forms of asexual reproduction enhance the likelihood of stable transmission of epigenetic marks across generations compared to sexual reproduction. However, direct tests of these predicted sexual–asexual differences are virtually lacking. Stable transmission of DNA methylation, transcriptomes, and phenotypes from parent to clonal offspring are demonstrated in various asexual species, and clonal genotypes from natural populations show habitat-specific DNA methylation. We discuss how these initial observations can be extended to demonstrate an epigenetic contribution to adaptation.

Adaptation of flowering phenology and fitness-related traits across environmental gradients in the widespread Campanula rotundifolia

Plant populations need to adjust to climate warming through phenotypic plasticity or evolution of trait means. We performed a common-garden experiment with European populations of Campanula rotundifolia to investigate current adaptation in fitness-related traits and the potential for future adaptation. The common garden was situated in Switzerland and contained plants from 18 populations from four regions: Central Europe, The Netherlands, Scandinavia and the Swiss Alps. We assessed current adaptation with trait–environment correlations, and we compared molecular marker with trait differentiation to investigate past selection. How traits may change under future climate warming was investigated via selection analysis. Trait–trait correlations were performed to reveal genetic constraints. The majority of analysed phenotypic traits showed regional differentiation and all traits showed indications of past selection. Flowering duration decreased with latitude and elevation, suggesting adaptation to growing season length. The Central European populations performed best, indicating home-site advantage. Selection analysis showed positive selection on fitness-related traits whereas phenological traits showed less clear patterns. Trait–trait correlations were mostly neutral or favourable to selection. This study suggests that flowering phenology and other fitness-related traits of C. rotundifolia are adapted to the current climatic conditions and have the potential to evolve under climate change

Data from: The epigenetic footprint of poleward range-expanding plants in apomictic dandelions

Epigenetic modifications, such as DNA methylation variation, can generate heritable phenotypic variation independent of the underlying genetic code. However, epigenetic variation in natural plant populations is poorly documented and little understood. Here, we test whether northward range expansion of obligate apomicts of the common dandelion (Taraxacum officinale) is associated with DNA methylation variation. We characterized and compared patterns of genetic and DNA methylation variation in greenhouse-reared offspring of T. officinale that were collected along a latitudinal transect of northward range expansion in Europe. Genetic AFLP and epigenetic MS-AFLP markers revealed high levels of local diversity and modest but significant heritable differentiation between sampling locations and between the southern, central and northern regions of the transect. Patterns of genetic and epigenetic variation were significantly correlated, reflecting the genetic control over epigenetic variation and/or the accumulation of lineage-specific spontaneous epimutations, which may be selectively neutral. In addition, we identified a small component of DNA methylation differentiation along the transect that is independent of genetic variation. This epigenetic differentiation might reflect environment-specific induction or, in case the DNA methylation variation affects relevant traits and fitness, selection of heritable DNA methylation variants. Such generated epigenetic variants might contribute to the adaptive capacity of individual asexual lineages under changing environments. Our results highlight the potential of heritable DNA methylation variation to contribute to population differentiation along ecological gradients. Further studies are needed using higher resolution methods to understand the functional significance of such natural occurring epigenetic differentiation

Genetic and Epigenetic Differences Associated with Environmental Gradients in Replicate Populations of Two Salt Marsh Perennials

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation‐sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site‐specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients