Sequence-independent identification of active LTR retrotransposons in Arabidopsis

Detection of retrotransposons capable of contemporary transposition is hampered by the replicative nature of their movement and is usually limited to fortuitous observations of new integration events causing visible phenotypes. To circumvent this shortcoming, we developed a screening strategy for novel active retrotransposons containing long terminal repeats (LTR-TEs). Our approach is based on specific recovery of an LTR region that is part of the linear extrachromosomal DNA (ecDNA) synthetized in the reverse transcription step of the LTR-TE replication/transposition cycle. The method is inexpensive and straightforward and does not require prior knowledge of the retroelement sequence. Here we demonstrate the high sensitivity and specificity of this approach using Arabidopsis mutants with known retrotransposon activities. Using this method, we then identified a novel and mobile retroelement in the Landsberg erecta Arabidopsis ecotype that is absent in the annotated reference genome of Col-0. The cost-effective procedure presented here can be used to identify transposition-competent LTR-retrotransposons in a broad variety of biological specimens, independent of their sequence annotation.This work was supported by European Research Council (EVOBREED) [322621]; and Gatsby Fellowship [AT3273/GLE]

Crystal structure of the high temperature phase of strontium barium niobate

Pure and undoped strontium-barium niobate Sr0:40Ba0:60Nb2O6 (SBN40) single crystals grown by the Czochralski method were investigated by single crystal X-ray diffraction methods. The study below TC (429 K for SBN40) confirmed the structure with P4bm space group. Above this temperature the structure transforms into the paraelectric, centrosymmetric one with P4=mbm space group. Analysis of the recorded diffraction patterns allowed to observe several signs of crystal structure modulation. On the registered diffraction images satellite reflections were found. A modulation vector q = ( ; ; ), where = 0:3075(6) (at room temperature) was found and it was similar to that occurring in the SBN61. In addition, above the phase transition temperature on the (hk) planes with l integer a weak diffuse scattering was observed

Regulation of rice root development by a retrotransposon acting as a microRNA sponge

It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.This work was supported by European Research Council 492 (EVOBREED) [322621]; Gatsby Fellowship [AT3273/GLE]

Biomartr: genomic data retrieval with R

$\textbf{MOTIVATION}$: Retrieval and reproducible functional annotation of genomic data are crucial in biology. However, the current poor usability and transparency of retrieval methods hinders reproducibility. Here we present an open source R package, $\textit{biomartr}$, which provides a comprehensive easy-to-use framework for automating data retrieval and functional annotation for meta-genomic approaches. The functions of biomartr achieve a high degree of clarity, transparency and reproducibility of analyses. $\textbf{RESULTS}$: The $\textit{biomartr}$ package implements straightforward functions for bulk retrieval of all genomic data or data for selected genomes, proteomes, coding sequences and annotation files present in databases hosted by the National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EMBL-EBI). In addition, $\textit{biomartr}$ communicates with the BioMartr database for functional annotation of retrieved sequences. Comprehensive documentation of $\textit{biomartr}$ functions and five tutorial vignettes provide step-by-step instructions on how to use the package in a reproducible manner. $\textbf{AVAILABILITY AND IMPLEMENTATION}$: The open source $\textit{biomartr}$ package is available at https://github.com/HajkD/biomartr and https://cran.r-project.org/web/packages/biomartr/index.htmlThis work was supported by an European Research Council grant named EVOBREED [grant number 322621] (to JP) and a Gatsby Fellowship [grant number AT3273/GLE] (to JP)

Quantifying community resilience to riverine hazards in Bangladesh

Every year, 30–70% of Bangladesh is inundated with flood waters, which combined with erosion, affect between 10 and 70 million people annually. Rural riverine communities in Bangladesh have long been identified as some of the poorest populations, most vulnerable to riverine hazards. However, these communities have, for generations, also developed resilience strategies – considered as the combination of absorptive, adaptive, and transformative approaches – to manage significant flooding and erosion. It is not clear whether such existing strategies are sufficient to generate resilience in the face of increasing hazards and growing pressures for land. In this study, we quantify community resilience to flooding and erosion of 35 of the most poverty-stricken and exposed communities in riverine Bangladesh by applying the systematic resilience measurement framework provided by the Flood Resilience Measurement for Communities tool. The low levels of resilience observed in the riverine communities, as well as their continued focus on enhancing absorptive capacities are alarming, especially in the face of growing climate threats and continued population growth. Innovative transformative responses are urgently required in riverine Bangladesh, which align with and complement ongoing community-centred efforts to enhance rural resilience to riverine hazards

Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylase of lysine 9 of histone 3 (IBM1), a subset of body-methylated genes acquires non-CpG methylation. This was shown to alter their expression and affect plant development. It is not clear why only certain body-methylated genes gain non-CpG methylation in the absence of IBM1 and others do not. Here we describe a link between CpG methylation and the establishment of methylation in the CpHpG context that explains the two classes of body-methylated genes. We provide evidence that external cytosines of CpCpG sites can only be methylated when internal cytosines are methylated. CpCpG sites methylated in both cytosines promote spreading of methylation in the CpHpG context in genes protected by IBM1. In contrast, CpCpG sites remain unmethylated in IBM1-independent genes and do not promote spread of CpHpG methylation.European Research Council [322621]; Gatsby Foundation [AT3273/GLE]. Funding for open access charge: Gatsby Foundation [AT3273/GLE]

Developmental Restriction of Retrotransposition Activated in Arabidopsis by Environmental Stress

Retrotransposons (RTs) may rapidly increase in copy number due to periodic bursts of transposition. Such bursts are mutagenic and thus potentially deleterious. However, certain transposition-induced gain-of-function or regulatory mutations may be of selective advantage. How an optimal balance between these opposing effects arises is not well characterized. Here, we studied transposition bursts of a heat-activated retrotransposon family in Arabidopsis. We recorded a high inter- and intra-plant variation in the number and chromosomal position of new insertions, which usually did not affect plant fertility and were equally well transmitted through male and female gametes, even though 90% of them were within active genes. We found that a highly heterogeneous distribution of these new retroelement copies result from a combination of two mechanisms, of which the first prevents multiple transposition bursts in a given somatic cell lineage that later contributes to differentiation of gametes, and the second restricts the regulatory influence of new insertions towards neighbouring chromosomal DNA. As a whole, such regulatory characteristics of this family of RTs ensure its rapid but stepwise accumulation in plant populations experiencing transposition bursts accompanied by high diversity of chromosomal sites harbouring new RT insertions.This work was supported by European Research Council (EVOBREED) [322621] and Gatsby Fellowship [AT3273/GLE]