miRA: adaptable novel miRNA identification in plants using small RNA sequencing data

BACKGROUND: MicroRNAs (miRNAs) are short regulatory RNAs derived from longer precursor RNAs. miRNA biogenesis has been studied in animals and plants, recently elucidating more complex aspects, such as non-conserved, species-specific, and heterogeneous miRNA precursor populations. Small RNA sequencing data can help in computationally identifying genomic loci of miRNA precursors. The challenge is to predict a valid miRNA precursor from inhomogeneous read coverage from a complex RNA library: while the mature miRNA typically produces many sequence reads, the remaining part of the precursor is covered very sparsely. As recent results suggest, alternative miRNA biogenesis pathways may lead to a more diverse miRNA precursor population than previously assumed. In plants, the latter manifests itself in e.g. complex secondary structures and expression from multiple loci within precursors. Current miRNA identification algorithms often depend on already existing gene annotation, and/or make use of specific miRNA precursor features such as precursor lengths, secondary structures etc. Consequently and in view of the emerging new understanding of a more complex miRNA biogenesis in plants, current tools may fail to characterise organism-specific and heterogeneous miRNA populations. RESULTS: miRA is a new tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations. miRA requires small RNA sequencing data and a corresponding reference genome, and evaluates precursor secondary structures and precursor processing accuracy; key parameters can be adapted based on the specific organism under investigation. We show that miRA outperforms the currently best plant miRNA prediction tools both in sensitivity and specificity, for data involving Arabidopsis thaliana and the Volvocine algae Chlamydomonas reinhardtii; the latter organism has been shown to exhibit a heterogeneous and complex precursor population with little cross-species miRNA sequence conservation, and therefore constitutes an ideal model organism. Furthermore we identify novel miRNAs in the Chlamydomonas-related organism Volvox carteri. CONCLUSIONS: We propose miRA, a new plant miRNA identification tool that is well adapted to complex precursor populations. miRA is particularly suited for organisms with no existing miRNA annotation, or without a known related organism with well characterized miRNAs. Moreover, miRA has proven its ability to identify species-specific miRNAs. miRA is flexible in its parameter settings, and produces user-friendly output files in various formats (pdf, csv, genome-browser-suitable annotation files, etc.). It is freely available at https://github.com/mhuttner/miRA .The authors acknowledge funding from the Deutsche Forschungsgemeinschaft (SFB 960), the Bavarian Genome Research Network (BayGene), and the Bavarian Biosystems Network (BioSysNet)

Disentangling effects of nuclear structure in heavy element formation

Forming the same heavy compound nucleus with different isotopes of the projectile and target elements allows nuclear structure effects in the entrance channel (resulting in static deformation) and in the dinuclear system to be disentangled. Using three isotopes of Ti and W, forming 232Cm, with measurement spanning the capture barrier energies, alignment of the heavy prolate deformed nucleus is shown to be the main reason for the broadening of the mass distribution of the quasifission fragments as the beam energy is reduced. The complex, consistently evolving mass-angle correlations that are observed carry more information than the integrated mass or angular distributions, and should severely test models of quasifission

Reconstructing breakup at sub-barrier energies

Using a position sensitive detector array, back-angle coincidence measurements of breakup fragments at sub-barrier energies has enabled the complete characterisation of the breakup processes in the reactions of 6,7Li with 208Pb. Breakup processes and the

RNAModR: Functional analysis of mRNA modifications in R

Motivation: Research in the emerging field of epitranscriptomics is increasingly generating comprehensive maps of chemical modifications in messenger RNAs (mRNAs). A computational framework allowing a reproducible and standardised analysis of these mRNA modification data is missing, but will be crucial for reliable functional meta-gene analyses and cross-study comparisons. Results: We have developed RNAModR, an open-source and R-based set of methods, to analyse and visualise the transcriptome-wide distribution of mRNA modifications. RNAModR allows the statistical evaluation of the mRNA modification site distribution relative to null sites on a meta-gene level, providing insight into the functional role of these mRNA modifications on e.g. mRNA structure and stability. Availability and implementation: RNAModR is available under the GNU General Public License (GPL) as an R-package from https://github.com/mevers/RNAMod

Determination of the angular distribution of evaporation residues following transmission through the superconducting solenoidal separator SOLITAIRE

A highly efficient superconducting solenoidal fusion product separator has been developed at the Australian National University in order to enable separation and detection of evaporation residues following heavy-ion collisions. The determination of absol

The emerging epitranscriptomics of long noncoding RNAs

The pervasive transcription of genomes into long noncoding RNAs has been amply demonstrated in recent years and garnered much attention. Similarly, emerging 'epitranscriptomics' research has shown that chemically modified nucleosides, thought to be largely the domain of tRNAs and other infrastructural RNAs, are far more widespread and can exert unexpected influence on RNA utilization. Both areas are characterized by the often-ephemeral nature of the subject matter in that few individual examples have been fully assessed for their molecular or cellular function, and effects might often be subtle and cumulative. Here we review available information at the intersection of these two exciting areas of biology, by focusing on four RNA modifications that have been mapped transcriptome-wide: 5-methylcytidine, N6-methyladenosine, pseudouridine as well as adenosine to inosine (A-to-I) editing, and their incidence and function in long noncoding RNAs. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.This work was supported by a grant from the National Health and Medical Research Council of Australia (#1061551) to T.P

Influence of entrance-channel magicity and isospin on quasi-fission

The role of spherical quantum shells in the competition between fusion and quasi-fission is studied for reactions forming heavy elements. Measurements of fission fragment mass distributions for different reactions leading to similar compound nuclei have been made near the fusion barrier. In general, more quasi-fission is observed for reactions with non-magic nuclei. However, the 40Ca+ 208Pb reaction is an exception, showing strong evidence for quasi-fission, though both nuclei are doubly magic. Time-dependent Hartree-Fock calculations predict fast equilibration of N/Z in the two fragments early in the collision. This transfer of nucleons breaks the shell effect, causing this reaction to behave more like a non-magic one in the competition between fusion and quasi-fission. Future measurements of fission in reactions with exotic beams should be able to test this idea with larger N/Z asymmetries

Quasifission and Shell Effects in Reactions Forming 266Sg

The role of shell effects in reactions forming the heavy element 266Sg was investigated using the Mass Angle Distribution technique. For the 34S + 232Th reaction the doubly magic shell closure at 208Pb was found to strongly influence asymmetric quasifiss

Insights into the mechanisms and time-scales of breakup of 6,7 Li

Using a back-angle detector array covering 117° to 167°, coincidence measurements of breakup fragments at sub-barrier energies have enabled the complete characterisation of the breakup processes in the reactions of 6,7Li with 208Pb. Those breakup proce