RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements

We present RibEx (riboswitch explorer), a web server capable of searching any sequence for known riboswitches as well as other predicted, but highly conserved, bacterial regulatory elements. It allows the visual inspection of the identified motifs in relation to attenuators and open reading frames (ORFs). Any of the ORF's or regulatory elements' sequence can be obtained with a click and submitted to NCBI's BLAST. Alternatively, the genome context of all other genes regulated by the same element can be explored with our genome context tool (GeConT). RibEx is available at

Theoretical and empirical quality assessment of transcription factor-binding motifs

Position-specific scoring matrices (PSSMs) are routinely used to predict transcription factor (TF)-binding sites in genome sequences. However, their reliability to predict novel binding sites can be far from optimum, due to the use of a small number of training sites or the inappropriate choice of parameters when building the matrix or when scanning sequences with it. Measures of matrix quality such as E-value and information content rely on theoretical models, and may fail in the context of full genome sequences. We propose a method, implemented in the program ‘matrix-quality’, that combines theoretical and empirical score distributions to assess reliability of PSSMs for predicting TF-binding sites. We applied ‘matrix-quality’ to estimate the predictive capacity of matrices for bacterial, yeast and mouse TFs. The evaluation of matrices from RegulonDB revealed some poorly predictive motifs, and allowed us to quantify the improvements obtained by applying multi-genome motif discovery. Interestingly, the method reveals differences between global and specific regulators. It also highlights the enrichment of binding sites in sequence sets obtained from high-throughput ChIP-chip (bacterial and yeast TFs), and ChIP–seq and experiments (mouse TFs). The method presented here has many applications, including: selecting reliable motifs before scanning sequences; improving motif collections in TFs databases; evaluating motifs discovered using high-throughput data sets

Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera

How chromosome gene organization and gene content evolve among distantly related and structurally malleable genomes remains unresolved. This is particularly the case when considering different insect orders. We have compared the highly contiguous genome assemblies of the lepidopteran Danaus plexippus and the dipteran Drosophila melanogaster, which shared a common ancestor around 290 Ma. The gene content of 23 out of 30 D. plexippus chromosomes was significantly associated with one or two of the six chromosomal elements of the Drosophila genome, denoting common ancestry. Despite the phylogenetic distance, 9.6% of the 1-to-1 orthologues still reside within the same ancestral genome neighbourhood. Furthermore, the comparison D. plexippus–Bombyx mori indicated that the rates of chromosome repatterning are lower in Lepidoptera than in Diptera, although still within the same order of magnitude. Concordantly, 14 developmental gene clusters showed a higher tendency to retain full or partial clustering in D. plexippus, further supporting that the physical association between the SuperHox and NK clusters existed in the ancestral bilaterian. Our results illuminate the scope and limits of the evolution of the gene organization and content of the ancestral chromosomes to the Lepidoptera and Diptera while helping reconstruct portions of the genome in their most recent common ancestor

miR-7 is recruited to the High Molecular Weight 1 RNA-induced silencing complex in CD8+ T cells upon activation and suppresses IL-2 signaling

Increasing evidence suggests mammalian Argonaute (Ago) proteins partition into distinct complexes within cells, but there is still little biochemical or functional understanding of the miRNAs differentially associated with these complexes. In naïve T cells, Ago2 is found almost exclusively in low molecular weight (LMW) complexes which are associated with miRNAs but not their target mRNAs. Upon T-cell activation, a proportion of these Ago2 complexes move into a newly formed high molecular weight (HMW) RNA-induced silencing complex (RISC), which is characterized by the presence of the GW182 protein that mediates translational repression. Here, we demonstrate distinct partitioning of miRNAs and isomiRs in LMW versus HMW RISCs upon antigen-mediated activation of CD8 + T cells. We identify miR-7 as highly enriched in HMW RISC and demonstrate that miR-7 inhibition leads to increased production of IL-2 and up-regulation of the IL-2 receptor, the transferrin receptor, CD71 and the amino acid transporter, CD98. Our data support a model where recruitment of miR-7 to HMW RISC restrains IL-2 signaling and the metabolic processes regulated by IL-2. </p

Genome evolution in three species of cactophilic drosophila

We report genomes of two species of cactophilic Drosophila: Drosophila arizonae and D. navojoa. These two are the closest relatives of D. mojavensis, forming the D. mojavensis cluster. D. mojavensis and D. arizonae diverged from D. navojoa ∼5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species are also separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a past role of the inversions in preventing gene flow, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions

Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection

Cross-kingdom small RNA trafficking between hosts and microbes modulates gene expression in the interacting partners during infection. However, whether other RNAs are also transferred is unclear. Here, we discover that host plant Arabidopsis thaliana delivers mRNAs via extracellular vesicles (EVs) into the fungal pathogen Botrytis cinerea. A fluorescent RNA aptamer reporter Broccoli system reveals host mRNAs in EVs and recipient fungal cells. Using translating ribosome affinity purification profiling and polysome analysis, we observe that delivered host mRNAs are translated in fungal cells. Ectopic expression of two transferred host mRNAs in B. cinerea shows that their proteins are detrimental to infection. Arabidopsis knockout mutants of the genes corresponding to these transferred mRNAs are more susceptible. Thus, plants have a strategy to reduce infection by transporting mRNAs into fungal cells. mRNAs transferred from plants to pathogenic fungi are translated to compromise infection, providing knowledge that helps combat crop diseases.</p