MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts.

BACKGROUND: Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines have traditionally focused on particular biotypes, making assumptions that are not fullfilled by total-RNA-seq datasets. Transcripts from distinct RNA biotypes vary in length, biogenesis, and function, can overlap in a genomic region, and may be present in the genome with a high copy number. Consequently, reads from total-RNA-seq libraries may cause ambiguous genomic alignments, demanding for flexible quantification approaches. RESULTS: Here we present Multi-Graph count (MGcount), a total-RNA-seq quantification tool combining two strategies for handling ambiguous alignments. First, MGcount assigns reads hierarchically to small-RNA and long-RNA features to account for length disparity when transcripts overlap in the same genomic position. Next, MGcount aggregates RNA products with similar sequences where reads systematically multi-map using a graph-based approach. MGcount outputs a transcriptomic count matrix compatible with RNA-sequencing downstream analysis pipelines, with both bulk and single-cell resolution, and the graphs that model repeated transcript structures for different biotypes. The software can be used as a python module or as a single-file executable program. CONCLUSIONS: MGcount is a flexible total-RNA-seq quantification tool that successfully integrates reads that align to multiple genomic locations or that overlap with multiple gene features. Its approach is suitable for the simultaneous estimation of protein-coding, long non-coding and small non-coding transcript concentration, in both precursor and processed forms. Both source code and compiled software are available at https://github.com/hitaandrea/MGcount .

Epigenetic Alterations of Repeated Relapses in Patient-matched Childhood Ependymomas.

Recurrence is frequent in pediatric ependymoma (EPN). Our longitudinal integrated analysis of 30 patient-matched repeated relapses (3.67 ± 1.76 times) over 13 years (5.8 ± 3.8) reveals stable molecular subtypes (RELA and PFA) and convergent DNA methylation reprogramming during serial relapses accompanied by increased orthotopic patient derived xenograft (PDX) (13/27) formation in the late recurrences. A set of differentially methylated CpGs (DMCs) and DNA methylation regions (DMRs) are found to persist in primary and relapse tumors (potential driver DMCs) and are acquired exclusively in the relapses (potential booster DMCs). Integrating with RNAseq reveals differentially expressed genes regulated by potential driver DMRs (CACNA1H, SLC12A7, RARA in RELA and HSPB8, GMPR, ITGB4 in PFA) and potential booster DMRs (PLEKHG1 in RELA and NOTCH, EPHA2, SUFU, FOXJ1 in PFA tumors). DMCs predicators of relapse are also identified in the primary tumors. This study provides a high-resolution epigenetic roadmap of serial EPN relapses and 13 orthotopic PDX models to facilitate biological and preclinical studies.

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes.

BACKGROUND: Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. RESULTS: Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. CONCLUSION: Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.

Evaluation of growth/no growth interface of Listeria monocytogenes growing on stainless steel surfaces, detached from biofilms or in suspension, in response to pH and NaCl.

The present study aimed to describe the growth/no growth interface of Listeria monocytogenes at three potential states of growth in industrial environments, namely attached, (Att), detached (Det) from a biofilm, or in a planktonic state (suspended; Plan). A 3-strain composite of L. monocytogenes cells was left to colonize stainless steel (SS) surfaces in tryptic soy broth supplemented with 0.6% yeast extract (TSBYE) at 20 °C for 72 h and then transferred to TSBYE at 30 different pH and NaCl concentrations, which were renewed every two days during incubation at 10 °C. Survival of attached population was observed at optimal conditions (pH 7.2, a(w) 0.996), whereas at 4.5-8.0% salt and/or pH<6.0, reduction of attached population on SS surfaces was observed. PFGE patterns showed that 91% of the cells colonizing the SS coupons after 30 days, at any pH and a(w) conditions, belonged to a single strain. Furthermore, the change in the probability of a single cell to initiate growth (P(in)) over time, as well as the number of cells needed (CN) for growth initiation of planktonically growing Plan and Det L. monocytogenes cells were evaluated based on MPN Tables. An ordinary logistic regression model was also used to describe the growth/no growth interface of varying inoculation levels (from <10 to 10(4)CFU/ml) of Plan and Det cells in response to pH and a(w). Although both cell types demonstrated similar growth limits at populations of 10(2)-10(4)CFU/ml, higher numbers of Det than Plan cells were needed (CN) in order to initiate growth at low a(w) and pH. Individual Plan cells reached higher maximum levels of probability of growth initiation (P(max)) and had shorter times to reach P(max)/2 (t(au)), compared to their Det counterparts. Data on growth potential of cells in suspension, attached or detached status, may assist in ranking the risk from different sources of contamination. In addition, they may establish the link between the behavior of L. monocytogenes in foods and its origin from the processing plant. The latter link is important component of biotraceability.