Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle.

The coordinated action of transcriptional and post-transcriptional machineries shapes gene expression programs at steady state and determines their concerted response to perturbations. We have developed Nanodynamo, an experimental and computational workflow for quantifying the kinetic rates of nuclear and cytoplasmic steps of the RNA life cycle. Nanodynamo is based on mathematical modelling following sequencing of native RNA from cellular fractions and polysomes.

Depletion of Mettl3 in cholinergic neurons causes adult-onset neuromuscular degeneration.

Motor neuron (MN) demise is a hallmark of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Post-transcriptional gene regulation can control RNA's fate, and defects in RNA processing are critical determinants of MN degeneration. N-methyladenosine (mA) is a post-transcriptional RNA modification that controls diverse aspects of RNA metabolism.

Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain.

A comprehensive understanding of molecular changes during brain aging is essential to mitigate cognitive decline and delay neurodegenerative diseases. The interpretation of mRNA alterations during brain aging is influenced by the health and age of the animal cohorts studied. Here, we carefully consider these factors and provide an in-depth investigation of mRNA splicing and dynamics in the aging mouse brain, combining short- and long-read sequencing technologies with extensive bioinformatic analyses.

Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing.

N6-methyladenosine (m6A) is the most abundant internal eukaryotic mRNA modification, and is involved in the regulation of various biological processes. Direct Nanopore sequencing of native RNA (dRNA-seq) emerged as a leading approach for its identification. Several software were published for m6A detection and there is a strong need for independent studies benchmarking their performance on data from different species, and against various reference datasets.

Co-occurrence of symptoms after radiochemotherapy in locally advanced cervix cancer patients: a cluster analysis.

Background: State of the art combined radiochemotherapy and image-guided brachytherapy for locally advanced cervical cancer (LACC) has shown improved disease control and survival as well as a significant reduction of organ related morbidity. However, LACC cancer survivors are still experiencing a spectrum of symptoms. The aim of this study was to identify co-occurring symptoms in cervix cancer survivors by using patient-reported outcome and physician assessed morbidity.

Haplotype based testing for a better understanding of the selective architecture.

Background: The identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are available, allele frequency changes at SNP positions are often used for this purpose. Here we provide a new testing approach that uses haplotype frequencies instead of allele frequencies.

Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization.

Background: The spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational signatures can be found using non-negative matrix factorization (NMF). To extract the mutational signatures we have to assume a distribution for the observed mutational counts and a number of mutational signatures.

Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions.

Motivation: Approaches such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) represent the standard for the identification of binding sites of DNA-associated proteins, including transcription factors and histone marks. Public repositories of omics data contain a huge number of experimental ChIP-seq data, but their reuse and integrative analysis across multiple conditions remain a daunting task.

Results: We present the Combinatorial and Semantic Analysis of Functional Elements (CombSAFE), an efficient computational method able to integrate and take advantage of the valuable and numerous, but heterogeneous, ChIP-seq data publicly available in big data repositories.

New insight into the catalytic -dependent and -independent roles of METTL3 in sustaining aberrant translation in chronic myeloid leukemia.

Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm caused by the presence of tyrosine kinase BCR-ABL1 fusion protein, which deregulate transcription and mRNA translation. Tyrosine kinase inhibitors (TKIs) are the first-choice treatment. However, resistance to TKIs remains a challenge to cure CML patients.

Computational methods for RNA modification detection from nanopore direct RNA sequencing data.

The covalent modification of RNA molecules is a pervasive feature of all classes of RNAs and has fundamental roles in the regulation of several cellular processes. Mapping the location of RNA modifications transcriptome-wide is key to unveiling their role and dynamic behaviour, but technical limitations have often hampered these efforts. Nanopore direct RNA sequencing is a third-generation sequencing technology that allows the sequencing of native RNA molecules, thus providing a direct way to detect modifications at single-molecule resolution.

Identification of Genes Post-Transcriptionally Regulated from RNA-seq: The Case Study of Liver Hepatocellular Carcinoma.

The field of transcriptional regulation generally assumes that changes in transcripts levels reflect changes in transcriptional status of the corresponding gene. While this assumption might hold true for a large population of transcripts, a considerable and still unrecognized fraction of the variation might involve other steps of the RNA lifecycle, that is the processing of the premature RNA, and degradation of the mature RNA. Discrimination between these layers requires complementary experimental techniques, such as RNA metabolic labeling or block of transcription experiments.

Multiple haplotype reconstruction from allele frequency data.

Because haplotype information is of widespread interest in biomedical applications, effort has been put into their reconstruction. Here, we propose an efficient method, called haploSep, that is able to accurately infer major haplotypes and their frequencies just from multiple samples of allele frequency data. Even the accuracy of experimentally obtained allele frequencies can be improved by re-estimating them from our reconstructed haplotypes.

The use of small-bore wire-guided chest drains for the management of feline pyothorax: A retrospective case series.

Background: Pyothorax in cats is routinely managed, at least initially, with thoracic tube placement associated with systemic antimicrobial administration. Traditionally, large-bore trocar-type thoracostomy tubes have preferentially been used for the drainage of thick material from the pleural space. In recent years, the use of small-bore wire-guided thoracic drains has increased in both small animals and in humans.

Dynamics of transcriptional and post-transcriptional regulation.

Despite gene expression programs being notoriously complex, RNA abundance is usually assumed as a proxy for transcriptional activity. Recently developed approaches, able to disentangle transcriptional and post-transcriptional regulatory processes, have revealed a more complex scenario. It is now possible to work out how synthesis, processing and degradation kinetic rates collectively determine the abundance of each gene's RNA.

Translation is required for miRNA-dependent decay of endogenous transcripts.

Post-transcriptional repression of gene expression by miRNAs occurs through transcript destabilization or translation inhibition. mRNA decay is known to account for most miRNA-dependent repression. However, because transcript decay occurs co-translationally, whether target translation is a requirement for miRNA-dependent transcript destabilization remains unknown.

Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling.

The quantification of the kinetic rates of RNA synthesis, processing, and degradation are largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT-, a computational method based on the mathematical modeling of premature and mature RNA expression that is able to quantify kinetic rates from steady-state or time course total RNA-seq data without requiring any information on nascent transcripts. Our approach outperforms available solutions, closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcript half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions in which nascent transcription cannot be readily profiled.

INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species.

The abundance of RNA species and their response to perturbations are set by the kinetics rates of RNA synthesis, processing, and degradation. However, the visualization, interpretation, and manipulation of these data require familiarity with mathematical modeling and command line tools. INSPEcT-GUI is an R-Shiny interface that allows researchers without specific training to effortlessly explore how the fine kinetic regulation of the RNA life cycle can shape gene expression programs.

Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts.

It has been known for a few decades that transcripts can be marked by dozens of different modifications. Yet, we are just at the beginning of charting these marks and understanding their functional impact. High-quality methods were developed for the profiling of some of these marks, and approaches to finely study their impact on specific phases of the RNA life-cycle are available, including RNA metabolic labeling.

Ontology-driven integrative analysis of omics data through Onassis.

Public repositories of large-scale omics datasets represent a valuable resource for researchers. In fact, data re-analysis can either answer novel questions or provide critical data able to complement in-house experiments. However, despite the development of standards for the compilation of metadata, the identification and organization of samples still constitutes a major bottleneck hampering data reuse.

A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons.

The histone demethylase LSD1 is a key chromatin regulator that is often deregulated in cancer. Its ortholog, dLsd1 plays a crucial role in Drosophila oogenesis; however, our knowledge of dLsd1 function is insufficient to explain its role in the ovary. Here, we have performed genome-wide analysis of dLsd1 binding in the ovary, and we document that dLsd1 is preferentially associated to the transcription start site of developmental genes.

Benchmarking software tools for detecting and quantifying selection in evolve and resequencing studies.

Background: The combination of experimental evolution with whole-genome resequencing of pooled individuals, also called evolve and resequence (E&R) is a powerful approach to study the selection processes and to infer the architecture of adaptive variation. Given the large potential of this method, a range of software tools were developed to identify selected SNPs and to measure their selection coefficients.

Results: In this benchmarking study, we compare 15 test statistics implemented in 10 software tools using three different scenarios.

An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation.

Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size, accompanied by activation of energy-producing and anabolic pathways, widespread chromatin decompaction, and elevated transcriptional activity. These changes depend upon prior induction of the Myc transcription factor, but how Myc controls them remains unclear. We addressed this issue by profiling the response to LPS stimulation in wild-type and c-myc-deleted primary mouse B-cells.

Prognostic Significance of Organ Dysfunction in Cats With Polytrauma.

Polytrauma is a common emergency condition in small animals and is frequently associated with higher morbidity and mortality rates compared to minor trauma. Multiple Organ Dysfunction Syndrome (MODS) is a major complication of extensive traumatic injury, carrying a high risk of death despite intensive care treatment. Little is known about the prevalence and the prognostic impact of MODS in feline polytrauma.