Biology subjects

Richard, H.

Publications and source records attributed to Richard, H..

8 recordsLinked to original sources

bioRxiv2026

phyloDS: phylogeny-aware differential splicing across species, beyond reference annotations

Alternative splicing diverges rapidly between species, yet its comparative analysis lags far behind that of gene expression: junction orthology is defined on a single reference genome, species are treated as independent samples, and detected shifts are rarely grounded in sequence-level evidence. We present phyloDS, an RNA-seq--driven framework that resolves all three limitations. phyloDS defines orthologous splice junctions on multiple sequence alignments of one-to-one orthologous genes, tests their differential usage with a regularized Ornstein--Uhlenbeck model, and cross-validates detected shifts against splice-site predictions made from genomic sequence alone. Applied to primate brain and rodent heart transcriptomes, phyloDS recovered up to 2.9-fold more shared orthologous splice junctions than a reference-based strategy and kept type~I error near nominal where competing methods inflate it more than two-fold. It identified 234 and 502 differentially used orthologous splice junctions in hominoids and mole-rats (86 and 141 unannotated), revealing a mitochondrial and contractile splicing signature in mole-rats.

bioinformatics↗

bioRxiv2025

Assessment of pharmacokinetics, safety, and neuroprotective efficacy of an adjunct intramuscular verapamil therapy in a rat model of organophosphate DFP-induced status epilepticus

Lethal organophosphate (OP) exposure leads to status epilepticus (SE), which, despite standard-of-care therapy, is associated with acute mortality and long-term morbidities. Neuronal injury and inflammation are reported following OP-SE, and drugs targeted at these processes have produced beneficial outcomes. Verapamil (VPM) is a calcium-channel blocker used as an antihypertensive drug. It exhibits neuroprotective and anti-inflammatory actions in experimental models of CNS injuries. Here, we investigated the feasibility of an adjunctive intramuscular (i.m.) VPM therapy in OP Diisopropyl Fluorophosphate (DFP)-induced SE. We also investigated the safety and toxicity of i.m. VPM and compared its pharmacokinetic (PK) profile to oral (p.o.) administration. Rats were injected with DFP (4 mg/kg, s.c.). One minute later, atropine (0.5 mg/kg, i.m.) and 2-PAM (25 mg/kg, i.m.) were injected, and at 1-hour post-SE, midazolam (1.78 mg/kg, i.m.) was administered. Rats were then treated with VPM (10 mg/kg, i.m, 3 days). Histological analysis was conducted to assess neuronal injury and injection-site pathology. In a separate group of rats, PK studies were conducted on blood and brain homogenates treated once with saline or VPM (10 mg/kg, p.o. or i.m.). Our data demonstrated that following DFP-SE, i.m. VPM achieved higher blood and brain levels and exhibited a favorable PK profile compared to p.o. route. VPM therapy did not cause significant muscle pathology and produced a robust neuroprotective response. Our studies provide evidence that the i.m. route is an effective method for delivering VPM following SE producing significant neuroprotective outcomes compared to treatment with the standard-of-care alone in OP-SE.

pharmacology and toxicology↗

bioRxiv2024

Reannotation of the zebra finch genome reveals undiscovered transcriptional complexity

The zebra finch has become a paradigmatic model system to mechanistically investigate vocal communication from genes to behavior. Here, we report 1) a comprehensive map of the polyadenylated fraction of the transcriptome of the male zebra finch telencephalon at two ages, during the song learning phase at 50 days and when fully adult at 2 years as well as 2) as an expanded and refined annotation of the zebra finch genome based on our transcriptome data. Using high-throughput next generation sequencing of paired-end strand- specific cDNA fragments, we detected over 50% of the annotated protein coding transcripts (ENSEMBL v.55) in the telencephalon at both stages. We exploited the information gained from the paired-end sequence reads and from reads falling onto splice junctions to update the existing annotation (ENS55) with new transcript structures and alternative splicing events. The dataset allowed to refine 2822 of the available gene models by extending them in the 3-UTR and to detect 11391 undiscovered transcriptional units in non-coding regions. Our results illustrate the value of continuously incorporating new transcriptional evidence into existing annotations.

molecular biology↗

bioRxiv2023

Charting the alternative usage of protein repeated regions in evolution and its implication for protein interactions

Alternative splicing of repeats in proteins provides a mechanism for rewiring and fine-tuning protein interaction networks. In this work, we developed a robust and versatile method, ASPRING, to identify alternatively spliced protein repeats from gene annotations. ASPRING leverages evolutionary meaningful alternative splicing-aware hierarchical graphs to provide maps between protein repeats sequences and 3D structures. We re-think the definition of repeats by explicitly accounting for transcript diversity across several genes/species. Using a stringent sequence-based similarity criterion, we detected over 5,000 evolutionary conserved repeats by screening virtually all human protein-coding genes and their orthologs across a dozen species. Through a joint analysis of their sequences and structures, we extracted specificity-determining sequence signatures and assessed their implication in experimentally resolved and modelled protein interactions. Our findings demonstrate the widespread alternative usage of protein repeats in modulating protein interactions and open avenues for targeting repeat-mediated interactions. HighlightsO_LIRobust detection of alternatively used repeated protein regions in evolution C_LIO_LIThe approach relies on sequence similarity and identifies conserved signatures C_LIO_LIMapping of the repeats onto protein isoform 3D models predicted by AlphaFold C_LIO_LI5 000 repeats detected over the human coding fraction, about one third disordered C_LIO_LIAssessment of the structural coverage of their interactions with protein partners C_LI

bioinformatics↗

bioRxiv2023

decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods

BackgroundThe analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. ResultsWe analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker. ConclusionsdecOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies.

bioinformatics↗

bioRxiv2020

Assessing Conservation of Alternative Splicing with Evolutionary Splicing Graphs

Understanding how protein function has evolved and diversified is of great importance for human genetics and medicine. Here, we tackle the problem of describing the whole transcript variability observed in several species by generalising the definition of splicing graph. We provide a practical solution to building parsimonious evolutionary splicing graphs where each node is a minimal transcript building block defined across species. We show a clear link between the functional relevance, tissue-regulation and conservation of AS events on a set of 50 genes. By scaling up to the whole human protein-coding genome, we identify a few thousands of genes where alternative splicing modulates the number and composition of pseudo-repeats. We have implemented our approach in ThorAxe, an efficient, versatile, and robust computational tool freely available at https://github.com/PhyloSofS-Team/thoraxe. The results are accessible and can be browsed interactively at http://www.lcqb.upmc.fr/ThorAxe.

bioinformatics↗

bioRxiv2017

PureCLIP: Capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data

iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP, a hidden Markov model based approach, which simultaneously performs peak calling and individual crosslink site detection. It explicitly incorporates RNA abundances and, for the first time, non-specific sequence biases. On both simulated and real data, PureCLIP is more accurate in calling crosslink sites than other state-of-the-art methods and has a higher agreement across replicates. Link: https://github.com/skrakau/PureCLIP.

bioinformatics↗

bioRxiv2017

Transcripts evolutionary conservation and structural dynamics give insights into the role of alternative splicing for the JNK family.

Alternative splicing and alternative initiation/termination transcription sites, have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms. We reconstruct phylogenetic forests relating 60 transcripts from the c-Jun N-terminal kinase (JNK) family observed in 7 species. We identify two alternative splicing events of ancient origin and show that they induce subtle changes on the proteins structural dynamics. We highlight a previously uncharacterized transcript whose predicted structure seems stable in solution. We further demonstrate that orphan transcripts, for which no phylogeny could be reconstructed, display peculiar sequence and structural properties. Our approach is implemented in PhyloSofS (Phylogenies of Splicing Isoforms Structures), a fully automated computational tool freely available at https://github.com/PhyloSofS-Team/PhyloSofS.

bioinformatics↗