Biology subjects

Derrien, T.

Publications and source records attributed to Derrien, T..

8 recordsLinked to original sources

bioRxiv2025

Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework

AO_SCPLOWBSTRACTC_SCPLOWCircular RNAs (circRNAs) are unique non-coding RNAs with covalently closed loop structures formed through backsplicing events. Their stability, tissue-specific expression patterns, and potential as disease biomarkers have garnered increasing attention. However, their circular structure and diverse size range pose challenges for conventional sequencing technologies. Long-read Oxford Nanopore (ONT) sequencing offers promising capabilities for capturing entire circRNA molecules without fragmentation, yet the effectiveness of bioinformatic tools for analyzing this data remains understudied. This study presents the first comprehensive benchmark comparison of three specialized tools for circRNA detection from ONT long-read data: CIRI-long (Zhang et al., 2021), IsoCIRC (Xin et al., 2021), and circNICK-Irs (Rahimi et al., 2021). To address the lack of standardized evaluation frameworks, we developed a novel computational pipeline, open-source and freely available, to generate realistic simulated circRNA ONT long-read datasets. Our pipeline integrates several molecular features of circRNAs extracted from established databases and real datasets into NanoSim tool (Hafezqorani et al., 2020) and outputs FASTQ reads reflecting therefore biological diversity and technical properties. We systematically assessed tool performance across key metrics, including precision, recall, specificity, accuracy, and F1 score. Our analysis revealed distinct performance profiles: while all tools exhibited high specificity, they varied in precision and their ability to detect different circRNA subtypes, often showing limited sensitivity and precision. Notably, the overlap in detected circRNAs among tools was relatively low. Additionally, computational efficiency varied significantly across the tools. This suggests that relying on a single tool might not be ideal, and combining tools or improving algorithms could be necessary for more accurate circRNA detection from ONT data. This benchmark provides valuable insights for researchers selecting appropriate tools for circRNA studies using ONT sequencing. Furthermore, our customizable simulation framework, offering a resource to optimize detection approaches and advance bioinformatic tool development for circRNA research is freely available at: https://gitlab.com/bioinfog/circall/nano-circ.

bioinformatics↗

bioRxiv2025

Facilitating genome annotation using ANNEXA and long-read RNA sequencing

With the advent of complete genome assemblies, genome annotation has become essential for the functional interpretation of genomic data. Long-read RNA sequencing (LR-RNAseq) technologies have significantly improved transcriptome annotation by enabling full-length transcript reconstruction for both coding and non-coding RNAs. However, challenges such as transcript fragmentation and incomplete isoform representation persist, highlighting the need for robust quality control (QC) strategies. This study presents ANNEXA, a pipeline designed to enhance genome annotation using LR-RNAseq data while also providing QC for reconstructed genes and transcripts. ANNEXA integrates two transcriptome reconstruction tools, StringTie2 and Bambu, applying stringent filtering criteria to improve annotation accuracy. It also incorporates deep learning models to evaluate transcription start sites (TSSs) and employs the tool FEELnc for the systematic annotation of long non-coding RNAs (lncRNAs). Additionally, the pipeline offers intuitive visualisations for comparative analyses of coding and non-coding repertoires. Benchmarking against multiple reference annotations revealed distinct patterns of sensitivity and precision for both known and novel genes and transcripts and mRNAs and lncRNAs. To demonstrate its utility, ANNEXA was applied in a comparative oncology study involving LR-RNAseq of two human and eight canine cancer cell lines. The pipeline successfully identified novel genes and transcripts across species, expanding the catalog of protein-coding and lncRNA annotations in both species. Implemented in Nextflow for scalability and reproducibility, ANNEXA is available as an open-source tool: https://github.com/IGDRion/ANNEXA.

bioinformatics↗

bioRxiv2021

Canine oral melanoma genomic and transcriptomic study defines two molecular subgroups with different therapeutical targets

Mucosal melanoma (MM) is a rare and aggressive clinical cancer that occurs mostly in the head, neck, and anogenital regions. Despite recent advances in genetics and the development of revolutionary treatments, such as immunotherapy, the prognosis for MM remains poor. Canine MM shares several clinical, histological, and genetic features with its human counterpart, offering a relevant spontaneous and immunocompetent model to decipher the genetic bases and explore treatment options for human MM. We performed an integrative genomic and transcriptomic analysis of 32 canine MM samples, which allowed us to identify two molecular subgroups differing in microenvironment and structural variant (SV) content. The overexpression of genes related to the microenvironment and T-cell response was associated with tumors harboring a lower content of structural variants, whereas the overexpression of pigmentation-related pathways and oncogenes such as TERT were associated with a high SV burden. To detail the SVs, especially those with focal amplifications, whole-genome sequencing was performed on four canine MM cell lines. We showed that focal amplifications characterized complex chromosomal rearrangements targeting oncogenes such as MDM2 or CDK4 and a recurrently amplified region on canine chromosome 30, comprising the genes TRPM7, GABPB1, USP8, and SPPL2A, were candidate oncogenes for MM. We showed that the copy numbers of these genes were significantly correlated with their expression levels. Finally, we demonstrated that the genes TRPM7, GABPB1, and SPPL2A play a role in cell proliferation; thus, these may be considered new candidate oncogenes for human MM. Our findings suggest the existence of two MM molecular subgroups that may benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies. These results illustrate the relevance of dog models for deciphering genetic mechanisms in spontaneous MM, along with the potential to screen for efficient targeted therapies for rare and aggressive cancers in humans.

cancer biology↗

bioRxiv2020

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long non-coding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3 end of LINE-1_Cfs (i.e., LINE-1_Cf 3-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation. SignificanceAdvancements in long-read DNA sequencing technologies provide more comprehensive views of genomes. We used long-read sequences to assemble a Great Dane dog genome that provides several improvements over the existing reference derived from a Boxer dog. Assembly comparisons revealed that gaps in the Boxer assembly often occur at the beginning of protein-coding genes and have a high-GC content, which likely reflects limitations of previous technologies in resolving GC-rich sequences. Dimorphic LINE-1 and SINEC retrotransposon sequences represent the predominant differences between the Great Dane and Boxer assemblies. Proof-of-principle experiments demonstrated that expression of a canine LINE-1 could promote the retrotransposition of itself and a SINEC_Cf consensus sequence in cultured human cells. Thus, ongoing retrotransposon activity may contribute to canine genetic diversity.

genomics↗

bioRxiv2020

The tree that hides the forest: identification of common predisposing loci in several hematopoietic cancers and several dog breeds.

Histiocytic sarcoma (HS) is a rare but aggressive cancer in humans and dogs. The spontaneous canine model, with the clinical, epidemiological and histological similarities with human HS and specific breed predispositions, is a unique model/opportunity to unravel the genetic bases of this cancer. In this study, we aimed to identify germline risk factors associated with the development of HS in canine predisposed breeds. We used a methodology that combined several genome-wide association studies in a multi-breed and multi-cancer approach, as well as targeted next generation sequencing, and imputation combining several breeds (Bernese mountain dog, Rottweiler, flat coated retriever and golden retriever) and three haematopoietic cancers (HS, lymphoma and mast cell tumor). Results showed that we not only refined the previously identified HS risk CDKN2A locus but we identified new loci on canine chromosomes 2, 5, 12, 14, 20, 26 and X. Capture and targeted sequencing of specific loci pointed towards the existence of regulatory variants in non coding regions and/or methylation mechanisms linked to risk haplotypes, leading to strong cancer predispositions in specific dog breeds. Our results showed that these canine cancer predisposing loci appear to be due to the additive effect of several risk haplotype involved also in other haematopoietic cancers such lymphoma or mast cell tumor, illustrating the pleiotropic nature of these canine cancer loci as observed in human oncology, thus reinforcing the interest of predisposed dog breeds to study cancer initiation and progression.

genetics↗

bioRxiv2019

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Our vision of DNA transcription and splicing has changed dramatically with the introduction of short-read sequencing. These high-throughput sequencing technologies promised to unravel the complexity of any transcriptome. Generally gene expression levels are well-captured using these technologies, but there are still remaining caveats due to the limited read length and the fact that RNA molecules had to be reverse transcribed before sequencing. Oxford Nanopore Technologies has recently launched a portable sequencer which offers the possibility of sequencing long reads and most importantly RNA molecules. Here we generated a full mouse transcriptome from brain and liver using the Oxford Nanopore device. As a comparison, we sequenced RNA (RNA-Seq) and cDNA (cDNA-Seq) molecules using both long and short reads technologies and tested the TeloPrime preparation kit, dedicated to the enrichment of full-length transcripts. Using spike-in data, we confirmed that expression levels are efficiently captured by cDNA-Seq using short reads. More importantly, Oxford Nanopore RNA-Seq tends to be more efficient, while cDNA-Seq appears to be more biased. We further show that the cDNA library preparation of the Nanopore protocol induces read truncation for transcripts containing internal runs of Ts. This bias is marked for runs of at least 15 Ts, but is already detectable for runs of at least 9 Ts and therefore concerns more than 20% of expressed transcripts in mouse brain and liver. Finally, we outline that bioinformatics challenges remain ahead for quantifying at the transcript level, especially when reads are not full-length. Accurate quantification of repeat-associated genes such as processed pseudogenes also remains difficult, and we show that current mapping protocols which map reads to the genome largely over-estimate their expression, at the expense of their parent gene. The entire dataset is available from http://www.genoscope.cns.fr/externe/ONT_mouse_RNA.

bioinformatics↗

bioRxiv2018

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig.

BackgroundFunctional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project (http://www.fragencode.org) aimed to profile the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells).\n\nResultsRNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically Associating Domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species.\n\nConclusionsWe report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.

genomics↗

bioRxiv2018

Characterisation and functional predictions of canine long non-coding RNAs

Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and humans through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.

genomics↗