Biology subjects

Bergeron, D.

Publications and source records attributed to Bergeron, D..

3 recordsLinked to original sources

bioRxiv2026

NANOCUTSIGHT: A NANOPORE-SEQUENCING APPROACH AND ANALYSIS PIPELINE TO ASSESS GENOME EDITING EFFICACY IN VARIOUS CELL POPULATIONS

Genome editing has revolutionized biomedical sciences and is now an essential tool to define molecular pathways through genetic interaction and loss-of-function studies. Through its diverse variations, it allows for the generation of specific knockout cell lines or organisms, as well as the creation of endogenously edited gene regions. While high-throughput methodologies exist to map CRISPR/Cas9 genetic modifications, the validation of guide efficiencies in cell populations is often performed through analysis of the targeted gene product by western blotting or by deconvolution of Sanger sequencing chromatograms using TIDE or ICE assays. Here, we highlight a rapid nanopore sequencing pipeline, which we have named NanoCutSight, to quantify the percentage of indels at a specific genomic locus and to identify the types of modifications generated. We also benchmarked the methodology on various guide RNAs and in both cultured cell and organoid models. We believe that NanoCutSight will simplify the analysis of complex sample editing and enable the rapid screening of edited samples.

bioinformatics↗

bioRxiv2025

Splicing Isoforms Associated to TGFb-Induced Myofibroblast Activation

Myofibroblast differentiation is a key process in developmental biology and involved in numerous physiopathology. The gene expression program orchestrating fibroblast to myofibroblast differentiation, as well as its recapitulation by TGF{beta} stimulation in vitro, is relatively well characterized. Intriguingly, it is known that the splicing isoform EDA+FN1 is a marker and driver of myofibroblast differentiation, but the alternative splicing landscape of myofibroblast is unknown. Here, we performed a high-throughput transcriptomic approach by RNA-Seq in a primary skin fibroblast line and uncover more than 250 splicing isoforms associated with TGF{beta}-induced myofibroblasts using two different bioinformatic pipelines. This splicing profile highlights a distinct layer of regulation when compared to the global gene expression profile of myofibroblasts. A 5 alternative splicing event (ASE) signature [ACTN1-19A/19B; COL5A1-64A/64B; COL6A3 exon 4; FLNA exon 30 and TPM1-6a/6b] was further validated by ddPCR and AS-PCR and retrieved in publicly available RNA-Seq datasets describing other TGF{beta}-stimulated lung and skin fibroblasts. Surprisingly, TGF{beta} does not induce an EDA+FN1 splicing shift, although it stimulates global fibronectin expression. Thus, we conclude that the 5 ASEs signature may be used as putative universal myofibroblast markers and be of functional significance to myofibroblast formation and biology.

genomics↗

bioRxiv2021

Dynamics and modulation of the human snoRNome

BackgroundSmall nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. ResultsWe used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver and brain). We identified 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. 59% of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, as opposed to only 16% of the correlated non-coding host gene/snoRNA pairs. ConclusionsOur results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.

genomics↗