Julien Jarroux
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View article: A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain
A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain Open
View article: A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types
A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types Open
View article: NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas
NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas Open
View article: Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state
Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state Open
Measuring splicing and chromatin accessibility simultaneously in frozen tissues remains challenging. Here we combined single-cell isoform RNA sequencing and assay for transposase accessible chromatin (ScISOr–ATAC) to interrogate the correl…
View article: Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types
Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types Open
Spatial long-read technologies are becoming increasingly common but lack nanometer- and therefore often single-cell resolution. This leaves the question unanswered of whether spatially variable isoforms represent spatial variability within…
View article: A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types
A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types Open
Genome-wide single-cell and spatial long-read approaches have gained traction, but mostly lack single-cell resolution - and yield limited read lengths. Here, we introduce spatial ISOform sequencing (Spl-ISO-Seq), which reveals exons and po…
View article: NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas
NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas Open
SUMMARY To overcome the paucity of known tumor-specific surface antigens in pediatric high-grade glioma (pHGG), we contrasted splicing patterns in pHGGs and normal brain samples. Among alternative splicing events affecting extracellular pr…
View article: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics Open
RNA isoform diversity, produced via alternative splicing, and alternative usage of transcription start and poly(A) sites, results in varied transcripts being derived from the same gene. Distinct isoforms can play important biological roles…
View article: ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer’s Disease
ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer’s Disease Open
Multimodal measurements have become widespread in genomics, however measuring open chromatin accessibility and splicing simultaneously in frozen brain tissues remains unconquered. Hence, we devised Single-Cell-ISOform-RNA sequencing couple…
View article: Accumulation of lncRNAs in cytoplasm upon DIS3 depletion leads to production of cryptic peptides detected in Multiple Myeloma.
Accumulation of lncRNAs in cytoplasm upon DIS3 depletion leads to production of cryptic peptides detected in Multiple Myeloma. Open
View article: DIS3 ribonuclease prevents the cytoplasmic accumulation of lncRNAs carrying non-canonical ORFs.
DIS3 ribonuclease prevents the cytoplasmic accumulation of lncRNAs carrying non-canonical ORFs. Open
Some of the long noncoding (lnc)RNAs harbor potential to produce functional micro peptides. Despite their increasing significance, the regulatory dynamics of cytoplasmic lncRNA expression, decay, and translation remain poorly understood. H…
View article: From words to complete phrases: insight into single-cell isoforms using short and long reads
From words to complete phrases: insight into single-cell isoforms using short and long reads Open
The profiling of gene expression patterns to glean biological insights from single cells has become commonplace over the last few years. However, this approach overlooks the transcript contents that can differ between individual cells and …
View article: DIS3 ribonuclease prevents the cytoplasmic accumulation of lncRNAs carrying non-canonical ORFs, which represent a source of cancer immunopeptides.
DIS3 ribonuclease prevents the cytoplasmic accumulation of lncRNAs carrying non-canonical ORFs, which represent a source of cancer immunopeptides. Open
Around 12% of multiple myeloma (MM) cases harbour mutations in DIS3 , which encodes an RNA decay enzyme that controls the turnover of some long noncoding RNAs (lncRNAs). Although lncRNAs, by definition, do not encode proteins, some can be …
View article: Mouse SIRV and simulated data used in the IsoQuant publication
Mouse SIRV and simulated data used in the IsoQuant publication Open
This dataset contain main simulated and SIRV sequencing data used in the IsoQuant publication. - Reduced mouse GENCODE vM26 annotation: 15% of expressed isoforms removed, expression profile based on real mouse brain sequencing data; also c…
View article: Mouse SIRV and simulated data used in the IsoQuant publication
Mouse SIRV and simulated data used in the IsoQuant publication Open
This dataset contain main simulated and SIRV sequencing data used in the IsoQuant publication. - Reduced mouse GENCODE vM26 annotation: 15% of expressed isoforms removed, expression profile based on real mouse brain sequencing data; also c…
View article: Accurate isoform discovery with IsoQuant using long reads
Accurate isoform discovery with IsoQuant using long reads Open
View article: Comparing 10x Genomics single-cell 3’ and 5’ assay in short-and long-read sequencing
Comparing 10x Genomics single-cell 3’ and 5’ assay in short-and long-read sequencing Open
Barcoding strategies are fundamental to droplet-based single-cell sequencing, and understanding the biases and caveats between approaches is essential. Here, we comprehensively evaluated both short and long reads of the cDNA obtained throu…
View article: Mouse SIRV and simulated data used in the IsoQuant publication
Mouse SIRV and simulated data used in the IsoQuant publication Open
This dataset contain main simulated and SIRV sequencing data used in the IsoQuant publication. NOTE: SIRVs BAM file contains ONT R9.4 data, R10.4 data that was used in the publication is available in the newer version. - R…
View article: IsoQuant: a tool for accurate novel isoform discovery with long reads
IsoQuant: a tool for accurate novel isoform discovery with long reads Open
Long reads are reshaping RNA biology. However, determining alternative isoforms from long-read RNA data is a complex and incompletely solved problem even when the reference genome is known. Here we present IsoQuant - a reference-based tool…
View article: Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue Open
View article: Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types
Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types Open
Single-nuclei RNA-Seq is being widely employed to investigate cell types, especially of human brain and other frozen samples. In contrast to single-cell approaches, however, the majority of single-nuclei RNA counts originate from partially…
View article: HOTAIR lncRNA promotes epithelial–mesenchymal transition by redistributing LSD1 at regulatory chromatin regions
HOTAIR lncRNA promotes epithelial–mesenchymal transition by redistributing LSD1 at regulatory chromatin regions Open
View article: Caractérisation fonctionnelle des longs ARN non codants associés à la transition épithélio-mésenchymateuse
Caractérisation fonctionnelle des longs ARN non codants associés à la transition épithélio-mésenchymateuse Open
In the last decade, new high-throughput sequencing techniques have revealed the complexity of the human transcriptome, allowing the characterization of long non-coding (lnc)RNAs. These transcripts have been reported as very specific to tis…
View article: HOTAIR promotes an epithelial-to-mesenchymal transition through relocation of the histone demethylase Lsd1
HOTAIR promotes an epithelial-to-mesenchymal transition through relocation of the histone demethylase Lsd1 Open
Summary Epithelial-to-mesenchymal transition (EMT) drives a loss of epithelial traits by neoplastic cells enabling metastasis and recurrence in cancer. HOTAIR emerged as one of the most renowned long noncoding RNAs promoting EMT mostly as …