A5060798410- RNA modifications and cancer
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Genetic and Kidney Cyst Diseases
- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetics and Neurodevelopmental Disorders
- Bioinformatics and Genomic Networks
- Autophagy in Disease and Therapy
- Lung Cancer Treatments and Mutations
- MicroRNA in disease regulation
- Machine Learning in Bioinformatics
- interferon and immune responses
- Birth, Development, and Health
- Sex and Gender in Healthcare
- Viral Infections and Immunology Research
Institute for Molecular Medicine Finland
2023-2024
University of Helsinki
2023-2024
Centre National de la Recherche Scientifique
2016-2023
Centre de Recherche en Neurosciences de Lyon
2018-2023
Inserm
2016-2023
Laboratoire de Biométrie et Biologie Evolutive
2018-2023
Université Claude Bernard Lyon 1
2016-2023
École Normale Supérieure de Lyon
2016-2022
Institut national de recherche en informatique et en automatique
2018-2021
Centre Inria de l'Université Grenoble Alpes
2018-2020
Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named “Exon Ontology,” based on terms corresponding well-characterized protein features organized an ontology tree. Exon Ontology conceptually similar Gene...
The Repressor Element 1-silencing transcription factor (REST) represses a number of neuronal genes in non-neuronal cells or undifferentiated neural progenitors. Here, we report that the DEAD box RNA helicase DDX17 controls important REST-related processes are critical during early phases differentiation. First, associates with REST, promotes its binding to promoter subset REST-targeted and co-regulates REST transcriptional repression activity. During differentiation, observed downregulation...
Abstract Genome-wide analyses estimate that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most start by mapping the reads an annotated reference genome, but some a de novo assembly reads. In this paper, we present systematic comparison mapping-first approach (F RL ine ) and assembly-first (K is S plice ). We applied these independent datasets found...
Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations RNU4ATAC , transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi–Linder (TALS/MOPD1), Roifman (RFMN), Lowry–Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on few RFMN patient cells, none performed...
Abstract Besides analyses of specific alternative splicing (AS) variants, little is known about AS regulatory pathways and programs involved in anticancer drug resistance. Doxorubicin widely used breast cancer chemotherapy. Here, we identified 1723 events 41 factors regulated a cell model acquired resistance to doxorubicin. An RNAi screen on the studied ZRANB2 SYF2, whose depletion partially reversed doxorubicin By RNA-seq resistant cells, found that controlled by SYF2 were enriched...
In the human genome, about 750 genes contain one intron excised by minor spliceosome. This spliceosome comprises its own set of snRNAs, among which U4atac. Its noncoding gene, RNU4ATAC, has been found mutated in Taybi-Linder (TALS/microcephalic osteodysplastic primordial dwarfism type 1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes. These rare developmental disorders, whose physiopathological mechanisms remain unsolved, associate ante- post-natal growth retardation, microcephaly, skeletal...
Abstract Background Variation in X chromosome inactivation (XCI) human-induced pluripotent stem cells (hiPSCs) can impact their ability to model biological sex biases. The gene-wise landscape of gene dosage remains unresolved female hiPSCs. To characterize patterns de-repression and escape from inactivation, we performed a systematic survey allele specific expression 165 hiPSC lines. Results XCI erosion is non-random primarily affects genes that human tissues. Individual cell lines vary the...
Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed allow an accurate quantification of splicing. Here, we show that IAV infection human lung cells induces widespread alterations splicing, overall increase exon inclusion and decrease intron retention. Over half the mRNAs differential splicing undergo no significant abundance or their 3' end...
Biallelic variants in RNU4ATAC, a non-coding gene transcribed into the minor spliceosome component U4atac snRNA, are responsible for three rare recessive developmental diseases, namely Taybi-Linder/MOPD1, Roifman and Lowry-Wood syndromes. Next-generation sequencing of clinically heterogeneous cohorts (children with either suspected genetic disorder or congenital microcephaly) recently identified mutations this gene, illustrating how profoundly these technologies modifying testing assessment....
Despite the initial efficacy of using tyrosine kinase inhibitors epidermal growth factor receptors (EGFR-TKIs) for treating patients with non-small cell lung cancer (NSCLC), resistance inevitably develops. Recent studies highlight a link between alternative splicing and drug response. Therefore, we aimed to identify deregulated events that play role in EGFR-TKI. By RNA sequencing, reverse-transcription PCR (RT-PCR), interference, showed overexpression splice variant autophagic gene ATG16-L1...
Abstract Epigenetic variation in the X chromosome inactivation (XCI) of human induced pluripotent stem cells (hiPSCs) can impact their ability to accurately model biological sex biases. However, gene-wise landscape escape from XCI remains unresolved female hiPSCs. To characterize patterns inactivation, we performed a systematic survey allele specific expression (ASE) 165 hiPSC lines. The analysis revealed that was non-random and affected primarily genes also tissues. individual cell lines...
Abstract To elaborate on the origins of established male-female differences in several brain-related phenotypes, we assessed patterns transcriptomic sex biases developing and adult human forebrain. We find an abundance expression (sex-DE) prenatal brain, driven by both hormonal sex-chromosomal factors, considerable consistency effects between with little sex-DE exclusive to Sex-DE was not enriched genes associated brain disorder, consistent systematic characteristics these (e.g. constraint)....
Abstract Genome-wide analyses reveal that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most start by mapping the reads an annotated reference genome, but some a de novo assembly reads. In this paper, we present systematic comparison mapping-first approach (F RL ine ) and assembly-first (K is S plice ). These approaches event-based, as they focus on...
Abstract In the human genome, about 750 genes contain one intron excised by minor spliceosome. This spliceosome comprises its own set of snRNAs, among which U4atac. Its non-coding gene, RNU4ATAC , has been found mutated in Taybi-Linder (MOPD1/TALS), Roifman (RFMN) and Lowry-Wood syndromes (LWS). These rare developmental disorders, whose physiopathological mechanisms remain unsolved, associate ante- post-natal growth retardation, microcephaly, skeletal dysplasia, intellectual disability,...