A5035856613- RNA Research and Splicing
- RNA modifications and cancer
- MicroRNA in disease regulation
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Genomics and Phylogenetic Studies
- Advanced biosensing and bioanalysis techniques
- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- Reproductive Biology and Fertility
- Chromosomal and Genetic Variations
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- RNA Interference and Gene Delivery
- Genetics, Aging, and Longevity in Model Organisms
- Epigenetics and DNA Methylation
- Circular RNAs in diseases
- Plant Disease Resistance and Genetics
- Sperm and Testicular Function
- Reproductive biology and impacts on aquatic species
- Pluripotent Stem Cells Research
- Immune cells in cancer
- Fish biology, ecology, and behavior
- Developmental Biology and Gene Regulation
- Immune Cell Function and Interaction
- Immune Response and Inflammation
Yale University
2016-2025
SIB Swiss Institute of Bioinformatics
2008-2014
University of Geneva
2008-2014
Imperial College London
2008-2012
In liver, most metabolic pathways are under circadian control, and hundreds of protein-encoding genes thus transcribed in a cyclic fashion. Here we show that rhythmic transcription extends to the locus specifying miR-122, highly abundant, hepatocyte-specific microRNA. Genetic loss-of-function gain-of-function experiments have identified orphan nuclear receptor REV-ERBalpha as major regulator mir-122 transcription. Although due its long half-life mature miR-122 accumulates at nearly constant...
MicroRNAs, or miRNAs, post-transcriptionally repress the expression of protein-coding genes. The human genome encodes over 1000 miRNA genes that collectively target majority messenger RNAs (mRNAs). Base pairing so-called ‘seed’ region with mRNAs identifies many thousands putative targets. Evaluating strength resulting mRNA repression remains challenging, but is essential for a biologically informative ranking potential To address these challenges, predictors may use thermodynamic,...
Cpf1 is a novel class of CRISPR-Cas DNA endonucleases, with wide range activity across different eukaryotic systems. Yet, the underlying determinants this variability are poorly understood. Here, we demonstrate that LbCpf1, but not AsCpf1, ribonucleoprotein complexes allow efficient mutagenesis in zebrafish and Xenopus. We show temperature modulates by controlling its ability to access genomic DNA. This effect stronger on explaining lower efficiency ectothermic organisms. capitalize property...
We report the whole-genome sequence of common marmoset (Callithrix jacchus). The 2.26-Gb genome a female was assembled using Sanger read data (6×) and shotgun strategy. A first analysis has permitted comparison with genomes apes Old World monkeys identification specific features that might contribute to unique biology this diminutive primate, including genetic changes may influence body size, frequent twinning chimerism. observed positive selection in growth hormone/insulin-like factor genes...
Nanoscale chromatin organization regulates gene expression. Although is notably reprogrammed during zygotic genome activation (ZGA), the of regulatory factors this universal process remains unclear. In work, we developed expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription in vivo. ChromExM embryos ZGA revealed how pioneer factor Nanog interacts with nucleosomes RNA polymerase II (Pol II), providing direct visualization transcriptional elongation as...
MicroRNAs (miRNAs) posttranscriptionally repress the expression of protein-coding genes. Based on partial complementarity between miRNA and messenger RNA pairs with a mandatory so-called ‘seed’ sequence, many thousands potential targets can be identified. Our open-source software library, miRmap, ranks these biologically meaningful criterion, repression strength. MiRmap combines thermodynamic, evolutionary, probabilistic sequence-based features, which cover features from TargetScan, PITA,...
The awakening of the genome after fertilization is a cornerstone animal development. However, mechanisms that activate silent are poorly understood. Here, we show transcriptional competency regulated by Brd4- and P300-dependent histone acetylation in zebrafish. Live imaging transcription revealed activation, beginning at miR-430 locus, gradual stochastic. We activation does not require slowdown cell cycle through translation maternally inherited mRNAs. Among these, enhancer regulators P300...
This protocol describes how to generate and genotype mutants using an optimized CRISPR–Cas9 genome-editing system in zebrafish (CRISPRscan). Because single guide RNAs (sgRNAs) have variable efficiency when targeting specific loci, our starts by explaining use the web tool CRISPRscan design highly efficient sgRNAs. The algorithm is based on results of integrated analysis more than 1000 sgRNAs zebrafish, which uncovered predictive factors that influence Cas9 activity. Next, we describe easily...
Abstract The requirement for Cas nucleases to recognize a specific PAM is major restriction genome editing. SpCas9 variants SpG and SpRY, recognizing NGN NRN PAMs, respectively, have contributed increase the number of editable genomic sites in cell cultures plants. However, their use has not been demonstrated animals. Here we study nuclease activity SpRY by targeting 40 zebrafish C. elegans . Delivered as mRNA-gRNA or ribonucleoprotein (RNP) complexes, were able induce mutations vivo, albeit...
The subcellular localization of mRNAs plays a pivotal role in biological processes, including cell migration. For instance, β-actin mRNA and its associated RNA-binding protein (RBP), ZBP1/IGF2BP1, are recruited to focal adhesions (FAs) support localized synthesis, crucial for However, whether other RBPs also localize at FAs remains unclear. Here, we identify hundreds that enriched (FA-mRNAs). FA-mRNAs share characteristics with stress granule (SG) found ribonucleoprotein (RNP) complexes the...
Sertoli cells (SCs) are the central, essential coordinators of spermatogenesis, without which germ cell development cannot occur. We previously showed that Dicer, an RNaseIII endonuclease required for microRNA (miRNA) biogenesis, is absolutely to mature, survive, and ultimately sustain development. Here, using isotope-coded protein labeling, a technique relative quantification by mass spectrometry, we investigated impact cell-Dicer subsequent miRNA loss on testicular proteome. found that,...
Abstract Arginine, a semiessential amino acid implicated in diverse cellular processes, is substrate for two arginases—Arg1 and Arg2—having different expression patterns functions. Although appropriately regulated Arg1 critical immune responses, this has not been documented Arg2. We show that Arg2 the dominant enzyme dendritic cells (DCs) repressed by microRNA-155 (miR155) during their maturation. miR155 known to be strongly induced various mouse human DC subsets response maturation signals,...
Posttranscriptional regulation plays a crucial role in shaping gene expression. During the maternal-to-zygotic transition (MZT), thousands of maternal transcripts are regulated. However, how different
MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation metazoan genes. The mature ∼22-nt long RNA molecules processed from genome-encoded stem-loop structured precursor Hundreds such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers estimated. miROrtho database (http://cegg.unige.ch/mirortho) presents results a comprehensive...
MicroRNAs (miRNAs) are regulatory noncoding RNAs that affect the production of a significant fraction human mRNAs via post-transcriptional regulation. Interindividual variation miRNA expression levels is likely to influence target genes and may therefore contribute phenotypic differences in humans, including susceptibility common disorders. The extent which genetically controlled largely unknown. In this report, we assayed miRNAs primary fibroblasts from 180 European newborns GenCord project...
Abstract Rotating cilia at the vertebrate left-right organizer (LRO) generate an asymmetric leftward flow, which is sensed by cells left LRO margin. Ciliary activity of calcium channel Pkd2 crucial for flow sensing. How this signal further processed and relayed to laterality-determining Nodal cascade in lateral plate mesoderm (LPM) largely unknown. We previously showed that down-regulates mRNA expression inhibitor Dand5 sensory cells. De-repression co-expressed Nodal, complexed with TGFß...