A5000049746- MicroRNA in disease regulation
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Developmental Biology and Gene Regulation
- Mosquito-borne diseases and control
- Invertebrate Immune Response Mechanisms
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- Insect symbiosis and bacterial influences
- RNA modifications and cancer
- RNA regulation and disease
- Neurobiology and Insect Physiology Research
- Coral and Marine Ecosystems Studies
- Genetics, Aging, and Longevity in Model Organisms
- Marine Ecology and Invasive Species
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Single-cell and spatial transcriptomics
- Protist diversity and phylogeny
- RNA Interference and Gene Delivery
- Circular RNAs in diseases
- Hippo pathway signaling and YAP/TAZ
- Insect Resistance and Genetics
- Kruppel-like factors research
Science for Life Laboratory
2018-2024
Stockholm University
2018-2024
Max Planck Society
2014-2015
Institut de génétique et de biologie moléculaire et cellulaire
2003-2009
Institute of Gene Biology
1998-2007
Inserm
2003
Centre National de la Recherche Scientifique
2003
Russian Academy of Sciences
2001
We present here miRTrace, the first algorithm to trace microRNA sequencing data back their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately (> 99%) assigns real simulated 14 important animal plant groups, sensitively detects parasitic infection in mammals, discovers primate origin of single cells. Applying our over 700 public datasets, we...
Abstract MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants animals. They thought to have evolved convergently these lineages hypothesized played a role the evolution multicellularity. In line with this hypothesis, miRNAs so far only been described few unicellular eukaryotes. Here, we investigate presence Amoebozoa, focusing on species belonging Acanthamoeba, Physarum dictyostelid taxonomic groups, representing range multicellular lifestyles. that...
Abstract We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to new server and creation computational mirror, we have expanded database with addition 33 invertebrate species, including representatives 5 previously unsampled phyla, 6 mammal species. now contains entries for 21 822 genes (5160 these from species) belonging 1743 families. The inclusion species allowed us refine both evolutionary node appearance number genes/families,...
Malaria inflicts the highest rate of morbidity and mortality among vector-borne diseases. The dramatic bottleneck parasite numbers that occurs in gut obligatory mosquito vector provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzed Plasmodium falciparum development gut, from unfertilized female gametes through first 20 h after blood feeding, including zygote ookinete stages. This study revealed temporal gene expression ApiAP2 family...
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or regulation, which are only attainable at transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost historical skins extant canids, but no attempts been made so far on We extract,...
The siRNA and piRNA pathways have been shown in insects to be essential for regulation of gene expression defence against exogenous endogenous genetic elements (viruses transposable elements). vast majority small RNAs produced by the originate from repetitive or (TE). In D. melanogaster, TE-derived siRNAs piRNAs are involved genome surveillance maintenance integrity. medically relevant malaria mosquito Anopheles gambiae TEs constitute 12-16% size. Genetic variations induced TE activities...
Abstract MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions cells. Here we have overcome these limitations by fusing the effector protein Argonaute2 RNA editing domain ADAR2, allowing detection transcriptome-wide in single miRNAs guide fusion natural transcripts, causing them undergo A>I editing, which can be...
We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to new server and creation computational mirror, we have expanded database with addition 33 invertebrate species, including representatives 5 previously unsampled phyla, 6 mammal species. now contains entries for 21,822 genes (5,160 these from species) belonging 1743 families. The inclusion species allowed us refine both evolutionary node appearance number genes/families, as well...
The best characterized chromatin insulator in Drosophila is the Suppressor of Hairy wing binding region contained within gypsy retrotransposon. Although cellular functions have been suggested, no role has found yet for multitude endogenous sites. Here we show that two sites intergenic between yellow gene and Achaete-scute complex form a functional insulator. Genetic analysis shows at least proteins, Modifier MDG4, required activity this insulator, are involved transcriptional regulation...
Previous large-scale studies have uncovered many features that determine the processing of microRNA (miRNA) precursors; however, they been conducted in vitro. Here, we introduce MapToCleave, a method to simultaneously profile thousands distinct RNA structures living cells. We find miRNA precursors with stable lower basal stem are more efficiently processed and also higher expression vivo tissues from 20 animal species. systematically compare importance known novel sequence structural test...
Abstract Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role stem cells largely unexplored. We here perform nuclear knockdown of mouse embryonic cells, causing the de-regulation 320 genes aberrant splicing 90 transcripts, some which potentially affecting translated protein sequence. find evidence that directly interacts bodies aberrantly spliced it locates upstream down-regulated at their putative enhancer regions,...
Abstract Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation cell cycle. We apply a tailored experimental design that eliminates these confounders, report thousands intrinsically covarying pairs in mouse embryonic stem cells. These covariations form network with biological properties, outlining known novel interactions. provide first evidence...
The GATA factor Pannier activates proneural achaete/scute ( ac/sc ) expression during development of the sensory organs Drosophila through enhancer binding. Chip bridges with (Ac/Sc)–Daughterless heterodimers bound to promoter and facilitates enhancer–promoter communication required for development. We show here that this is regulated by Osa, which recruited Chip. Osa belongs Brahma chromatin remodeling complexes we negatively regulates . Consequently, also play an essential role repression...
miRNAs are short noncoding RNA molecules that regulate gene expression by inhibiting translation or inducing degradation of target mRNAs. often expressed as polycistronic transcripts, so-called miRNA clusters, containing several precursors. The largest mammalian cluster, the miR-379-410 is primarily during embryonic development and in adult brain; however, downstream regulation this cluster not well understood. Here, we investigated adenosine deamination to inosine (RNA editing) deaminase...
Abstract MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants animals. They thought to have evolved convergently these lineages hypothesized played a role the evolution multicellularity. In line with this hypothesis, miRNAs so far only been described few unicellular eukaryotes. Here, we investigate presence Amoebozoa, focusing on species belonging Acanthamoeba , Physarum dictyostelid taxonomic groups, representing range multicellular lifestyles. that...
Previously we described highly unstable mutations in the yellow locus, induced by chimeric element and consisting of sequences from a distally located 1A unique genomic region, flanked identical copies an internally deleted 1.2-kb P element. Here show that sequence, which is part can be transmitted to AS-C successive inversion reinversion generated yellow- AS-C-located elements. The contains regulatory region specifically blocks wing body enhancers simultaneously stimulates expression...
Abstract MicroRNAs are small RNA molecules that can repress the expression of protein coding genes post-transcriptionally. Previous studies have shown microRNAs also alternative functions including target noise buffering and co-expression, but these observations been limited to a few microRNAs. Here we systematically study microRNA in mouse embryonic stem cells, by genetically deleting Drosha - leading global loss We apply complementary single-cell RNA-seq methods variation targets...
Abstract Single-cell RNA sequencing studies into gene co-expression patterns could yield important new regulatory and functional insights, but have so far been limited by the confounding effects of cell differentiation cycle. We apply a tailored experimental design that eliminates these confounders, report >80,000 intrinsically covarying pairs in mouse embryonic stem cells. These covariances form network with biological properties, outlining known novel interactions. provide first...