A5016966335- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- RNA regulation and disease
- Marine Ecology and Invasive Species
- Mosquito-borne diseases and control
- Circular RNAs in diseases
- Invertebrate Immune Response Mechanisms
- Molecular Biology Techniques and Applications
- Insect symbiosis and bacterial influences
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Heat shock proteins research
- RNA Interference and Gene Delivery
- Cancer Genomics and Diagnostics
- Skin Protection and Aging
- Planarian Biology and Electrostimulation
- Spaceflight effects on biology
- Advanced biosensing and bioanalysis techniques
- Protist diversity and phylogeny
- Chromatin Remodeling and Cancer
- FOXO transcription factor regulation
Stockholm University
2016-2025
Science for Life Laboratory
2016-2025
Centre for Genomic Regulation
2013-2019
Universitat Pompeu Fabra
2013-2019
Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública
2013-2019
Hospital Del Mar
2013-2015
Hospital del Mar Research Institute
2015
Municipal Institute for Medical Research
2015
Instituto de Salud Carlos III
2015
Max Delbrück Center
2008-2013
microRNAs (miRNAs) are a large class of small non-coding RNAs which post-transcriptionally regulate the expression fraction all animal genes and important in wide range biological processes. Recent advances high-throughput sequencing allow miRNA detection at unprecedented sensitivity, but computational task accurately identifying miRNAs background sequenced remains challenging. For this purpose, we have designed miRDeep2, substantially improved algorithm identifies canonical non-canonical...
Abstract Background MicroRNAs (miRNAs) are established regulators of development, cell identity and disease. Although nearly two thousand human miRNA genes known new ones continuously discovered, no attempt has been made to gauge the total content genome. Results Employing an innovative computational method on massively pooled small RNA sequencing data, we report 2,469 novel candidates which 1,098 validated by in-house published experiments. Almost 300 robustly expressed in a neuronal system...
Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences conserved across the kingdom. In addition, unique mechanistically well understood features can clearly distinguish bona fide miRNAs from myriad other small generated by cells. However, making this distinction is not a common practice and, thus, surprisingly, heterogeneous quality of available miRNA...
Abstract We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for annotation nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers flatworms. 2.1 now consists 75 spanning over ∼800 million years animal evolution, contains a total number 16 670 microRNAs from 1549 families. Over 6000 were added in this using ∼550...
Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration tissue homeostasis have been shown to depend on PIWI, a molecule required for Piwi-interacting RNA (piRNA) expression in planarians. Nevertheless, the full complement piRNAs microRNAs (miRNAs) this organism has yet be defined. Here we report large-scale cloning sequencing small RNAs from Schmidtea...
Abstract The exosome is a ribonucleolytic complex that plays important roles in RNA metabolism. Here we show the necessary for repair of DNA double-strand breaks (DSBs) human cells and clearance an essential step homologous recombination. Transcription DSB-flanking sequences results production damage-induced long non-coding RNAs (dilncRNAs) engage DNA-RNA hybrid formation. Depletion EXOSC10, catalytic subunit, leads to increased dilncRNA levels. Moreover, targeting ssDNA-binding protein RPA...
Hsf1 is an ancient transcription factor that responds to protein folding stress by inducing the heat-shock response (HSR) restore perturbed proteostasis. Hsp70 chaperones negatively regulate activity of via stress-responsive mechanisms are poorly understood. Here, we have reconstituted budding yeast Hsf1-Hsp70 activation complexes and find surplus inhibits DNA-binding activity. binds its canonical substrate binding domain regulates During heat shock, out-titrated misfolded proteins derived...
Abstract Combined measurements of mRNA and protein expression in single cells enable in-depth analysis cellular states. We present SPARC, an approach that combines single-cell RNA-sequencing with proximity extension essays to simultaneously measure global 89 intracellular proteins individual cells. show fails accurately reflect abundance at the time measurement, although direction changes is agreement during neuronal differentiation. Moreover, levels transcription factors better predict...
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...
miRNAs are small 22-nucleotide RNAs that can post-transcriptionally regulate gene expression. It has been proposed dietary plant enter the human bloodstream and host transcripts; however, these findings have widely disputed. We here conduct first comprehensive meta-study in field, surveying presence abundances of cross-species (xenomiRs) 824 sequencing data sets from various tissues body fluids. find xenomiRs commonly present (17%) fluids (69%); low, comprising 0.001% miRNA counts. Further,...
Recent studies suggest that transcription takes place at DNA double-strand breaks (DSBs), transcripts DSBs are processed by Drosha and Dicer into damage-induced small RNAs (diRNAs), diRNAs required for repair. However, have been mostly detected in reporter constructs or repetitive sequences, their existence endogenous loci has questioned recent reports. Using the homing endonuclease I-PpoI, we investigated diRNA production genetically unperturbed human mouse cells. I-PpoI is an ideal tool to...
We have identified and validated a spaceflight-associated microRNA (miRNA) signature that is shared by rodents humans in response to simulated, short-duration long-duration spaceflight. Previous studies miRNAs regulate rodent responses spaceflight low-Earth orbit, we confirmed the expression of these proposed reacting simulated conditions. Moreover, astronaut samples from NASA Twins Study signatures miRNA sequencing, single-cell RNA sequencing (scRNA-seq), assay for transposase accessible...
Over the last few years, number of microRNAs in human genome has become a controversially debated issue. Several publications reported thousands putative novel not included curated microRNA gene database MirGeneDB and repository miRBase. Recently, by using sequencing ∼300 tissues cell lines, RNA atlas, an expanded inventory annotations, was published, reporting microRNAs. We, developers established prediction tools hosts MirGeneDB, raise concerns about frequently applied functional...
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,...
While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified swine. Because of the close phylogenetic distance to humans, pigs serve as suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs key regulators and their aberrant expression leads malignancy. Here, we present identification hundreds apparently novel porcine intestine. MiRNAs were first by means deep sequencing followed miRNA precursor...
MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies different organisms, research on global profiling pre-miRNAs is limited. Here, using massive parallel sequencing, we performed characterization both mouse and precursor miRNAs. total, 87 369 704 252 003 sequencing reads 887 281 miRNAs were obtained, respectively....