A5027898382- Genetic diversity and population structure
- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Forensic and Genetic Research
- RNA regulation and disease
- Evolution and Genetic Dynamics
- Cancer-related molecular mechanisms research
- Archaeology and ancient environmental studies
- Epigenetics and DNA Methylation
- Immune Cell Function and Interaction
- Cytomegalovirus and herpesvirus research
- Animal Behavior and Reproduction
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Aquaculture disease management and microbiota
- Tuberculosis Research and Epidemiology
- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Yersinia bacterium, plague, ectoparasites research
- Mycobacterium research and diagnosis
- NF-κB Signaling Pathways
- Plant and animal studies
University of Bern
2020-2024
SIB Swiss Institute of Bioinformatics
2011-2024
École Polytechnique Fédérale de Lausanne
2010-2020
Protein Research Foundation
2007
Osaka University
2007
European Bioinformatics Institute
2006-2007
SummaryThe maintenance of H3K9 and DNA methylation at imprinting control regions (ICRs) during early embryogenesis is key to the regulation imprinted genes. Here, we reveal that ZFP57, its cofactor KAP1, associated effectors bind selectively H3K9me3-bearing, DNA-methylated allele ICRs in ES cells. KAP1 deletion induces a loss heterochromatin marks ICRs, whereas deleting ZFP57 or DNMTs leads ICR demethylation. Accordingly, find with hemimethylated DNA-binding NP95. Finally, identify...
In the southern region of United States, such as in Louisiana and Texas, there are autochthonous cases leprosy among native-born Americans with no history foreign exposure. same region, well Mexico, wild armadillos infected Mycobacterium leprae.
Mobile elements are important evolutionary forces that challenge genomic integrity. Long interspersed element-1 (L1, also known as LINE-1) is the only autonomous transposon still active in human genome. It displays an unusual pattern of evolution, with, at any given time, a single L1 lineage amplifying to thousands copies before getting replaced by new lineage, likely under pressure host restriction factors, which act notably silencing expression during early embryogenesis. Here, we...
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well processes timing their differentiation, remain largely unknown. Demogenomic modeling high-quality ancient genomes reveals that early farmers Anatolia emerged from a multiphase mixing Asian population with strongly bottlenecked western hunter-gatherer after last glacial maximum. Moreover, ancestors went through period extreme drift during westward range expansion, contributing highly...
Reverse transcription-derived sequences account for at least half of the human genome. Although these retroelements are formidable motors evolution, they can occasionally cause disease, and accordingly inactivated during early embryogenesis through epigenetic mechanisms. In mouse, endogenous retroviruses, important mediators this process tetrapod-specific KRAB-containing zinc finger proteins (KRAB-ZFPs) their cofactor TRIM28. The present study demonstrates that KRAB/TRIM28-mediated...
TRIM28 is critical for the silencing of endogenous retroviruses (ERVs) in embryonic stem (ES) cells. Here, we reveal that an essential impact this process protection cellular gene expression early embryos from perturbation by cis -acting activators contained within these retroelements. In TRIM28-depleted ES cells, repressive chromatin marks at ERVs are replaced histone modifications typical active enhancers, stimulating transcription nearby genes, notably those harboring bivalent promoters....
De novo DNA methylation is an essential aspect of the epigenetic reprogramming that takes place during early development, yet factors responsible for its instatement at particular genomic loci are poorly defined. Here, we demonstrate KRAB-ZFP-mediated recruitment KAP1 to in embryonic stem cells (ESCs) induces cytosine methylation. This process preceded by H3K9 trimethylation, and genome-wide analyses reveal it spreads over short distances from KAP1-binding sites so as involve nearby CpG...
TRIM28 is a corepressor that mediates transcriptional silencing by establishing local heterochromatin. Here, we show deletion of in neural progenitor cells (NPCs) results high-level expression two groups endogenous retroviruses (ERVs): IAP1 and MMERVK10C. We find NPCs use TRIM28-mediated histone modifications to dynamically regulate transcription ERVs, which contrast other somatic cell types using DNA methylation. also derepression ERVs influences dynamics through the activation nearby genes...
Human cytomegalovirus (HCMV) is a highly prevalent pathogen that induces life-long infections notably through the establishment of latency in hematopoietic stem cells (HSC). Bouts reactivation are normally controlled by immune system, but can be fatal immuno-compromised individuals such as organ transplant recipients. Here, we reveal HCMV human CD34+ HSC reflects recruitment on viral genome KAP1, master co-repressor, together with HP1 and SETDB1 histone methyltransferase, which results...
During hematopoiesis, lineage- and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. We explored role KRAB-containing zinc finger proteins (KRAB-ZFPs) their cofactor KAP1 this process. In mice, hematopoietic-restricted deletion Kap1 resulted severe hypoproliferative anemia. Kap1-deleted erythroblasts failed induce mitophagy-associated genes retained mitochondria. This was due persistent expression microRNAs...
Endogenous retroelements (EREs) account for about half of the mouse or human genome, and their potential as insertional mutagens transcriptional perturbators is suppressed by early embryonic epigenetic silencing. Here, we asked how ERE control maintained during generation induced pluripotent stem cells (iPSCs), this procedure involves profound remodeling. We found that all EREs tested were markedly up-regulated reprogramming either fibroblasts, CD34 + cells, primary hepatocytes. At iPSC...
Microbial communities in recirculating aquaculture systems (RAS) play a role system success, nutrient cycling, and water quality. Considering the increasing socio-economic of fish farming, e.g., regarding food security, an in-depth understanding microbial is also relevant from management perspective, especially growth, development, welfare farmed animal. However, current data on composition within RAS patchy, which partly attributable to diverging method choices that render comparative...
The liver is characterized by sexually dimorphic gene expression translating into sex-specific differences in lipid, drug, steroid hormone, and xenobiotic metabolism, with distinct responses of males females to environmental challenges. Here, we investigated the role Krüppel-associated box (KRAB)-associated protein 1 (KAP1) epigenetic regulator this process. Liver-specific KAP1 knockout (KO) led strikingly phenotypic disturbances, including male-predominant steatosis hepatic tumors...
Chromatin remodeling at specific genomic loci controls lymphoid differentiation. Here, we investigated the role played in this process by Kruppel-associated box (KRAB)-associated protein 1 (KAP1), universal cofactor of KRAB-zinc finger proteins (ZFPs), a tetrapod-restricted family transcriptional repressors. T-cell-specific Kap1-deleted mice displayed significant expansion immature thymocytes, imbalances CD4+/CD8+ cell ratios, and altered responses to TCR TGFβ stimulation when compared...
Antimicrobial resistance (AMR) in Enterobacterales, particularly extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec), poses a significant public health concern. Widespread antimicrobial use exerts selection pressure, driving the persistence and spread of resistant bacteria diverse environments. While ESBL-Ec is well-documented clinical agricultural settings, its presence reservoirs remains poorly understood. This study assessed prevalence, AMR profiles, genetic diversity...
Highly coordinated transcription networks orchestrate the self-renewal of pluripotent stem cell and earliest steps mammalian development. KRAB-containing zinc finger proteins represent largest group factors encoded by genomes higher vertebrates including mice humans. Together with their putatively universal cofactor KAP1, they have been implicated in events as diverse silencing endogenous retroelements, maintenance imprinting embryonic cells, although genomic targets specific functions...
Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected different places at times. This heterogeneous sampling can be an issue for demographic inferences results in biased parameters incorrect model choice if properly considered. When explicitly accounted for, it result very complex models high data dimensionality that difficult to analyse. In this paper, we formally study the impact of such spatial temporal heterogeneity on...
Abstract Background KRAB-ZFPs (Krüppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors responsible for formation of facultative heterochromatin. We have recently shown that KRAB/KAP1 can mediate long-range repression through heterochromatin spreading, but also demonstrated this process is at times countered endogenous...
Abstract European and African natural populations of Drosophila melanogaster have been the focus several studies aiming at inferring demographic adaptive processes based on genetic variation data. However, in these analyses little attention has given to gene flow between samples. Here we present a dataset consisting 14 fully sequenced haploid genomes sampled from population northern species range (Umeå, Sweden). We co-analyzed this new data with an compare likelihood competing scenarios for...
The KRAB-containing zinc finger (KRAB-ZF) proteins represent the largest family of transcription factors (TFs) in humans, yet for great majority, their function and specific genomic target remain unknown. However, it has been shown that a large fraction these genes arose from segmental duplications, they have expanded gene number throughout vertebrate evolution. To determine whether this expansion is linked to selective pressures acting on different domains, we manually curated all KRAB-ZF...