A5017962316- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Cancer-related molecular mechanisms research
- Plant Reproductive Biology
- Molecular Biology Techniques and Applications
- Gene Regulatory Network Analysis
- Circadian rhythm and melatonin
- Insect-Plant Interactions and Control
- Genetic and phenotypic traits in livestock
- Epigenetics and DNA Methylation
- Plant Parasitism and Resistance
- Plant-Microbe Interactions and Immunity
- Plant Virus Research Studies
- Genetic Mapping and Diversity in Plants and Animals
- Coffee research and impacts
- Endoplasmic Reticulum Stress and Disease
- Plant nutrient uptake and metabolism
- Genetics, Aging, and Longevity in Model Organisms
- Plant tissue culture and regeneration
- Cancer-related gene regulation
- Adipose Tissue and Metabolism
University of Lausanne
2019-2024
Centro Universitário Filadélfia
2022
SIB Swiss Institute of Bioinformatics
2014-2021
École Polytechnique Fédérale de Lausanne
2012-2019
John Innes Centre
2009-2012
Norwich Research Park
2009-2012
Rothamsted Research
2012
University of Trieste
2006-2011
University of Molise
2009
University of Padua
2006
We present an update of EPDNew (http://epd.vital-it.ch), a recently introduced new part the Eukaryotic Promoter Database (EPD) which has been described in more detail previous NAR Issue. EPD is old database experimentally characterized eukaryotic POL II promoters, are conceptually defined as transcription initiation sites or regions. EPDnew collection automatically compiled, organism-specific promoter lists complementing corpus manually compiled entries EPD. This exclusively derived from...
We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next generation sequencing (NGS) data. Thanks to abundant release new high-throughput transcript mapping data (CAGE, TSS-seq, GRO-cap) database could be extended plant and fungal species. further report expansion mass genome annotation (MGA) repository...
Programmed ribosomal frameshifting is a key event during translation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome that allows synthesis viral RNA-dependent polymerase and downstream proteins. Here, we present cryo-electron microscopy structure translating mammalian ribosome primed for on RNA. The adopts pseudoknot lodges at entry to messenger (mRNA) channel generate tension in mRNA promote frameshifting, whereas nascent polyprotein forms distinct...
The ribotoxic stress response (RSR) is a signaling pathway in which the p38- and c-Jun N-terminal kinase (JNK)-activating mitogen-activated protein (MAP3K) ZAKα senses stalling and/or collision of ribosomes. Here, we show that reactive oxygen species (ROS)-generating agents trigger ribosomal impairment activation. Conversely, zebrafish larvae deficient for are protected from ROS-induced pathology. Livers mice fed ROS-generating diet exhibit ZAKα-activating changes elongation dynamics....
Abstract In common with a range of environmental and biological stresses, heat shock results in the accumulation misfolded proteins collection downstream consequences for cellular homeostasis growth. Within this complex array responses, sensing responses to specific subcellular compartments involves chaperones, transcriptional regulators, expression profiles. Using (ectopic protein virus infection) chemical triggers accumulation, we have profiled features response cytosol (i.e., cytoplasmic...
The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years.A promoter represented by single position in the genome, typically major transcription start site (TSS).EPD primarily serves biologists interested analysing motif content, chromatin structure or DNA methylation status co-regulated subsets.Initially, evidence came from TSS mapping experiments...
Over the next decade, wheat grain production must increase to meet demand of a fast growing human population. One strategy this challenge is raise productivity by optimizing plant stature. The Reduced height 8 (Rht8) semi-dwarfing gene one few, together with Green Revolution genes, reduce stature (Triticum aestivum L.), and improve lodging resistance, without compromising yield. Rht8 widely used in dry environments such as Mediterranean countries where it increases adaptability. With recent...
Physical damage can strongly affect plant growth, reducing the biomass of developing organs situated at a distance from wounds. These effects, previously studied in leaves, require activation jasmonate (JA) signalling. Using novel assay involving repetitive cotyledon wounding Arabidopsis seedlings, we uncovered function JA suppressing cell division and elongation roots. Regulatory signalling components were then manipulated to delineate their relative impacts on root growth. The new...
Translation initiation is the major regulatory step defining rate of protein production from an mRNA. Meanwhile, impact nonuniform ribosomal elongation rates largely unknown. Using a modified ribosome profiling protocol based on footprints two closely packed ribosomes (disomes), we have mapped collisions transcriptome-wide in mouse liver. We uncover that stacking elongating onto paused occurs frequently and scales with translation rate, trapping ∼10% translating disome state. A distinct...
Abstract The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome browser, queried or analyzed via web interfaces, exported standard formats (FASTA, BED, CSV) subsequent analysis with other tools. Recent work has focused on the improvement EPD promoter viewers, which use UCSC Genome Browser as...
Impairment of translation can lead to collisions ribosomes, which constitute an activation platform for several ribosomal stress-surveillance pathways. Among these is the ribotoxic stress response (RSR), where sensing by MAP3K ZAKα leads p38 and JNK kinases. Despite insights, physiological ramifications impairment downstream RSR signaling remain elusive. Here, we show that stalling ribosomes sufficient activate ZAKα. In amino acid deprivation full nutrient starvation, impacts on ensuing...
Abstract During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding rRNA secondary structures and therefore function. Along with pseudouridine, methylation the 2′-hydroxyl ribose moiety (Nm) is most abundant modification rRNAs. The majority Nm eukaryotes placed Fibrillarin, a conserved methyltransferase belonging to ribonucleoprotein complex guided C/D box small nucleolar (C/D snoRNAs). These impact interactions...
The RNA-binding proteins FCA and FPA were identified based on their repression of the flowering time regulator FLC but have since been shown to widespread roles in Arabidopsis thaliana genome. Here, we use whole-genome tiling arrays show that a wide spectrum genes transposable elements are misexpressed fca-9 fpa-7 (fcafpa) double mutant at two stages seedling development. There was significant bias for misregulated genomic segments mapping 3′ region genes. In addition, large number...
The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from standard code, including reassignment two arginine codons to stop codons. required for translation termination at these noncanonical release newly synthesized polypeptides not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy...
Plant cells can change their identity based on positional information, a mechanism that confers developmental plasticity to plants. This ability, common distinct multicellular organisms, is particularly relevant for plant phloem cells. Protophloem sieve elements (PSEs), one type of conductive cells, act as the main organizers pole, which comprises four cell files organized in conserved pattern. Here, we report how Arabidopsis roots generate reservoir meristematic competent swap identities....
Abstract Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway that important for the elimination of faulty, and regulation normal, mRNAs. The molecular details early steps in NMD are not fully understood but previous work suggests activation occurs as consequence ribosome stalling at termination codon (TC). To test this hypothesis, we established an vitro translation-coupled toeprinting assay based on lysates from human cells allows monitoring occupancy TC...
Despite the vital roles of jasmonoyl-isoleucine (JA-Ile) in governing plant growth and environmental acclimation, it remains unclear what intracellular processes lead to its induction. Here, we provide compelling genetic evidence that mechanical osmotic regulation turgor pressure represents a key elicitor JA-Ile biosynthesis. After identifying cell wall mutant alleles KORRIGAN1 (KOR1) with elevated seedling roots, found ectopic resulted from nonautonomous signals deriving enlarged cortex...
Open chromatin regions host DNA regulatory motifs that are accessible to transcription factors and the transcriptional machinery. In Arabidopsis, responses light heavily regulated at level. Shade, for example, can limit photosynthesis is rapidly perceived by phytochromes as a reduction of red far-red ratio (LRFR). Under shade, become inactive, enabling PHYTOCHROME INTERACTING FACTORs (PIFs), particularly PIF7, promote genome-wide reprogramming essential LRFR responses. An initial strong fast...
Abstract To gain insight into the mechanistic link between translation termination and nonsense-mediated mRNA decay (NMD), we depleted ribosome recycling factor ABCE1 in human cells, resulting an upregulation of NMD-sensitive mRNAs. Suppression NMD on these mRNAs occurs prior to their SMG6-mediated endonucleolytic cleavage. depletion caused stalling at codons (TCs) increased occupancy 3′ UTRs, implying enhanced TC readthrough. knockdown indeed rate readthrough continuation different reading...
Seasonal seawater temperature increases define optimal growth conditions for Dinoflagellate species which can reach high concentrations in water column and also filter-feeding organisms like Mytilus galloprovincialis. Commonly produced by Dinophysis Prorocentrum spp., okadaic acid (OA) its analogues are responsible the Diarrheic Shellfish Poisoning (DSP) syndrome humans. Closure of shellfishing grounds is therefore recommended EU when DSP toxin levels shellfish exceed 16 μg OA 100 g(-1)...
Article10 December 2020Open Access Source DataTransparent process Translation is required for miRNA-dependent decay of endogenous transcripts Adriano Biasini orcid.org/0000-0003-3908-1381 Department Computational Biology, University Lausanne, Switzerland Search more papers by this author Baroj Abdulkarim Stefano de Pretis Center Genomic Sciences, Istituto Italiano di Tecnologia (IIT), Milano, Italy Jennifer Y Tan orcid.org/0000-0003-1064-1162 Rajika Arora Institute Molecular Health ETHZ,...
Nonsense-mediated messenger RNA (mRNA) decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or processing errors. While additional roles in physiological control of mRNA stability have emerged, possible functions mammalian physiology vivo remain unclear. Here, we created conditional mouse allele allows converting the NMD effector nuclease SMG6 wild-type to domain-mutant protein. We find down-regulation affects function...
Metabolic reprogramming is considered as a hallmark of cancer and clinically exploited novel target for therapy. The E2F transcription factor-1 (E2F1) regulates various cellular processes, including proliferative metabolic pathways, acts, depending on the molecular context, an oncogene or tumor suppressor. latter evident by observation that E2f1-knockout mice develop spontaneous tumors, uterine sarcomas. This dual role warrants detailed investigation how E2F1 loss impacts pathways related to...