A5059941956- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Chromatin Remodeling and Cancer
- RNA Research and Splicing
- Protein Degradation and Inhibitors
- Bioinformatics and Genomic Networks
- Immune responses and vaccinations
- Histone Deacetylase Inhibitors Research
- Biomedical Text Mining and Ontologies
- Immune cells in cancer
- Estrogen and related hormone effects
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Fungal and yeast genetics research
- Immune Response and Inflammation
- Gene expression and cancer classification
- Retinoids in leukemia and cellular processes
- S100 Proteins and Annexins
- Acute Myeloid Leukemia Research
- Bone Metabolism and Diseases
- DNA Repair Mechanisms
- RNA Interference and Gene Delivery
Radboud University Nijmegen
2016-2025
Radboud Institute for Molecular Life Sciences
2016-2025
Radboud University Medical Center
2016-2025
SIB Swiss Institute of Bioinformatics
2023
Phoenix Bioinformatics
2023
University of Padua
2023
University College London
2023
Stanford University
2023
University at Buffalo, State University of New York
2023
University of Southern California
2023
Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding functions of genes and gene products. Here, we report advances consortium over past two years. new GO-CAM annotation framework was notably improved, formalized model with a computational schema to check validate rapidly increasing repository 2838 GO-CAMs. In addition, describe impacts several collaborations refine GO 10% increase in number annotations,...
Epigenetic reprogramming of myeloid cells, also known as trained immunity, confers nonspecific protection from secondary infections. Using histone modification profiles human monocytes with the Candida albicans cell wall constituent β-glucan, together a genome-wide transcriptome, we identified induced expression genes involved in glucose metabolism. Trained display high consumption, lactate production, and ratio nicotinamide adenine dinucleotide (NAD(+)) to its reduced form (NADH),...
Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate and susceptibility to secondary infections. We characterized transcriptomes epigenomes in four primary cell types: monocytes vitro-differentiated naïve, tolerized, macrophages. Inflammatory metabolic pathways were modulated macrophages, including decreased inflammasome activation, we...
Innate immune memory is the phenomenon whereby innate cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components lipopolysaccharide (LPS). We apply an integrated epigenomic approach characterize molecular events involved in LPS-induced tolerance a time-dependent manner. Mechanistically, LPS-treated fail accumulate active histone marks at promoter and enhancers of genes lipid metabolism phagocytic pathways. Transcriptional inactivity...
Natalya Yudkovsky, Colin Logie, Steven Hahn, and Craig L. Peterson Molecular Cellular Biology Program, University of Washington, The Fred Hutchinson Cancer Research Center; Center the Howard Hughes Medical Institute, Seattle Washington 98109 USA; Program in Medicine Department Biochemistry Biology, Massachusetts School, Worcester, 01605 USA
Background Nucleosome translocation along DNA is catalyzed by eukaryotic SNF2-type ATPases. One class of SNF2-ATPases distinguished the presence a C-terminal bromodomain and conserved from yeast to man plants. This SNF2 enzymes forms rather large protein complexes that are collectively called SWI/SNF complexes. They involved in transcription repair. Two broad types have been reported literature; PBAF BAF. These inclusion or not polybromo several ARID subunits. Here we investigated human...
Site-specific recombination offers a potential way to alter living genome by design in precise and stable manner. This requires strategies which can be used regulate the event. We describe strategy FLP recombinase activity relies on expressing as fusion protein with steroid hormone receptor ligand binding domains (LBDs). In absence of cognate LBD, is extremely low. Upon administration, rapidly induced. These results outline basis for inducible expression or disruption based recombination....
Nucleosome positioning dictates eukaryotic DNA compaction and access. To predict nucleosome positions in a statistical mechanics model, we exploited the knowledge that nucleosomes favor sequences with specific periodically occurring dinucleotides. Our model is first to capture both dyad position within few base pairs, free binding energy 2 k B T , for all known sequences. By applying Percus’s equation derived landscape, isolate sequence effects on genome-wide occupancy from other factors may...
Abstract Background Topologically associating domains (TADs) are genomic regions of self-interaction. Additionally, it is known that TAD boundaries enriched in CTCF binding sites. In turn, sites to be asymmetric, whereby the convergent configuration a pair leads formation chromatin loop vivo. However, date, has been unclear how reconcile structure with CTCF-based loops. Results We approach this problem by analysing site strengths and classifying clusters along genome on basis their relative...
Abstract A comprehensive, computable representation of the functional repertoire all macromolecules encoded within human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating structured body information about gene functions, which now includes experimental findings reported in more than 175,000 publications genes experimentally tractable model organisms 1,2 . Here, we describe results large,...
Post-translational histone modifications abound and regulate multiple nuclear processes. Most are targeted to the amino-terminal domains of histones. Here we report identification characterization acetylation lysine 56 within core domain H3. In crystal structure nucleosome, contacts DNA. Phenotypic analysis suggests that is critical for function it modulates formamide resistance, ultraviolet radiation sensitivity, sensitivity hydroxyurea. We show acetylated form H3 (H3-K56) present during...
SWI-SNF is an ATP-dependent chromatin remodeling complex that disrupts DNA-histone interactions. Several studies of activity on mononucleosome substrates have suggested leads to novel, accessible nucleosomes which persist in the absence continuous ATP hydrolysis. In contrast, we reported SWI-SNF-dependent nucleosomal arrays rapidly reversed after removal ATP. One possibility these contrasting results are due different assays used; alternatively, lability SWI-SNF-remodeled state might be...