Angelika Merkel
A5026388196- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Cancer-related gene regulation
- RNA and protein synthesis mechanisms
- Genetic Syndromes and Imprinting
- Chromosomal and Genetic Variations
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- Immune responses and vaccinations
- Immune cells in cancer
- Genetics and Neurodevelopmental Disorders
- RNA Research and Splicing
- Inflammatory Bowel Disease
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Immune Cell Function and Interaction
- Viral Infectious Diseases and Gene Expression in Insects
- Genetic diversity and population structure
- Immune Response and Inflammation
- Multiple Myeloma Research and Treatments
- Bat Biology and Ecology Studies
- Autism Spectrum Disorder Research
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
Josep Carreras Leukaemia Research Institute
2022-2025
Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol
2023
Centro Nacional de Análisis Genómico
2014-2019
Centre for Genomic Regulation
2012-2018
Pompeu Fabra University
2011-2018
Government of Catalonia
2015
Departament de Salut
2015
University of Otago
2013
Institut thématique Génétique, génomique et bioinformatique
2012
University of Canterbury
2008
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue these is not yet available their characteristic localizations also poorly understood. Because RNA represents direct output genetic information encoded by genomes a significant proportion cell's regulatory capabilities focused on its synthesis, processing, transport, modification translation, generation such crucial for...
The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical experimental approaches to investigate these genes been hampered by the lack comprehensive lncRNA annotation. Here, we present analyze most complete annotation date, produced GENCODE consortium within framework ENCODE project comprising 9277 manually annotated producing 14,880 transcripts. Our analyses...
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits fascinating combination reptilian and mammalian characters. For example, platypuses have coat fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; males are equipped with venom similar that reptiles. Analysis first aligned these features genetic innovations. find reptile proteins been co-opted independently from same gene families; milk protein genes conserved despite...
Abstract Newly growing evidence highlights the essential role that epitranscriptomic marks play in development of many cancers; however, little is known about and implications altered epitranscriptome deposition prostate cancer. Here, we show transfer RNA N 7 -methylguanosine (m G) transferase METTL1 highly expressed primary advanced tumours. Mechanistically, find depletion causes loss m G tRNA methylation promotes biogenesis a novel class small non-coding RNAs derived from 5'tRNA fragments....
While analyzing the DNA methylome of multiple myeloma (MM), a plasma cell neoplasm, by whole-genome bisulfite sequencing and high-density arrays, we observed highly heterogeneous pattern globally characterized regional hypermethylation embedded in extensive hypomethylation. In contrast to widely reported promoter-associated CpG islands (CGIs) cancer, hypermethylated sites MM, as opposed normal cells, were located outside unexpectedly associated with intronic enhancer regions defined B cells...
The most striking characteristic of CHO cells is their adaptability, which enables efficient production proteins as well growth under a variety culture conditions, but also results in genomic and phenotypic instability. To investigate the relative contribution epigenetic modifications towards phenotype evolution, comprehensive genome epigenome data are presented for six related cell lines, both response to perturbations (different conditions media selection specific with increased transient...
Neutrophils are short-lived blood cells that play a critical role in host defense against infections. To better comprehend neutrophil functions and their regulation, we provide complete epigenetic overview, assessing important functional features of differentiation stages from bone marrow-residing progenitors to mature circulating cells. Integration chromatin modifications, methylation, transcriptome dynamics reveals an enforced regulation differentiation, for cellular such as release...
A healthy immune system requires cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability.We apply a novel analytical approach measure compare variability genome-wide across CD14+CD16- monocytes, CD66b+CD16+ neutrophils, CD4+CD45RA+ naïve T from the same 125 individuals. We discover substantially increased in neutrophils compared monocytes cells. In genes with hypervariable expression are found implicated...
Preclinical ulcerative colitis is poorly defined. We aimed to characterize the preclinical systemic inflammation in colitis, using a comprehensive set of proteins.We obtained plasma samples biobanked from individuals who developed later life (n = 72) and matched healthy controls 140) within population-based screening cohort. measured 92 proteins related proximity extension assay. The biologic relevance these findings was validated an inception cohort patients with 101) 50). To examine...
DNA methylation is essential for normal embryogenesis and development in mammals can be captured at single base pair resolution by whole genome bisulfite sequencing (WGBS). Current available analysis tools are becoming rapidly outdated as they lack sensible functionality efficiency to handle large amounts of data now commonly created.We developed gemBS, a fast high-throughput bioinformatics pipeline specifically designed scale BS-Seq that combines high performance BS-mapper (GEM3) variant...
Abstract Aim To assess the pathobiological and translational importance of whole-blood transcriptomic analysis in inflammatory bowel disease [IBD]. Methods We analysed expression profiles from paired-end sequencing a discovery cohort 590 Europeans recruited across six countries IBD Character initiative (newly diagnosed patients with Crohn’s [CD; n = 156], ulcerative colitis [UC; 167], controls [n 267]), exploring differential [DESeq2], co-expression networks [WGCNA], transcription factor...
Abstract Background Epigenetic alterations may provide valuable insights into gene–environment interactions in the pathogenesis of inflammatory bowel disease [IBD]. Methods Genome-wide methylation was measured from peripheral blood using Illumina 450k platform a case-control study an inception cohort (295 controls, 154 Crohn’s [CD], 161 ulcerative colitis [UC], 28 IBD unclassified [IBD-U)] with covariates age, sex and cell counts, deconvoluted by Houseman method. Genotyping performed...
TDP-43 is a DNA/RNA-binding protein that regulates gene expression and its malfunction in neurons has been causally associated with multiple neurodegenerative disorders. Although progress made understanding the functions of neurons, little known about role endothelial cells (ECs), angiogenesis vascular function. Using inducible EC-specific knockout mice, we showed required for sprouting angiogenesis, barrier integrity blood vessel stability. Postnatal deletion leaded to retinal...
DNA methylation and the localization post-translational modification of nucleosomes are interdependent factors that contribute to generation distinct phenotypes from genetically identical cells. With 112 whole-genome bisulfite sequencing datasets BLUEPRINT Epigenome Project, we analyzed global development patterns during lineage commitment maturation a range immune system effector cells cancers arise them. We show clear trends in innate adaptive arms human system, both globally relation...
Introduction The HIV regulatory protein Tat enhances viral transcription and also modifies host gene expression, affecting cell functions like cycle apoptosis. Residual expression of is detected in blood other tissues even under antiretroviral treatment. Cohort studies have indicated that, despite virologic suppression, people with (PWH) are at increased risk comorbidities linked to chronic inflammation, accelerated immune ageing, cellular senescence, sometimes associated abnormal genomic...
Short tandem repeats, specifically microsatellites, are widely used genetic markers, associated with human diseases, and play an important role in various regulatory mechanisms evolution. Despite their importance, much is yet unknown about mutational dynamics. The increasing availability of genome data has led to several silico studies microsatellite evolution which have produced a vast range algorithms software for repeat detection. Documentation these tools often sparse, or provided format...
The existence of dynamic cellular phenotypes in changing environmental conditions is major interest for cell biologists who aim to understand the mechanism and sequence regulation gene expression. In context therapeutic protein production by Chinese Hamster Ovary (CHO) cells, a detailed temporal understanding cell-line behavior control necessary achieve more predictable reliable process performance. Of particular are data on dynamic, temporally resolved transcriptional genes response altered...
Global investigation of histone marks in acute myeloid leukemia (AML) remains limited. Analyses 38 AML samples through integrated transcriptional and chromatin mark analysis exposes 2 major subtypes. One subtype is dominated by patients with NPM1 mutations or MLL-fusion genes, shows activation the regulatory pathways involving HOX-family genes as targets, displays high self-renewal capacity stemness. The second enriched for RUNX1 spliceosome mutations, suggesting potential interplay between...
Abstract Motivation: The avalanche of data arriving since the development NGS technologies have prompted need for developing fast, accurate and easily automated bioinformatic tools capable dealing with massive datasets. Among most productive applications is sequencing cellular RNA, known as RNA-Seq. Although RNA-Seq provides similar or superior dynamic range than microarrays at lower cost, lack standard user-friendly pipelines a bottleneck preventing from becoming transcriptome analysis....
Rett syndrome (RTT) is a severe neurodevelopmental disease caused almost exclusively by mutations to the MeCP2 gene. This may be regarded as synaptopathy, with impairments affecting synaptic plasticity, inhibitory and excitatory transmission network excitability. The complete understanding of mechanisms behind how transcription factor so profoundly affects mammalian brain are yet determined. What known, that involvement in activity-dependent expression programs critical link between this...
Abstract Background A healthy immune system requires cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. Results We applied a novel analytical approach measure compare variability genome-wide across CD14 + CD16 − monocytes, CD66b neutrophils, CD4 CD45RA naïve T cells, from the same 125 individuals. discovered substantially increased in neutrophils compared monocytes cells. In genes with hypervariable...