A5101443561- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Nuclear Structure and Function
- Hereditary Neurological Disorders
- RNA modifications and cancer
- Cancer-related gene regulation
- Genomics and Chromatin Dynamics
- RNA regulation and disease
- Cancer Genomics and Diagnostics
- Neurological diseases and metabolism
- Neurological Disorders and Treatments
- Metabolism and Genetic Disorders
- Cardiomyopathy and Myosin Studies
- Epigenetics and DNA Methylation
- Genetic factors in colorectal cancer
- Muscle Physiology and Disorders
- Genetic Neurodegenerative Diseases
- DNA and Nucleic Acid Chemistry
- Peripheral Nerve Disorders
- Prion Diseases and Protein Misfolding
- Cerebrovascular and genetic disorders
- Intracerebral and Subarachnoid Hemorrhage Research
- Myasthenia Gravis and Thymoma
- Colorectal Cancer Screening and Detection
- Polyomavirus and related diseases
Aarhus University
2007-2023
Aarhus University Hospital
2013-2015
Institute of Human Genetics
2008
University of Bonn
1890
Charité - Universitätsmedizin Berlin
1884-1888
Humboldt-Universität zu Berlin
1887
<h3>Objective</h3> To develop an affordable and robust pipeline for selection of patient-specific somatic structural variants (SSVs) being informative about radicality the primary resection, response to adjuvant therapy, incipient recurrence treatment performed in relation diagnosis recurrence. <h3>Design</h3> We have established efficient procedures identification SSVs by next-generation sequencing subsequent quantification 3–6 plasma. The consequence intratumour heterogeneity on our...
Several aspects of eukaryotic mRNA processing are linked to transcription. In Saccharomyces cerevisiae, overexpression the export factor Sub2p suppresses growth defect hpr1 null cells, yet protein Hpr1p and associated THO complex implicated in transcriptional elongation. Indeed, we find that a pool heat shock HSP104 transcripts 3'-end truncated mutant as well sub2 backgrounds. Surprisingly, however, this can be suppressed by deletion 3'-5' exonuclease Rrp6p. This indicates incomplete RNAs...
A common method for calculating results from qPCR experiments is the comparative Ct method, also called 2(-ΔΔCt) method. However, several assumptions are included in and standard statistical analyses not directly applicable. Here, we describe a different X(0) result calculations analysis experiments. The differs by introducing conversion of exponentially related values into linearly values, which represent amount starting material experiment. Results calculated illustrated with technical...
In situ detection of RNA by hybridization with complementary probes is a powerful technique. Probe design critical parameter in successful target detection. We have evaluated the efficiency fluorescent DNA oligonucleotides modified to contain locked nucleic acid (LNA) residues. This increases thermal stability hybrids formed RNA. The LNA-based detect specific RNAs fixed yeast cells an far better than conventional oligonucleotide same sequence. Using this probe design, we were also able...
Abstract Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking complexes at serial timepoints. We apply tiCLIP to export adaptor, ALYREF; a component Nuclear Exosome Targeting (NEXT) complex, RBM7; and...
Myotonic dystrophy type 1 (DM1) is caused by CUG triplet expansions in the 3′ UTR of dystrophia myotonica protein kinase (DMPK) messenger ribonucleic acid (mRNA). The etiology this multi-systemic disease involves pre-mRNA splicing defects elicited ability CUG-expanded mRNA to 'sponge' factors muscleblind family. Although nuclear aggregation CUG-containing mRNPs distinct foci a hallmark DM1, mechanisms their homeostasis have not been completely elucidated. Here we show that DEAD-box helicase,...
In the yeast Saccharomyces cerevisiae , a common conditional phenotype associated with deletion or mutation of genes encoding mRNA export factors is rapid accumulation mRNAs in intranuclear foci, suggested to be near transcription sites. The nuclear RNA exosome has been implicated retaining RNAs these foci; on component Rrp6p, released. To determine exact location retained as well released mRNAs, we have used mutant strains analyze spatial relationship between newly synthesized heat shock...
Subcellular RNA localization plays an important role in development, cell differentiation, and migration. For a comprehensive description of the population protrusion localized mRNAs astrocytes we separated protrusions from bodies Boyden chamber performed high‐throughput direct sequencing. The with astrocyte encode proteins belonging to variety functional groups indicating involvement for palette cellular functions. mRNA encoding intermediate filament protein Nestin was among identified...
The intermediate filament network of astrocytes includes Glial fibrillary acidic protein (Gfap) as a major component. Gfap mRNA is alternatively spliced resulting in generation different isoforms where Gfapα the most predominant isoform. Gfapδ isoform expressed proliferating neurogenic developing human brain and adult mouse brain. Here we provide characterization protein. RT-qPCR analysis showed that expression coordinately increased post-natal period. Immunohistochemical staining samples...
The Boyden chamber assay has been developed for various cell migration and invasion protocols. One variant of the is pseudopodium isolation assay, which to identify RNA proteins localized in pseudopodia protrusions. Astrocytes are most abundant type CNS typically extend long cellular Increasing interest emerges concerning example growth mechanisms functions astrocytes respect brain development, re-uptake neurotransmitters synaptic cleft glial scar formation. Protein localization have...
Protrusions of cancer cells conferrers a vital function for cell migration and metastasis. Protein RNA localization mechanisms have been extensively examined shown to play pivotal roles the functional presence specific protein components in protrusions.To describe genome wide localized protrusions metastatic human breast line MDA-MB-231 we used Boyden chamber based methodology followed by direct mRNA sequencing.In hereby identified group protrusion some previously were described be...
Myotonic dystrophy type 1 (DM1) is the most common muscle in adults. The disease caused by a triplet expansion 3'end of myotonic protein kinase (DMPK) gene. In order to develop human cell model for investigation possible effects antisense and RNAi effector molecules we have used lentiviral mediated myoD-forced myogenesis DM1 patient fibroblasts. Transduced fibroblasts show multinuclear phenotype express differentiation marker myogenin. Furthermore, fluorescence situ hybridization (FISH)...
Abstract The three mammalian HP1 proteins, HP1α/CBX5, HP1β/CBX1, and HPγ/CBX3, are involved in chromatin packing gene regulation. HP1α protein is down‐regulated invasive compared to non‐invasive breast cancer cells a suppressor of cell migration invasion. In this report, we examined the background for down‐regulation cells. We identified strict correlation between at level mRNA level. was not caused by destabilization. Chromatin immunoprecipitation analysis showed decrease histone mark...
The three members of the human heterochromatin protein 1 (HP1) family proteins, HP1α, HP1β, and HPγ, are involved in chromatin packing epigenetic gene regulation. HP1α is encoded from CBX5 a suppressor metastasis. down-regulated at transcriptional level metastatic compared to non-metastatic breast cancer. shares bi-directional promoter structure with hnRNPA1 gene. But whereas expression cells, hnRNAP1 constant. Here, we address regulation Transient transfection transposon mediated...
In the yeast Saccharomyces cerevisiae, mutation of some effectors mRNA nuclear export leads to rapid accumulation HSP104 RNA in transcription site-associated foci. We have screened S. cerevisiae complement viable gene deletion mutants for their inability RNA. The 15 strains identified comprise deletions components THO, Thp1p/Sac3p, and pore complexes. all three mutant classes, retained overlaps site. Thus, an early block is general. Incubation strains, as well seven additional mutants, under...
(1) Background: Merkel cell carcinoma (MCC) is caused by the polyomavirus and UV radiation. Understanding of underlying biology limited, but identification prognostic markers may lead to better stratification for patients. (2) Methods: Ninety patients diagnosed with MCC (1996-2012) were included. Virus status was estimated polymerase chain reaction (qPCR) immunohistochemistry (IHC). Ulceration status, PD-L1, cd66b neutrophils, cd8 lymphocytes biomarkers vascularization (cd34 endothelial...
Our genes are post-transcriptionally regulated by microRNAs (miRNAs) inducing translational suppression and degradation of targeted mRNAs. Strategies to inhibit miRNAs in a spatiotemporal manner desired cell type or tissue, at developmental stage, can be crucial for understanding miRNA function pushing forward as feasible rationale genetic treatment disease. For such purposes, RNA polymerase II (RNA Pol II)-transcribed tough decoy (TuD) inhibitors particularly attractive. Here, we...