A5049667539- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Bacterial Genetics and Biotechnology
- MicroRNA in disease regulation
- Cervical Cancer and HPV Research
- Cancer-related molecular mechanisms research
- Distributed and Parallel Computing Systems
- Photosynthetic Processes and Mechanisms
- HIV Research and Treatment
- Enzyme Production and Characterization
- Cancer-related gene regulation
- Enzyme Structure and Function
- Advanced biosensing and bioanalysis techniques
- Cancer Genomics and Diagnostics
- DNA Repair Mechanisms
- Animal Genetics and Reproduction
- T-cell and Retrovirus Studies
- Forensic and Genetic Research
- Chromosomal and Genetic Variations
- Genetics, Aging, and Longevity in Model Organisms
- Evolution and Genetic Dynamics
University of Copenhagen
2014-2023
Tel Aviv University
2011-2013
Exact Sciences (United States)
2013
PharmacoGenetics (China)
2011
Abstract Methylation of guanosine on position N7 (m7G) internal RNA positions has been found in all domains life and have implicated human disease. Here, we present m7G Mutational Profiling sequencing (m7G-MaP-seq), which allows high throughput detection modifications at nucleotide resolution. In our method, modified are converted to abasic sites by reduction with sodium borohydride, directly recorded as cDNA mutations through reverse transcription sequenced. We detect increased mutation...
MicroRNAs (miRNA) are small RNA molecules of approximately 20 to 22 nucleotides that reduce expression proteins through mRNA degradation and/or translational silencing. Each known miRNA has a large number predicted targets. Members the let-7/miR-98 family miRNAs up-regulated at end embryonic development. Let-7 is often down-regulated early during cancer development, suggesting let-7-regulated oncofetal genes (LOG) may become reexpressed in cells. Using comparative bioinformatics, we have...
MicroRNAs (miRNAs) are short regulatory RNAs that down-regulate gene expression. They essential for cell homeostasis and active in many disease states. A major discovery is the ability of miRNAs to determine efficacy drugs, which has given rise field 'miRNA pharmacogenomics' through 'Pharmaco-miRs'. play a significant role pharmacogenomics by down-regulating genes important drug function. These interactions can be described as triplet sets consisting miRNA, target associated with gene. We...
miRNAs are small noncoding RNAs that regulate gene expression. We have used stable isotope labeling by amino acids in cell culture (SILAC) to investigate the effect of miRNA-1 on HeLa proteome. Expression 12 out 504 investigated proteins was repressed transfection. This set genes significantly overlaps with regulated been identified DNA array technology and predicted computational methods. Moreover, we find 3′-untranslated region for enriched complementary sites. Our findings demonstrate...
The development of vascular calcification (VC) in chronic uremia (CU) is a tightly regulated process controlled by factors promoting and inhibiting mineralization. Next-generation high-throughput RNA sequencing (RNA-seq) powerful sensitive tool for quantitative gene expression profiling the detection differentially expressed genes. In present study, we, first time, used RNA-seq to examine rat aorta transcriptomes from CU rats compared with control rats. Severe VC was induced rats, which lead...
Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the signal normalized to a no-reagent control correct background caused premature termination reverse transcriptase. Here, we introduce Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains ability reagents accurately probe structure, but also allows covalent coupling between SHAPES reagent and biotin molecule....
Hydroxyl Radical Footprinting (HRF) is a tried-and-tested method for analysis of the tertiary structure RNA and identification protein footprints on RNA. The hydroxyl radical reaction breaks accessible parts backbone, thereby allowing ribose accessibility to be determined by detection reverse transcriptase termination sites. Current methods HRF rely transcription single primer fluorescent fragments capillary electrophoresis. Here, we describe an accurate efficient massive...
RNase H cleaves RNA in RNA-DNA duplexes. It is present all domains of life as well multiple viruses and essential for mammalian development human immunodeficiency virus replication. Here, we developed a sequencing-based method to measure the cleavage thousands different duplexes thereby comprehensively characterized sequence preferences HIV-1, Escherichia coli enzymes. We find that catalytic E. have nearly identical preferences, which correlate with efficiency H-recruiting antisense...
Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation alternatively spliced (cassette) exons within mammals dipterans. We report a strikingly different pattern Caenorhabditis nematodes-more than 92% cassette from elegans are conserved briggsae and/or remanei. High extend minor-form (present minority transcripts) particularly pronounced for showing complex patterns splicing....
During preparation of a follow-up manuscript, the Authors have discovered that company which sold commercial enzymatic 'Recombinant Human RNASEH1' mislabelled preparation.The has confirmed actually used recombinant E.coli RNase H protein, not human enzyme.That implies whenever discussed sequence preferences H1 enzyme, they were in fact unknowingly instead describing properties E. coli enzyme.Below is Authors' assessment consequences reagent mislabeling on major conclusions paper.1.The...
The aim of pharmacogenomics is to identify individual differences in genome and transcriptome composition their effect on drug efficacy. MicroRNAs (miRNAs) are short noncoding RNAs that negatively regulate expression the majority animal genes, including many genes involved Consequently, miRNA among individuals could be an important factor contributing differential response. Pharmacogenomics can divided into target termed as pharmacodynamics (PD) transport metabolism pharmacokinetics (PK). To...
A large part of our current understanding gene regulation in Gram-positive bacteria is based on Bacillus subtilis, as it one the most well studied bacterial model systems. The rapid growth data concerning its molecular and genomic biology distributed across multiple annotation resources. Consequently, interpretation from further B. subtilis experiments becomes increasingly challenging both low- large-scale analyses. Additionally, structured RNA non-coding (ncRNA), operon structure, still...
Alternative splicing (AS) is an important contributor to proteome diversity and regarded as explanatory factor for the relatively low number of human genes compared with less complex animals. To assess evolutionary conservation AS its developmental regulation, we have investigated qualitative quantitative expression 21 orthologous alternative splice events through development 2 nematode species separated by 85–110 Myr time. We demonstrate that most these present in Caenorhabditis elegans are...
mRNA secondary structure influences translation. Proteins that modulate the around translation initiation region may regulate in plastids. To test this hypothesis, we exposed Arabidopsis thaliana to high light, which induces of psbA encoding D1 subunit photosystem II. We assayed by ribosome profiling and applied two complementary methods analyze vivo RNA structure: DMS-MaPseq SHAPE-seq. detected increased accessibility after light treatment, likely contributing observed increase facilitating...
Bacillus subtilis is a Gram-positive bacterium used as cell factory for protein production. Over the last decades, continued optimization of production strains has increased yields enzymes, such amylases, and made commercial applications feasible. However, current are still significantly lower than theoretically possible yield based on available carbon sources. In its natural environment, B. can respond to unfavorable growth conditions by differentiating into motile cells that use flagella...
The production of the alpha-amylase (AMY) enzyme in
Human papillomavirus type 16 (HPV-16) has the capacity to transform human primary keratinocytes. Maintenance of transformed phenotype requires constitutive expression oncoproteins E6 and E7. The low-risk HPV types express E7 from monocistronic mRNA, but for high-risk types, no mRNA that encodes as first open reading frame (ORF) been identified. We recently identified a transcription initiation site within ORF HPV-16 at nt 542. In present study we have characterized P542 promoter, which...
Abstract RNA sequencing (RNA‐seq) has become the preferred method for global quantification of bacterial gene expression. With continued improvements in technology and data analysis tools, most labor‐intensive expensive part an RNA‐seq experiment is preparation libraries, which also essential quality obtained. Here, we present a straightforward inexpensive basic protocol strand‐specific libraries from as well computational pipeline reads. The based on Illumina platform allows easy...
Abstract Background Within the last decade a large number of noncoding RNA genes have been identified, but this may only be tip iceberg. Using comparative genomics sequences that signals concordant with conserved secondary structures discovered in human genome. Moreover, genome wide transcription profiling tiling arrays indicate majority is transcribed. Results We combined array data structural predictions to search for novel and are expressed neuroblastoma cell line SK-N-AS. strategy, we...