A5017352127- RNA and protein synthesis mechanisms
- Malaria Research and Control
- Mosquito-borne diseases and control
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Retinoids in leukemia and cellular processes
- Estrogen and related hormone effects
- Complement system in diseases
- Advanced biosensing and bioanalysis techniques
- Vector-borne infectious diseases
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Invertebrate Immune Response Mechanisms
- DNA and Nucleic Acid Chemistry
- Transgenic Plants and Applications
- Insect and Arachnid Ecology and Behavior
- Hepatitis B Virus Studies
- Insect and Pesticide Research
- Protein Kinase Regulation and GTPase Signaling
- Hypothalamic control of reproductive hormones
- Plant Virus Research Studies
RIKEN Center for Integrative Medical Sciences
2011-2022
CellFree Sciences (Japan)
2014-2022
Leiden University Medical Center
2010
ID Pharma (Japan)
2004-2006
University of Gdańsk
2003
Gdańsk Medical University
2003
The Francis Crick Institute
2002
Laboratory of Molecular Genetics
2001
Karolinska Institutet
1992-1998
Inserm
1998
This study describes comprehensive polling of transcription start and termination sites analysis previously unidentified full-length complementary DNAs derived from the mouse genome. We identify 5' 3' boundaries 181,047 transcripts with extensive variation in arising alternative promoter usage, splicing, polyadenylation. There are 16,247 new protein-coding transcripts, including 5154 encoding proteins. Genomic mapping transcriptome reveals transcriptional forests, overlapping on both...
We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers DNA tags deriving from the initial 20 nucleotides 5′ end mRNAs. CAGE allows high-throughout profiling transcriptional start points (TSP), including promoter usage analysis. By analyzing four libraries (brain, cortex, hippocampus, cerebellum), we redefined more accurately TSPs 11-27% analyzed units that were hit. The frequency correlates well with results other analyses, such as...
Abstract Background DNA methylation in promoters is closely linked to downstream gene repression. However, whether a cause or consequence of repression remains an open question. If it cause, then may affect the affinity transcription factors (TFs) for their binding sites (TFBSs). consequence, caused by chromatin modification be stabilized methylation. Until now, these two possibilities have been supported only non-systematic evidence and they not tested on wide range TFs. An average promoter...
Finding and characterizing mRNAs, their transcription start sites (TSS), associated promoters is a major focus in post-genome biology. Mammalian cells have at least 5–10 magnitudes more TSS than previously believed, deeper sequencing necessary to detect all active given tissue. Here, we present new method for high-throughput of 5′ cDNA tags—DeepCAGE: merging the Cap Analysis Gene Expression with ultra-high-throughput sequence technology. We apply DeepCAGE characterize 1.4 million sequenced...
The pleiotropic effects of retinoids are mediated by nuclear receptors that activated 9-cis- or all-trans-retinoic acid to function as ligand-dependent transcription factors. In a yeast one-hybrid screen for proteins capable interacting with native retinoic receptor (RAR), we have isolated the T:G mismatch-specific thymine-DNA glycosylase (TDG), which initiates repair mismatches caused spontaneous deamination methylated cytosines. Here, report TDG can interact RAR and retinoid X (RXR) in...
A better method was developed for analysis and identification of protein DNA components gel-shift assays. The protein-DNA complexes, separated in polyacrylamide gels, were transferred onto stacked nitrocellulose anion-exchange membranes. proteins, bound to nitrocellulose, identified by immunoblotting, while the DNA, which only membrane, detected autoradiography. technique readily thyroid hormone receptors interacting with response elements representing inverted or direct repeats consensus...
Abstract Honey bee colonies exhibit an age-related division of labor, with worker bees performing discrete sets behaviors throughout their lifespan. These behavioral states are associated distinct brain transcriptomic states, yet little is known about the regulatory mechanisms governing them. We used CAGEscan (a variant Cap Analysis Gene Expression technique) for first time to characterize promoter regions differentially expressed genes during two (brood care (aka “nursing”) and foraging)...
Journal Article Thyroid hormone alters the DNA binding properties of chicken thyroid receptors α and β Get access Monika L. Andersson, Andersson Department Molecular Biology, Karolinska InstituteBox60400, S-1 401 Stockholm, Sweden Search for other works by this author on: Oxford Academic PubMed Google Scholar Kristina Nordström, Nordström Stephen Demczuk, Demczuk Matthias Harbers, Harbers Björn Vennström * To whom correspondence should be addressed Nucleic Acids Research, Volume 20, Issue...
Elmar vom Baur, Matthias Harbers, Soo-Jung Um, Arndt Benecke, Pierre Chambon, and Régine Losson Institut de Génétique et Biologie Moléculaire Cellulaire (IGBMC), Centre National la Recherche Scientifique–Institut Santé Médicale–Université Louis Pasteur (CNRS–INSERM–ULP), Collège France, 67404 Illkirch Cedex, France
Next-generation sequencing is excellently suited to evaluate the abundance of mRNAs study gene expression. Here we compare two alternative technologies, cap analysis expression (CAGE) and serial (SAGE), for same RNA samples. Along with quantifying levels, CAGE can be used identify tissue-specific transcription start sites, while SAGE monitors 3′-end usage. We both methods get more insight into transcriptional control myogenesis, studying differential in differentiated proliferating C2C12...
The global prevalence of malaria has decreased over the past fifteen years, but similar gains have not been realized against Plasmodium vivax because this species is less responsive to conventional control interventions aimed principally at P. falciparum. Approximately half all cases outside Africa are caused by vivax. This places dormant forms in human liver that cause repeated clinical attacks without involving another mosquito bite. diagnosis acute patent relies primarily on light...
Serological markers are a promising tool for surveillance and targeted interventions Plasmodium vivax malaria. P. is closely related to the zoonotic parasite knowlesi, which also infects humans. knowlesi co-endemic across much of South East Asia, making it important design serological that minimize cross-reactivity in this region. To determine degree IgG against panel markers, we assayed samples from human patients with antibody reactivity high proteins sequence identity their ortholog....
Most commonly used intercalating fluorescent dyes in DNA detection are lacking any sequence specificity, whereas so-called Exciton Primers can overcome this limitation by functioning as "sequence-specific dyes." After hybridization to complementary sequences, the fluorescence of provides sequence-specific signals for real-time monitoring amplification reactions. Applied SmartAmp2 mutation process, show high signal strength with low background leading a superior specificity and sensitivity...
Abstract Background Analyzing the RNA pool or transcription start sites requires effective means to convert into cDNA libraries for digital expression counting. With current high-speed sequencers, it is necessary flank cDNAs with specific adapters. Adding template-switching oligonucleotides reverse reactions most commonly used approach when working very small quantities of even from single cells. Results Here we compared performance DNA-RNA, DNA-LNA and DNA in during nanoCAGE library...
Multiplexed bead-based assays that use Luminex ® xMAP technology have become popular for measuring antibodies against proteins of interest in many fields, including malaria and more recently SARS-CoV-2/COVID-19. There are currently two formats widely used: non-magnetic beads or magnetic beads. Data lacking regarding the comparability results obtained using these types beads, run on different instruments. Whilst can only be flow-based instruments (such as 100/200™ Bio-Plex 200), both newer...