Anders Ranegaard Clausen

Anders Ranegaard Clausen
University of Gothenburg | GU · Department of Medical Biochemistry and Cell Biology

PhD, Genetics

About

61
Publications
4,811
Reads
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1,168
Citations
Citations since 2016
24 Research Items
840 Citations
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
Additional affiliations
March 2015 - present
University of Gothenburg
Position
  • Research Assistant
Description
  • Research in the field of Genome Instability and DNA Repair
April 2010 - February 2015
National Institute of Environmental Health Sciences
Position
  • Research in the field of DNA replication
December 2009 - April 2010
Lund University
Position
  • Crystallization of a plant thymidine kinase
Education
February 2005 - December 2009
Lund University
Field of study
  • Deoxyribonucleoside kinases in bacteria, plants and humans
September 1999 - June 2004
Technical University of Denmark
Field of study
  • Chemical Engineering

Publications

Publications (61)
Article
Full-text available
Ribonucleotides are frequently incorporated into DNA during replication in eukaryotes. Here we map genome-wide distribution of these ribonucleotides as markers of replication enzymology in budding yeast, using a new 5' DNA end-mapping method, hydrolytic end sequencing (HydEn-seq). HydEn-seq of DNA from ribonucleotide excision repair-deficient strai...
Article
Full-text available
Significance More than a million ribonucleotides may be incorporated into the mammalian nuclear genome during each round of DNA replication. When these ribonucleotides are not removed, they persist in the DNA template used for the next round of replication. Here we show that replicases stall when attempting to bypass ribonucleotides in DNA template...
Article
Full-text available
In both budding and fission yeast, a large number of ribonucleotides are incorporated into DNA during replication by the major replicative polymerases (Pols α, δ and ɛ). They are subsequently removed by RNase H2-dependent repair, which if defective leads to replication stress and genome instability. To extend these studies to humans, where an RNase...
Article
Full-text available
The in vivo role for RNase H1 in mammalian mitochondria has been much debated. Loss of RNase H1 is embryonic lethal and to further study its role in mtDNA expression we characterized a conditional knockout of Rnaseh1 in mouse heart. We report that RNase H1 is essential for processing of RNA primers to allow site-specific initiation of mtDNA replica...
Preprint
Full-text available
Ribonucleotides are estimated to be the most common non-canonical nucleotides transiently incorporated in DNA. Their presence or failure of their removal can affect genome stability and mutations in factors involved in dNTP pool maintenance or ribonucleotide removal can cause Aicardi-Goutières syndrome or promote certain human cancers. Here, we hav...
Article
Full-text available
Ribonucleotides are frequently incorporated into DNA and can be used as a marker of DNA replication enzymology. To investigate on a genome-wide scale, how E. coli pol V accesses undamaged chromosomal DNA during the SOS response, we mapped the location of ribonucleotides incorporated by steric gate variants of pol V across the entire E. coli genome....
Article
Full-text available
Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA) although aberrant mtDNA rNMP content has been identified in disease models....
Preprint
Full-text available
MtDNA integrity is important for mitochondrial function. We analysed mtDNA over the course of mouse lifespan and found that its integrity, as measured by electrophoretic mobility under denaturing conditions, decreased significantly in old animals whereas its ribonucleotide (rNMP) content increased with age. To investigate whether the rNMPs incorpor...
Article
Full-text available
Human mitochondrial DNA (mtDNA) replication is first initiated at the origin of H-strand replication. The initiation depends on RNA primers generated by transcription from an upstream promoter (LSP). Here we reconstitute this process in vitro using purified transcription and replication factors. The majority of all transcription events from LSP are...
Article
Full-text available
DNA polymerase η (pol η) is best known for its ability to bypass UV-induced thymine–thymine (T–T) dimers and other bulky DNA lesions, but pol η also has other cellular roles. Here, we present evidence that pol η competes with DNA polymerases α and δ for the synthesis of the lagging strand genome-wide, where it also shows a preference for T–T in the...
Article
Full-text available
Sequencing of whole cancer genomes has revealed an abundance of recurrent mutations in gene-regulatory promoter regions, in particular in melanoma where strong mutation hotspots are observed adjacent to ETS-family transcription factor (TF) binding sites. While sometimes interpreted as functional driver events, these mutations are commonly believed...
Data
Mutational burden and overall mutational signature for 221 melanomas. (a) Number of mutations in each sample, color-coded for pyrimidine-based nucleotide substitution. (b) Mutation frequency of each substitution type in different trinucleotide contexts, normalized for genomic trinucleotide background frequencies. (PDF)
Data
TTCCG-related recurrent mutations occur primarily in promoters rather than enhancers. (a) The location of recurrent mutations in melanoma relative to nearby annotated enhancers (analogous to Fig 1a which shows the position relative to nearby TSSs), based on chromHMM segmentation of Roadmap epigenomic data (E6 and E7 regions; genic enhancers and enh...
Data
Recurrent TTCCG-related promoter mutations. 291 recurrent promoter mutations (+/- 500 bp from TSS), all mutated in at least 5/221 tumors and flanked by TTCCG elements (+/-10 bp sequence context). (XLSX)
Data
The nucleotide excision repair (NER) pathway, with mutated genes in the four repair-deficient cell lines (S1 Table) highlighted in red. (PDF)
Data
Oligonucleotide sequences for CPD-seq. Illumina P5 and P7 adapters are indicated underlined and italicized respectively, and indexes are shown in bold and underline. Oligo 5ʹ modifications are also indicated. All oligos were from Integrated DNA technologies (Coralville, IA). * indicates a phosphorothioate bond. /3Ammo/ indicates a 3' Amino Modifier...
Data
Numerical data underlying graphs. (XLSX)
Data
Cell lines with DNA repair deficiencies and their verified homozygous mutations. Genotypes were verified by whole genome sequencing. (PDF)
Preprint
Full-text available
Sequencing of whole cancer genomes has revealed an abundance of recurrent mutations in gene-regulatory promoter regions, in particular in melanoma where strong mutation hotspots are observed adjacent to ETS-family transcription factor (TF) binding sites. While sometimes interpreted as functional driver events, these mutations have also been suggest...
Chapter
Ribonucleotides embedded within DNA render the DNA sensitive to the formation of single-stranded breaks under alkali conditions. Here, we describe a next-generation sequencing method called hydrolytic end sequencing (HydEn-seq) to map ribonucleotides inserted into the genome of Saccharomyce cerevisiae strains deficient in ribonucleotide excision re...
Article
Full-text available
Established approaches to estimate the number of ribonucleotides present in a genome are limited to the quantitation of incorporated ribonucleotides using short synthetic DNA fragments or plasmids as templates and then extrapolating the results to the whole genome. Alternatively, the number of ribonucleotides present in a genome may be estimated us...
Article
Full-text available
Significance Mitochondria are essential for energy production. However, a number of defects that affect the cellular levels of deoxyribonucleoside triphosphates (dNTPs), the building blocks of DNA, threaten the proper maintenance of mitochondrial DNA (mtDNA) and lead to human disease. We show that imbalances in the total cellular dNTP pool are tran...
Article
Full-text available
Author summary Human mitochondria contain a small double-stranded DNA genome (mtDNA) of only 16,569 base pairs (bp) that encodes 13 essential subunits of the oxidative phosphorylation system. Depletion of mtDNA and different types of mtDNA mutations cause mitochondrial disease, and are also implicated in biological ageing. For almost half a century...
Data
Spearmans coefficient was calculated for H-strand (HS) and L-strand (LS) in HydEn-seq and 5´-End-seq libraries for mtDNA isolated from HeLa cells. (PDF)
Data
Summarized signal at HincII sites in mtDNA in L-strand (upper left panel), mtDNA in H-strand (lower left panel), nuclear DNA in top strand (upper right panel), nuclear DNA in bottom strand (lower right panel). (PDF)
Data
5´-End-seq and HydEn-seq results at OriH. (PDF)
Article
Deoxyribonucleoside kinases (dNKs) salvage deoxyribonucleosides (dNs) and catalyze the rate limiting step of this salvage pathway by converting dNs into corresponding monophosphate forms. These enzymes serve as an excellent model to study duplicated genes and their evolutionary history. So far, among vertebrates only four mammalian dNKs have been s...
Article
Full-text available
Ribonucleotides are incorporated into genomes by DNA polymerases, they can be removed, and if not removed, they can have deleterious and beneficial consequences. Here, we describe an assay to quantify stable ribonucleotide incorporation by DNA polymerases in vitro, and an assay to probe for ribonucleotides in each of the two DNA strands of the yeas...
Article
Full-text available
Ribonucleotides incorporated during DNA replication are removed by RNase H2-dependent ribonucleotide excision repair (RER). In RER-defective yeast, topoisomerase 1 (Top1) incises DNA at unrepaired ribonucleotides, initiating their removal, but this is accompanied by RNA-DNA-damage phenotypes. Here we show that these phenotypes are incurred by a hig...
Article
Full-text available
Mutational heterogeneity must be taken into account when reconstructing evolutionary histories, calibrating molecular clocks, and predicting links between genes and disease. Selective pressures and various DNA transactions have been invoked to explain the heterogeneous distribution of genetic variation between species, within populations, and in ti...
Article
Deoxyribonucleoside kinases phosphorylate deoxyribonucleosides into the corresponding 5'-monophosphate deoxyribonucleosides to supply the cell with nucleic acid precursors. In mitochondrial fractions of the model plant Arabidopsis thaliana, we detected deoxyadenosine and thymidine kinase activities, while the cytosol fraction contained six-fold low...
Article
Fruit fly (Drosophila melanogaster) deoxyribonucleoside kinase (DmdNK; EC: 2.7.1.145) was characterized for its substrate specificity towards natural and non-natural nucleosides, confirming its potential in the enzymatic synthesis of modified nucleotides. DmdNK was adsorbed on a solid ion exchange support (bearing primary amino groups) achieving an...
Article
To maintain genome stability, mismatch repair of nuclear DNA replication errors must be directed to the nascent strand, likely by DNA ends and PCNA. Here we show that the efficiency of mismatch repair in Saccharomyces cerevisiae is reduced by inactivating RNase H2, which nicks DNA containing ribonucleotides incorporated during replication. In strai...
Article
Thymidine kinase 1 (TK1) provides a crucial precursor, thymidine monophosphate (dTMP), for nucleic acid synthesis, and the activity of TK1 increases up to 200-fold during the S-phase of cell division in humans. An important part of the regulatory check-points is the ATP and enzyme concentration-dependent transition of TK1 from a dimer with low cata...
Article
Deoxyribonucleotides are the building blocks of DNA and can be synthesized via de novo and salvage pathways. Deoxyribonucleoside kinases (EC 2.7.1.145) salvage deoxyribonucleosides by transfer of a phosphate group to the 5′ of a deoxyribonucleoside. This salvage pathway is well characterized in mammals, but in contrast, little is known about how pl...
Article
We have investigated the ability of the 3' exonuclease activity of Saccharomyces cerevisiae DNA polymerase ɛ (Pol ɛ) to proofread newly inserted ribonucleotides (rNMPs). During DNA synthesis in vitro, Pol ɛ proofreads ribonucleotides with apparent efficiencies that vary from none at some locations to more than 90% at others, with rA and rU being mo...
Article
Deoxyribonucleoside kinases (dNKs) are essential in the mammalian cell but their 'importance' in bacteria, especially aquatic ones, is less clear. We studied two aquatic bacteria, Gram-negative Flavobacterium psychrophilum JIP02/86 and Polaribacter sp. MED152, for their ability to salvage deoxyribonucleosides (dNs). Both had a Gram-positive-type th...
Article
The gene encoding thymidine kinase 1 from tomato (toTK1) has in combination with azidothymidine (AZT) recently been proposed as a powerful suicide gene for anticancer gene therapy. The toTK1/AZT combination has been demonstrated to have several advantages for the treatment of glioblastomas because AZT can easily penetrate the blood-brain barrier an...
Article
In the Pasteurella multocida genome only one putative deoxyribonucleoside kinase encoding gene, for thymidine kinase 1 (PmTK1), was identified. The PmTK1 gene was sub-cloned into Escherichia coli KY895 and it sensitized the host towards 2',2'-difluoro-deoxycytidine (gemcitabine, dFdC), 3'-azido-thymidine (AZT) and 5-fluoro-deoxyuridine (5F-dU). PmT...
Article
Full-text available
The prognosis for malignant gliomas remains poor, and new treatments are urgently needed. Targeted suicide gene therapy exploits the enzymatic conversion of a prodrug, such as a nucleoside analog, into a cytotoxic compound. Although this therapeutic strategy has been considered a promising regimen for central nervous system (CNS) tumors, several ob...
Article
Transfer of deoxyribonucleoside kinases (dNKs) into cancer cells increases the activity of cytotoxic nucleoside analogues. It has been shown that bacterial dNKs, when introduced into Escherichia coli, sensitize this bacterium toward nucleoside analogues. We studied the possibility of using bacterial dNKs, for example deoxyadenosine kinases (dAKs),...
Article
Drosophila melanogaster multisubstrate deoxyribonucleoside kinase (Dm-dNK) can additionally sensitize human cancer cell lines towards the anti-cancer drug gemcitabine. We show that this property is based on the Dm-dNK ability to efficiently phosphorylate gemcitabine. The 2.2A resolution structure of Dm-dNK in complex with gemcitabine shows that the...
Article
Full-text available
Deoxyribonucleoside kinases catalyze the rate limiting step during the salvage of deoxyribonucleosides and convert them into the corresponding monophosphate compounds. We have identified and characterized a unique multisubstrate deoxyribonucleoside kinase from plants. The phylogenetic relationship and biochemical properties suggest that this deoxyr...
Article
Full-text available
To investigate the bactericidal activity of antiviral and anticancer nucleoside analogues against a variety of pathogenic bacteria and characterize the activating enzymes, deoxyribonucleoside kinases (dNKs). Several FDA-approved nucleoside analogue drugs were screened for their potential bactericidal activity against several clinical bacterial isol...
Article
Full-text available
Common bacterial pathogens are becoming progressively more resistant to traditional antibiotics, representing a major public-health crisis. Therefore, there is a need for a variety of antibiotics with alternative modes of action. In our study, several nucleoside analogs were tested against pathogenic staphylococci and streptococci. We show that pyr...
Article
Thymidine kinase (TK) is the key enzyme in salvaging thymidine to produce thymidine monophosphate. Owing to its ability to phosphorylate nucleoside analogue prodrugs, TK has gained attention as a rate-limiting drug activator. We describe the structures of two bacterial TKs, one from the pathogen Bacillus anthracis in complex with the substrate dT,...
Article
Thymidine kinases (TKs) appear to be almost ubiquitous and are found in nearly all prokaryotes, eukaryotes, and several viruses. They are the key enzymes in thymidine salvage and activation of several anti-cancer and antiviral drugs. We show that bacterial TKs can be subdivided into 2 groups. The TKs from Gram-positive bacteria are more closely rel...
Article
Twenty-six fully sequenced archaeal genomes were searched for genes coding for putative deoxyribonucleoside kinases (dNKs). We identified only 5 human-like thymidine kinase 1 genes (TK1s) and none for non-TK1 kinases. Four TK1s were identified in the Euryarchaea and one was found in the Crenarchaea, while none was found in Nanoarchaeum. The identif...

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Projects (3)
Project
There are many mutations in DNA polymerases in cancer patients. However, it is very difficult to understand the function of those mutations. We use a new method called Hyd-En seq to study DNA polymerases functions. Our study model is yeast.
Project
It is not easy to study DNA polymerases functions in vivo. One way is to use steric gate mutants of the enzymes to track ribonucleotides they misincorporate in the genome. In our project, we study SOS response, pol V and strand specificity of this enzyme during DNA replication.
Project
To track ribonucleotide incorporation as a marker of genome-wide DNA replication enzymology and map ribonucleotide incorporation in genomes under physiological relevant conditions.