Ewa P. Malc
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View article: A Case Study of Genomic Instability in an Industrial Strain of Saccharomyces cerevisiae
A Case Study of Genomic Instability in an Industrial Strain of Saccharomyces cerevisiae Open
The Saccharomyces cerevisiae strain JAY270/PE2 is a highly efficient biocatalyst used in the production of bioethanol from sugarcane feedstock. This strain is heterothallic and diploid, and its genome is characterized by abundant …
View article: Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements
Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements Open
Break induced replication (BIR) is a double strand break repair pathway that can promote genetic instabilities similar to those observed in cancer. Instead of a replication fork, BIR is driven by a migration bubble where asynchronous synth…
View article: Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation
Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation Open
A single cancer genome can harbor thousands of clustered mutations. Mutation signature analyses have revealed that the origin of clusters are lesions in long tracts of single-stranded (ss) DNA damaged by apolipoprotein B mRNA editing enzym…
View article: The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions
The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions Open
Three-methyl cytosine (3meC) are toxic DNA lesions, blocking base pairing. Bacteria and humans express members of the AlkB enzymes family, which directly remove 3meC. However, other organisms, including budding yeast, lack this class of en…
View article: Congenital Midline Cervical Cleft: First Report and Genetic Analysis of Two Related Patients
Congenital Midline Cervical Cleft: First Report and Genetic Analysis of Two Related Patients Open
OBJECTIVES: Congenital midline cervical cleft (CMCC) is a rare congenital anterior neck anatomical anomaly. We present the case of two related patients (grandchild and maternal grandmother) who were both born with a congenital midline cerv…
View article: Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages
Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages Open
Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromere DNA sequences are dive…
View article: Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina
Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina Open
Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsida…
View article: Characterization of systemic genomic instability in budding yeast
Characterization of systemic genomic instability in budding yeast Open
Conventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time. We characterized the occurrence of bursts of genome-wide loss-of-heterozygosity (LOH) …
View article: Corrigendum to “APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast” [DNA Repair 53 (2017) 4–14]
Corrigendum to “APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast” [DNA Repair 53 (2017) 4–14] Open
View article: APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast
APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast Open
View article: The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions
The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions Open
Three-methyl cytosine (3meC) are toxic DNA lesions, blocking base pairing. Bacteria and humans express members of the AlkB enzymes family, which directly remove 3meC. However, other organisms, including budding yeast, lack this class of en…
View article: Author response: The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions
Author response: The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions Open
View article: The Shu Complex Prevents Mutagenesis and Cytotoxicity of Single-Strand Specific Alkylation Lesions
The Shu Complex Prevents Mutagenesis and Cytotoxicity of Single-Strand Specific Alkylation Lesions Open
Three-methyl cytosine (3meC) are toxic DNA lesions, blocking base pairing. Bacteria and humans, express members of the AlkB enzymes family, which directly remove 3meC. However, other organisms, including budding yeast, lack this class of e…
View article: Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina
Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina Open
Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsida…
View article: Metabolic potential, ecology and presence of endohyphal bacteria is reflected in genomic diversity of Mucoromycotina
Metabolic potential, ecology and presence of endohyphal bacteria is reflected in genomic diversity of Mucoromycotina Open
We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e. Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e. U. isabellina, U. vinacea ), two s…
View article: Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath
Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath Open
A perfluorocarbon nanodroplet formulation is shown to be an effective cavitation enhancement agent, enabling rapid and consistent fragmentation of genomic DNA in a standard ultrasonic water bath. This nanodroplet-enhanced method produces g…
View article: Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation
Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation Open
Ribonucleotides are frequently incorporated into DNA during eukaryotic replication. Here we map the genome-wide distribution of these ribonucleotides as markers of replication enzymology in budding yeast, using a new 5′-DNA end-mapping met…
View article: Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions
Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions Open
Mutations are typically perceived as random, independent events. We describe here non-random clustered mutations in yeast and in human cancers. Genome sequencing of yeast grown under chronic alkylation damage identified mutation clusters t…
View article: An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers
An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers Open
Dmitry Gordenin and colleagues use a yeast reporter strain to identify distinct mutagenic signatures for the cytosine deaminases APOBEC3A and APOBEC3B. They find that cancer samples with APOBEC3A-like mutation signatures have greater than …
View article: Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition
Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition Open
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 invoke…
View article: Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma
Atypical UV Photoproducts Induce Non-canonical Mutation Classes Associated with Driver Mutations in Melanoma Open
Somatic mutations in skin cancers and other ultraviolet (UV)-exposed cells are typified by C>T and CC>TT substitutions at dipyrimidine sequences; however, many oncogenic "driver" mutations in melanoma do not fit this UV signature. Here, we…
View article: Break-Induced Replication Is a Source of Mutation Clusters Underlying Kataegis
Break-Induced Replication Is a Source of Mutation Clusters Underlying Kataegis Open
Clusters of simultaneous multiple mutations can be a source of rapid change during carcinogenesis and evolution. Such mutation clusters have been recently shown to originate from DNA damage within long single-strand (ss) DNA formed at rese…
View article: Characterization of systemic genomic instability in budding yeast
Characterization of systemic genomic instability in budding yeast Open
Significance Mutations are generally thought to accumulate independently and gradually over many generations. Here, we combined complementary experimental approaches in budding yeast to track the appearance of chromosomal changes resulting…
View article: Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma Open
View article: Characterization of systemic genomic instability in budding yeast
Characterization of systemic genomic instability in budding yeast Open
Conventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time. We characterized the occurrence of bursts of genome-wide loss-of-heterozygosity (LOH) …
View article: The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts
The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts Open
Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome is associated with aging and cancer. Understanding the impacts of these processes on mutagenesis is fundamental to understanding the etiology…
View article: Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity
Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity Open
DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape and contributes to mutagenesis is unknown. Here, we describe genome-wide maps of DNA …
View article: APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication
APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication Open
APOBEC family cytidine deaminases have been recently implicated as powerful mutators of cancer genomes. How APOBECs, which are ssDNA specific enzymes, gain access to chromosomal DNA is unclear. To ascertain the chromosomal ssDNA substrates…
View article: Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages
Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages Open
Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromere DNA sequences are dive…
View article: Correction: Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation
Correction: Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation Open
[This corrects the article DOI: 10.1371/journal.pbio.3000464.].