Research articles and scholarly works

You can search for our papers on PubMed as follows, but be aware that there are other “wilson te” authors even at Michigan!

Reverse transcriptase meets DNA, again: Possible roles for transposable elements in host DNA repair
Moran JV, Wilson TE
Cell 185(20):3643-3645 (2022)
Recent News
Retrotransposons are selfish genetic elements that encode an enzyme, reverse transcriptase (RT), which converts the element-encoded RNA into DNA prior to or during genomic integration. New studies provide compelling evidence that a bacterial group II intron-like RT has adapted enzymatic activities associated with RTs to function in host DNA repair....
svCapture: Efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing
Wilson TE, Ahmed S, Higgins J, Salk JJ, Glover TW
bioRxiv (2022)
Recent News
Error-corrected sequencing of genomic targets enriched by probe-based capture has become a standard approach for detecting single-nucleotide variants (SNVs) and small insertion/deletions (indels) present at very low variant allele frequencies. Less attention has been given to strategies for comparable detection of rare structural variant (SV) junctions, where different error mechanisms...
Bur1 functions with TORC1 for vacuole-mediated cell cycle progression
Jin Y, Jin N, Oikawa Y, Benyair R, Koizumi M, Wilson TE, Ohsumi Y, Weisman LS
EMBO Rep 23(4):e53477 (2022)
The vacuole/lysosome plays essential roles in the growth and proliferation of many eukaryotic cells via the activation of target of rapamycin complex 1 (TORC1). Moreover, the yeast vacuole/lysosome is necessary for progression of the cell division cycle, in part via signaling through the TORC1 pathway. Here, we show that an...
Mapping yeast mitotic 5' resection at base resolution reveals the sequence and positional dependence of nucleases in vivo
Bazzano D, Lomonaco S, Wilson TE
Nucleic Acids Res 49(22):12607-12621 (2021)
Recent News
Resection of the 5'-terminated strand at DNA double-strand breaks (DSBs) is the critical regulated step in the transition to homologous recombination. Recent studies have described a multi-step model of DSB resection where endonucleolytic cleavage mediated by Mre11 and Sae2 leads to further degradation mediated by redundant pathways catalyzed by Exo1...
Locus-specific transcription silencing at the FHIT gene suppresses replication stress-induced copy number variant formation and associated replication delay
Park SH, Bennett-Baker P, Ahmed S, Arlt MF, Ljungman M, Glover TW, Wilson TE
Nucleic Acids Res 49(13):7507-7524 (2021)
Recent News
Impaired replication progression leads to de novo copy number variant (CNV) formation at common fragile sites (CFSs). We previously showed that these hotspots for genome instability reside in late-replicating domains associated with large transcribed genes and provided indirect evidence that transcription is a factor in their instability. Here, we compared...
Co-transcriptional splicing efficiencies differ within genes and between cell types
Bedi K, Magnuson BR, Narayanan I, Paulsen M, Wilson TE, Ljungman M
RNA 27(7):829-40 (2021)
Pre-mRNA splicing is carried out by the spliceosome and involves splice site recognition, removal of introns, and ligation of exons. Components of the spliceosome have been shown to interact with the elongating RNA polymerase II (RNAPII) which is thought to allow splicing to occur concurrently with transcription. However, little is...
Multiple metabolic signals including AMPK and PKA regulate glucose-stimulated double strand break resection in yeast
Lomonaco S, Bazzano D, Wilson TE
bioRxiv (2021)
Twin peaks: finding fragile sites with MiDAS-seq
Glover TW, Wilson TE
Cell Res 30(11):944-945 (2020)
Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing
Bedi K, Paulsen MT, Wilson TE, Ljungman M
NAR Genom Bioinform 2(1):lqz014 (2020)
MicroRNAs (miRNAs) are key contributors to gene regulatory networks. Because miRNAs are processed from RNA polymerase II transcripts, insight into miRNA regulation requires a comprehensive understanding of the regulation of primary miRNA transcripts. We used Bru-seq nascent RNA sequencing and hidden Markov model segmentation to map primary miRNA transcription units...
Double-strand breaks in motion: implications for chromosomal rearrangement
Wilson TE, Sunder S
Curr Genet 66(1):1-6 (2020)
DNA double-strand breaks (DSBs) must be rejoined properly to prevent the occurrence of serious genomic rearrangements associated with many human diseases. Non-homologous end joining (NHEJ) is a DSB repair mechanism known to protect genomic integrity that is also implicated in creating genomic translocations, inversions, deletions, and insertions. We recently investigated...
Frequency of DNA end joining in trans is not determined by the predamage spatial proximity of double-strand breaks in yeast
Sunder S, Wilson TE
Proc Natl Acad Sci U S A 116(19):9481-9490 (2019)
DNA double-strand breaks (DSBs) are serious genomic insults that can lead to chromosomal rearrangements if repaired incorrectly. To gain insight into the nuclear mechanisms contributing to these rearrangements, we developed an assay in yeast to measure cis (same site) vs. trans (different site) repair for the majority process of precise...
Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication
Flasch DA, Macia Á, Sánchez L, Ljungman M, Heras SR, García-Pérez JL, Wilson TE, Moran JV
Cell 177(4):837-851.e28 (2019)
L1 retrotransposon-derived sequences comprise approximately 17% of the human genome. Darwinian selective pressures alter L1 genomic distributions during evolution, confounding the ability to determine initial L1 integration preferences. Here, we generated high-confidence datasets of greater than 88,000 engineered L1 insertions in human cell lines that act as proxies for cells...
Identification of Suppressor of Clathrin Deficiency-1 (SCD1) and Its Connection to Clathrin-Mediated Endocytosis in Saccharomyces cerevisiae
Moorthy BT, Sharma A, Boettner DR, Wilson TE, Lemmon SK
G3 (Bethesda) 9(3):867-877 (2019)
Clathrin is a major coat protein involved in vesicle formation during endocytosis and transport in the endosomal/trans Golgi system. Clathrin is required for normal growth of yeast (Saccharomyces cerevisiae) and in some genetic backgrounds deletion of the clathrin heavy chain gene (CHC1) is lethal. Our lab defined a locus referred...
Effects of hydroxyurea on CNV induction in the mouse germline
Arlt MF, Rajendran S, Holmes SN, Wang K, Bergin IL, Ahmed S, Wilson TE, Glover TW
Environ Mol Mutagen 59(8):698-714 (2018)
Copy number variants (CNVs) are important in genome variation and genetic disease, with new mutations arising frequently in the germline and somatic cells. Replication stress caused by aphidicolin and hydroxyurea (HU) is a potent inducer of de novo CNVs in cultured mammalian cells. HU is used extensively for long-term management...
Fragile sites in cancer: more than meets the eye
Glover TW, Wilson TE, Arlt MF
Nat Rev Cancer 17(8):489-501 (2017)
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not...
Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53
Venkata Narayanan I, Paulsen MT, Bedi K, Berg N, Ljungman EA, Francia S, Veloso A, Magnuson B, di Fagagna FD, Wilson TE, Ljungman M
Sci Rep 7:43598 (2017)
In response to ionizing radiation (IR), cells activate a DNA damage response (DDR) pathway to re-program gene expression. Previous studies using total cellular RNA analyses have shown that the stress kinase ATM and the transcription factor p53 are integral components required for induction of IR-induced gene expression. These studies did...
Mechanisms of glycosylase induced genomic instability
Eyler DE, Burnham KA, Wilson TE, O'Brien PJ
PLoS One 12(3):e0174041 (2017)
Human alkyladenine DNA glycosylase (AAG) initiates base excision repair (BER) to guard against mutations by excising alkylated and deaminated purines. Counterintuitively, increased expression of AAG has been implicated in increased rates of spontaneous mutation in microsatellite repeats. This microsatellite mutator phenotype is consistent with a model in which AAG excises...
Molecular biology: Breaks in the brain
Glover TW, Wilson TE
Nature 532(7597):46-7 (2016)
Overhang polarity of chromosomal double-strand breaks impacts kinetics and fidelity of yeast non-homologous end joining
Liang Z, Sunder S, Nallasivam S, Wilson TE
Nucleic Acids Res 44(6):2769-81 (2016)
Non-homologous end joining (NHEJ) is the main repair pathway for DNA double-strand breaks (DSBs) in cells with limited 5' resection. To better understand how overhang polarity of chromosomal DSBs affects NHEJ, we made site-specific 5'-overhanging DSBs (5' DSBs) in yeast using an optimized zinc finger nuclease at an efficiency that...
Identifying transcription start sites and active enhancer elements using BruUV-seq
Magnuson B, Veloso A, Kirkconnell KS, de Andrade Lima LC, Paulsen MT, Ljungman EA, Bedi K, Prasad J, Wilson TE, Ljungman M
Sci Rep 5:17978 (2015)
BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the...
Large transcription units unify copy number variants and common fragile sites arising under replication stress
Wilson TE, Arlt MF, Park SH, Rajendran S, Paulsen M, Ljungman M, Glover TW
Genome Res 25(2):189-200 (2015)
Copy number variants (CNVs) resulting from genomic deletions and duplications and common fragile sites (CFSs) seen as breaks on metaphase chromosomes are distinct forms of structural chromosome instability precipitated by replication inhibition. Although they share a common induction mechanism, it is not known how CNVs and CFSs are related or...
Yeast DNA ligase IV mutations reveal a nonhomologous end joining function of BRCT1 distinct from XRCC4/Lif1 binding
Chiruvella KK, Renard BM, Birkeland SR, Sunder S, Liang Z, Wilson TE
DNA Repair (Amst) 24:37-45 (2014)
LIG4/Dnl4 is the DNA ligase that (re)joins DNA double-strand breaks (DSBs) via nonhomologous end joining (NHEJ), an activity supported by binding of its tandem BRCT domains to the ligase accessory protein XRCC4/Lif1. We screened a panel of 88 distinct ligase mutants to explore the structure–function relationships of the yeast Dnl4...
Pooled segregant sequencing reveals genetic determinants of yeast pseudohyphal growth
Song Q, Johnson C, Wilson TE, Kumar A
PLoS Genet 10(8):e1004570 (2014)
The pseudohyphal growth response is a dramatic morphological transition and presumed foraging mechanism wherein yeast cells form invasive and surface-spread multicellular filaments. Pseudohyphal growth has been studied extensively as a model of conserved signaling pathways controlling stress responses, cell morphogenesis, and fungal virulence in pathogenic fungi. The genetic contribution to...
Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications
Veloso A, Kirkconnell KS, Magnuson B, Biewen B, Paulsen MT, Wilson TE, Ljungman M
Genome Res 24(6):896-905 (2014)
The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-ß-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 individual genes in human cells....
Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA
Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Magnuson B, Wilson TE, Ljungman M
Methods 67(1):45-54 (2014)
Gene expression studies commonly examine total cellular RNA, which only provides information about its steady-state pool of RNA. It remains unclear whether differences in the steady-state reflects variable rates of transcription or RNA degradation. To specifically monitor RNA synthesis and degradation genome-wide, we developed Bru-Seq and BruChase-Seq. These assays are...
Release from myosin V via regulated recruitment of an E3 ubiquitin ligase controls organelle localization
Yau RG, Peng Y, Valiathan RR, Birkeland SR, Wilson TE, Weisman LS
Dev Cell 28(5):520-33 (2014)
Molecular motors transport organelles to specific subcellular locations. Upon arrival at their correct locations, motors release organelles via unknown mechanisms. The yeast myosin V, Myo2, binds the vacuole-specific adaptor Vac17 to transport the vacuole from the mother cell to the bud. Here, we show that vacuole detachment from Myo2 occurs...
Copy number variants are produced in response to low-dose ionizing radiation in cultured cells
Arlt MF, Rajendran S, Birkeland SR, Wilson TE, Glover TW
Environ Mol Mutagen 55(2):103-13 (2014)
Despite their importance to human genetic variation and disease, little is known about the molecular mechanisms and environmental risk factors that impact copy number variant (CNV) formation. While it is clear that replication stress can lead to de novo CNVs, for example, following treatment of cultured mammalian cells with aphidicolin...
Saccharomyces cerevisiae DNA ligase IV supports imprecise end joining independently of its catalytic activity
Chiruvella KK, Liang Z, Birkeland SR, Basrur V, Wilson TE
PLoS Genet 9(6):e1003599 (2013)
DNA ligase IV (Dnl4 in budding yeast) is a specialized ligase used in non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Although point and truncation mutations arise in the human ligase IV syndrome, the roles of Dnl4 in DSB repair have mainly been examined using gene deletions. Here, Dnl4...
Repair of double-strand breaks by end joining
Chiruvella KK, Liang Z, Wilson TE
Cold Spring Harb Perspect Biol 5(5):a012757 (2013)
Nonhomologous end joining (NHEJ) refers to a set of genome maintenance pathways in which two DNA double-strand break (DSB) ends are (re)joined by apposition, processing, and ligation without the use of extended homology to guide repair. Canonical NHEJ (c-NHEJ) is a well-defined pathway with clear roles in protecting the integrity...
Building on the past, shaping the future: the Environmental Mutagenesis and Genomics Society
Wilson TE, DeMarini DM, Dertinger SD, Engelward BP, Hanawalt PC, MacGregor JT, Smith-Roe SL, Witt KL, Yauk CL, Ljungman M, Schwartz JL, Klein CB
Environ Mol Mutagen 54(3):153-7 (2013)
In late 2012, the members of the Environmental Mutagen Society voted to change its name to the Environmental Mutagenesis and Genomics Society. Here, we describe the thought process that led to adoption of the new name, which both respects the rich history of a Society founded in 1969 and reflects...
Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia
Velusamy T, Palanisamy N, Kalyana-Sundaram S, Sahasrabuddhe AA, Maher CA, Robinson DR, Bahler DW, Cornell TT, Wilson TE, Lim MS, Chinnaiyan AM, Elenitoba-Johnson KS
Proc Natl Acad Sci U S A 110(8):3035-40 (2013)
Chronic lymphocytic leukemia (CLL) is the most common form of leukemia in adults in the Western hemisphere. Tumor-specific chromosomal translocations, characteristic findings in several human malignancies that directly lead to malignant transformation, have not been identified in CLL. Using paired-end transcriptome sequencing, we identified recurrent and reciprocal RNA chimeras involving...
Breaking news on fragile sites in cancer
Glover TW, Wilson TE
Cancer Cell 23(2):137-9 (2013)
Chromosome rearrangements in B lymphocytes can be initiated by AID-associated double strand breaks (DSBs), with others arising by unclear mechanisms. A recent study by Barlow and colleagues in Cell reports on genomic regions, termed early replicating fragile sites, that may explain many AID-independent DSBs and creates a compelling link between...
Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response
Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Tsan YC, Chang CW, Tarrier B, Washburn JG, Lyons R, Robinson DR, Kumar-Sinha C, Wilson TE, Ljungman M
Proc Natl Acad Sci U S A 110(6):2240-5 (2013)
Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, micro RNAs (miRNAs), and RNA-binding proteins. Here, we present bromouride labeling and sequencing (Bru-Seq) and bromouridine pulse-chase and sequencing (BruChase-Seq) to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at...
Genome-wide transcriptional effects of the anti-cancer agent camptothecin
Veloso A, Biewen B, Paulsen MT, Berg N, Carmo de Andrade Lima L, Prasad J, Bedi K, Magnuson B, Wilson TE, Ljungman M
PLoS One 8(10):e78190 (2013)
The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a "cleavable complex". To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment primarily affected transcription elongation. We also observed that camptothecin increased RNA...
Harnessing genomics to identify environmental determinants of heritable disease
Yauk CL, Lucas Argueso J, Auerbach SS, Awadalla P, Davis SR, DeMarini DM, Douglas GR, Dubrova YE, Elespuru RK, Glover TW, Hales BF, Hurles ME, Klein CB, Lupski JR, Manchester DK, Marchetti F, Montpetit A, Mulvihill JJ, Robaire B, Robbins WA, Rouleau GA, Shaughnessy DT, Somers CM, Taylor JG 6th, Trasler J, Waters MD, Wilson TE, Witt KL, Bishop JB
Mutat Res 752(1):6-9 (2013)
Next-generation sequencing technologies can now be used to directly measure heritable de novo DNA sequence mutations in humans. However, these techniques have not been used to examine environmental factors that induce such mutations and their associated diseases. To address this issue, a working group on environmentally induced germline mutation analysis...
De novo CNV formation in mouse embryonic stem cells occurs in the absence of Xrcc4-dependent nonhomologous end joining
Arlt MF, Rajendran S, Birkeland SR, Wilson TE, Glover TW
PLoS Genet 8(9):e1002981 (2012)
Spontaneous copy number variant (CNV) mutations are an important factor in genomic structural variation, genomic disorders, and cancer. A major class of CNVs, termed nonrecurrent CNVs, is thought to arise by nonhomologous DNA repair mechanisms due to the presence of short microhomologies, blunt ends, or short insertions at junctions of...
Replication stress and mechanisms of CNV formation
Arlt MF, Wilson TE, Glover TW
Curr Opin Genet Dev 22(3):204-10 (2012)
Copy number variants (CNVs) are widely distributed throughout the human genome, where they contribute to genetic variation and phenotypic diversity. De novo CNVs are also a major cause of numerous genetic and developmental disorders. However, unlike many other types of mutations, little is known about the genetic and environmental risk...
A recurrent loss-of-function alanyl-tRNA synthetase (AARS) mutation in patients with Charcot-Marie-Tooth disease type 2N (CMT2N)
McLaughlin HM, Sakaguchi R, Giblin W, Wilson TE, Biesecker L, Lupski JR, Talbot K, Vance JM, Züchner S, Lee YC, Kennerson M, Hou YM, Nicholson G, Antonellis A
Hum Mutat 33(1):244-53 (2012)
Charcot-Marie-Tooth (CMT) disease comprises a heterogeneous group of peripheral neuropathies characterized by muscle weakness and wasting, and impaired sensation in the extremities. Four genes encoding an aminoacyl-tRNA synthetase (ARS) have been implicated in CMT disease. ARSs are ubiquitously expressed, essential enzymes that ligate amino acids to cognate tRNA molecules. Recently,...
Hydroxyurea induces de novo copy number variants in human cells
Arlt MF, Ozdemir AC, Birkeland SR, Wilson TE, Glover TW
Proc Natl Acad Sci U S A 108(42):17360-5 (2011)
Copy number variants (CNVs) are widely distributed throughout the human genome, where they contribute to genetic variation and phenotypic diversity. Spontaneous CNVs are also a major cause of genetic and developmental disorders and arise frequently in cancer cells. As with all mutation classes, genetic and environmental factors almost certainly increase...
Comparison of constitutional and replication stress-induced genome structural variation by SNP array and mate-pair sequencing
Arlt MF, Ozdemir AC, Birkeland SR, Lyons RH Jr, Glover TW, Wilson TE
Genetics 187(3):675-83 (2011)
Copy-number variants (CNVs) are a major source of genetic variation in human health and disease. Previous studies have implicated replication stress as a causative factor in CNV formation. However, existing data are technically limited in the quality of comparisons that can be made between human CNVs and experimentally induced variants....
Discovery of mutations in Saccharomyces cerevisiae by pooled linkage analysis and whole-genome sequencing
Birkeland SR, Jin N, Ozdemir AC, Lyons RH Jr, Weisman LS, Wilson TE
Genetics 186(4):1127-37 (2010)
Many novel and important mutations arise in model organisms and human patients that can be difficult or impossible to identify using standard genetic approaches, especially for complex traits. Working with a previously uncharacterized dominant Saccharomyces cerevisiae mutant with impaired vacuole inheritance, we developed a pooled linkage strategy based on next-generation...
Compound heterozygosity for loss-of-function lysyl-tRNA synthetase mutations in a patient with peripheral neuropathy
McLaughlin HM, Sakaguchi R, Liu C, Igarashi T, Pehlivan D, Chu K, Iyer R, Cruz P, Cherukuri PF, Hansen NF, Mullikin JC, Biesecker LG, Wilson TE, Ionasescu V, Nicholson G, Searby C, Talbot K, Vance JM, Züchner S, Szigeti K, Lupski JR, Hou YM, Green ED, Antonellis A
Am J Hum Genet 87(4):560-6 (2010)
Charcot-Marie-Tooth (CMT) disease comprises a genetically and clinically heterogeneous group of peripheral nerve disorders characterized by impaired distal motor and sensory function. Mutations in three genes encoding aminoacyl-tRNA synthetases (ARSs) have been implicated in CMT disease primarily associated with an axonal pathology. ARSs are ubiquitously expressed, essential enzymes responsible for...
Regulation of the copper chaperone CCS by XIAP-mediated ubiquitination
Brady GF, Galbán S, Liu X, Basrur V, Gitlin JD, Elenitoba-Johnson KS, Wilson TE, Duckett CS
Mol Cell Biol 30(8):1923-36 (2010)
In order to balance the cellular requirements for copper with its toxic properties, an elegant set of mechanisms has evolved to regulate and buffer intracellular copper. The X-linked inhibitor of apoptosis (XIAP) protein was recently identified as a copper-binding protein and regulator of copper homeostasis, although the mechanism by which...
MLH1 deficiency enhances tumor cell sensitivity to ganciclovir
O'Konek JJ, Boucher PD, Iacco AA, Wilson TE, Shewach DS
Cancer Gene Ther 16(9):683-92 (2009)
Suicide gene therapy with herpes simplex virus thymidine kinase (HSV-TK) and ganciclovir (GCV) is notable for producing multi-log cytotoxicity in a unique pattern of delayed cytotoxicity in S-phase. As hydroxyurea, a ribonucleotide reductase inhibitor that activates mismatch repair, can increase sensitivity to GCV, we evaluated the role of MLH1, an...
Recruitment of Saccharomyces cerevisiae Dnl4-Lif1 complex to a double-strand break requires interactions with Yku80 and the Xrs2 FHA domain
Palmbos PL, Wu D, Daley JM, Wilson TE
Genetics 180(4):1809-19 (2008)
Nonhomologous end joining (NHEJ) in yeast depends on eight different proteins in at least three different functional complexes: Yku70-Yku80 (Ku), Dnl4-Lif1-Nej1 (DNA ligase IV), and Mre11-Rad50-Xrs2 (MRX). Interactions between these complexes at DNA double-strand breaks (DSBs) are poorly understood but critical for the completion of repair. We previously identified two...
Recruitment and dissociation of nonhomologous end joining proteins at a DNA double-strand break in Saccharomyces cerevisiae
Wu D, Topper LM, Wilson TE
Genetics 178(3):1237-49 (2008)
Nonhomologous end joining (NHEJ) is an important DNA double-strand-break (DSB) repair pathway that requires three protein complexes in Saccharomyces cerevisiae: the Ku heterodimer (Yku70-Yku80), MRX (Mre11-Rad50-Xrs2), and DNA ligase IV (Dnl4-Lif1), as well as the ligase-associated protein Nej1. Here we use chromatin immunoprecipitation from yeast to dissect the recruitment and...
Evidence that base stacking potential in annealed 3' overhangs determines polymerase utilization in yeast nonhomologous end joining
Daley JM, Wilson TE
DNA Repair (Amst) 7(1):67-76 (2008)
Nonhomologous end joining (NHEJ) directly rejoins DNA double-strand breaks (DSBs) when recombination is not possible. In Saccharomyces cerevisiae, the DNA polymerase Pol4 is required for gap filling when a short 3' overhang must prime DNA synthesis. Here, we examined further end variations to test specific hypotheses regarding Pol4 usage in...
Modes of interaction among yeast Nej1, Lif1 and Dnl4 proteins and comparison to human XLF, XRCC4 and Lig4
Deshpande RA, Wilson TE
DNA Repair (Amst) 6(10):1507-16 (2007)
The nonhomologous end joining (NHEJ) pathway of double-strand break repair depends on DNA ligase IV and its interacting partner protein XRCC4 (Lif1 in yeast). A third yeast protein, Nej1, interacts with Lif1 and supports NHEJ, similar to the distantly related mammalian Nej1 orthologue XLF (also known as Cernunnos). XRCC4/Lif1 and...
Increased recombination between active tRNA genes
Pratt-Hyatt MJ, Kapadia KM, Wilson TE, Engelke DR
DNA Cell Biol 25(6):359-64 (2006)
Transfer RNA genes are distributed throughout eukaryotic genomes, and are frequently found as multicopy families. In Saccharomyces cerevisiae, tRNA gene transcription by RNA polymerase III suppresses nearby transcription by RNA polymerase II, partially because the tRNA genes are clustered near the nucleolus. We have tested whether active transcription of tRNA...
Mutations of the Yku80 C terminus and Xrs2 FHA domain specifically block yeast nonhomologous end joining
Palmbos PL, Daley JM, Wilson TE
Mol Cell Biol 25(24):10782-90 (2005)
The nonhomologous end-joining (NHEJ) pathway of DNA double-strand break repair requires three protein complexes in Saccharomyces cerevisiae: MRX (Mre11-Rad50-Xrs2), Ku (Ku70-Ku80), and DNA ligase IV (Dnl4-Lif1-Nej1). Much is known about the interactions that mediate the formation of each complex, but little is known about how they act together during repair....
DNA joint dependence of pol X family polymerase action in nonhomologous end joining
Daley JM, Laan RL, Suresh A, Wilson TE
J Biol Chem 280(32):29030-7 (2005)
DNA double strand breaks (DSBs) can be rejoined directly by the nonhomologous end-joining (NHEJ) pathway of repair. Nucleases and polymerases are required to promote accurate NHEJ when the terminal bases of the DSB are damaged. The same enzymes also participate in imprecise rejoining and joining of incompatible ends, important mutagenic...
Abrogation of the Chk1-Pds1 checkpoint leads to tolerance of persistent single-strand breaks in Saccharomyces cerevisiae
Karumbati AS, Wilson TE
Genetics 169(4):1833-44 (2005)
In budding yeast, Apn1, Apn2, Tpp1, and Rad1/Rad10 are important enzymes in the removal of spontaneous DNA lesions. apn1 apn2 rad1 yeast are inviable due to accumulation of abasic sites and strand breaks with 3' blocking lesions. We found that tpp1 apn1 rad1 yeast exhibited slow growth but frequently gave...
Rejoining of DNA double-strand breaks as a function of overhang length
Daley JM, Wilson TE
Mol Cell Biol 25(3):896-906 (2005)
The ends of spontaneously occurring double-strand breaks (DSBs) may contain various lengths of single-stranded DNA, blocking lesions, and gaps and flaps generated by end annealing. To investigate the processing of such structures, we developed an assay in which annealed oligonucleotides are ligated onto the ends of a linearized plasmid which...
Nonhomologous end joining in yeast
Daley JM, Palmbos PL, Wu D, Wilson TE
Annu Rev Genet 39:431-51 (2005)
Nonhomologous end joining (NHEJ), the direct rejoining of DNA double-strand breaks, is closely associated with illegitimate recombination and chromosomal rearrangement. This has led to the concept that NHEJ is error prone. Studies with the yeast Saccharomyces cerevisiae have revealed that this model eukaryote has a classical NHEJ pathway dependent on...
Identification of DNA 3'-phosphatase active site residues and their differential role in DNA binding, Mg2+ coordination, and catalysis
Deshpande RA, Wilson TE
Biochemistry 43(26):8579-89 (2004)
DNA 3'-phosphatase (Tpp1) from Saccharomyces cerevisiae, a homologue of human polynucleotide kinase/3'-phosphatase, has been shown to participate in DNA damage repair by removing 3'-phosphate blocking lesions. Tpp1 shows similarity to the l-2-haloacid dehalogenase superfamily of enzymes. By comparison to phosphoserine phosphatase, a well-studied member of this family, we designed conservative...
The role of yeast DNA 3'-phosphatase Tpp1 and rad1/Rad10 endonuclease in processing spontaneous and induced base lesions
Karumbati AS, Deshpande RA, Jilani A, Vance JR, Ramotar D, Wilson TE
J Biol Chem 278(33):31434-43 (2003)
Tpp1 is a DNA 3'-phosphatase in Saccharomyces cerevisiae that is believed to act during strand break repair. It is homologous to one domain of mammalian polynucleotide kinase/3'-phosphatase. Unlike in yeast, we found that Tpp1 could confer resistance to methylmethane sulfonate when expressed in bacteria that lack abasic endonuclease/3'-phosphodiesterase function. This...
Non-homologous end-joining: bacteria join the chromosome breakdance
Wilson TE, Topper LM, Palmbos PL
Trends Biochem Sci 28(2):62-6 (2003)
The repair of DNA double-strand breaks by non-homologous end-joining (NHEJ) has long been thought to be restricted to eukaryotes. However, recent papers document the existence of operons encoding functional NHEJ complexes in some bacteria. These findings provide new evolutionary insights into the core biochemistry of this repair pathway, and suggest...
A genomics-based screen for yeast mutants with an altered recombination/end-joining repair ratio
Wilson TE
Genetics 162(2):677-88 (2002)
We recently described a yeast assay suitable for genetic screening in which simple religation nonhomologous end-joining (NHEJ) and single-strand annealing (SSA) compete for repair of an I-SceI-created double-strand break. Here, the required allele has been introduced into an array of 4781 MATa deletion mutants and each strain screened individually. Two...
Enhancement of Saccharomyces cerevisiae end-joining efficiency by cell growth stage but not by impairment of recombination
Karathanasis E, Wilson TE
Genetics 161(3):1015-27 (2002)
Cells can repair DNA double-strand breaks by both homologous and nonhomologous mechanisms. To explore the basis of pathway utilization, we developed both plasmid and chromosomal yeast repair assays in which breaks are created with restriction endonucleases so that nonhomologous end-joining (NHEJ) competes with the single-strand annealing (SSA) recombination pathway, which...
Repair of DNA strand breaks by the overlapping functions of lesion-specific and non-lesion-specific DNA 3' phosphatases
Vance JR, Wilson TE
Mol Cell Biol 21(21):7191-8 (2001)
In Saccharomyces cerevisiae, the apurinic/apyrimidinic (AP) endonucleases Apn1 and Apn2 act as alternative pathways for the removal of various 3'-terminal blocking lesions from DNA strand breaks and in the repair of abasic sites, which both result from oxidative DNA damage. Here we demonstrate that Tpp1, a homologue of the 3'...
Uncoupling of 3'-phosphatase and 5'-kinase functions in budding yeast. Characterization of Saccharomyces cerevisiae DNA 3'-phosphatase (TPP1)
Vance JR, Wilson TE
J Biol Chem 276(18):15073-81 (2001)
Polynucleotide kinase is a bifunctional enzyme containing both DNA 3'-phosphatase and 5'-kinase activities seemingly suited to the coupled repair of single-strand nicks in which the phosphate has remained with the 3'-base. We show that the yeast Saccharomyces cerevisiae is able to repair transformed dephosphorylated linear plasmids by non-homologous end joining...