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Telomeres are guardians of chromosomal integrity

Evelina Y Basenko
2013 Postdoc Journal  
In yeast, t-circles can be produced due to mutations in telomere-binding proteins and destabilization of telomeres and serve as templates in extensive telomere lengthening events (Basenko, Cesare et al  ... 
doi:10.14304/surya.jpr.v1n1.9 fatcat:yxblvdncmncgtesrp3lze44qji

EuPathDB: The Eukaryotic Pathogen Genomics Database Resource [chapter]

Susanne Warrenfeltz, Evelina Y. Basenko, Kathryn Crouch, Omar S. Harb, Jessica C. Kissinger, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco
2018 Msphere  
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are
more » ... with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polyso-mal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data.
doi:10.1007/978-1-4939-7737-6_5 pmid:29761457 fatcat:c6zfevdra5c7xn7f3qozklsy6i

Histone H1 limits DNA methylation in Neurospora crassa [article]

Michael Seymour, Lexiang Ji, Alex M Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y Basenko, Robert J Schmitz, Xiaoyu Zhang, Zachary A Lewis
2016 bioRxiv   pre-print
token=edunyawudnqntwr&acc=GS E76982) and #GSE70518 (Basenko et al. 2016) .  ...  Methylated regions in wild type were defined previously (Basenko et al. 2016) .  ... 
doi:10.1101/041285 fatcat:k7ndc66v75c2tejbvjow725rha

Histone H1 Limits DNA Methylation in Neurospora crassa

Michael Seymour, Lexiang Ji, Alex M. Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y. Basenko, Robert J. Schmitz, Xiaoyu Zhang, Zachary A. Lewis
2016 G3: Genes, Genomes, Genetics  
Methylated regions in the wild-type were defined previously (Basenko et al. 2016) .  ...  The percentage of total shared methylated sites (y-axis) vs. the level of methylation at individual cytosines (x-axis) is shown. (Bednar et al. 2016) .  ... 
doi:10.1534/g3.116.028324 pmid:27172195 pmcid:PMC4938642 fatcat:suhyghzbzfblblwr53eczzwpwe

Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination

Evelina Y. Basenko, Anthony J. Cesare, Shilpa Iyer, Jack D. Griffith, Michael J. McEachern
2009 Nucleic Acids Research  
Basenko and M. McEachern, unpublished data). It is quite possible that the proportion of single-stranded t-circles may also be naturally variable.  ... 
doi:10.1093/nar/gkp814 pmid:19858100 pmcid:PMC2800209 fatcat:mktr4h5hnrdtzeckjk3r26ezau

The LSH/DDM1 Homolog MUS-30 Is Required for Genome Stability, but Not for DNA Methylation in Neurospora crassa

Evelina Y. Basenko, Masayuki Kamei, Lexiang Ji, Robert J. Schmitz, Zachary A. Lewis, Gregory P. Copenhaver
2016 PLoS Genetics  
LSH/DDM1 enzymes are required for DNA methylation in higher eukaryotes and have poorly defined roles in genome maintenance in yeast, plants, and animals. The filamentous fungus Neurospora crassa is a tractable system that encodes a single LSH/DDM1 homolog (NCU06306). We report that the Neurospora LSH/DDM1 enzyme is encoded by mutagen sensitive-30 (mus-30), a locus identified in a genetic screen over 25 years ago. We show that MUS-30-deficient cells have normal DNA methylation, but are
more » ... tive to DNA damaging agents. MUS-30 is a nuclear protein, consistent with its predicted role as a chromatin remodeling enzyme, and levels of MUS-30 are increased following DNA damage. MUS-30 co-purifies with Neurospora WDR76, a homolog of yeast Changed Mutation Rate-1 and mammalian WD40 repeat domain 76. Deletion of wdr76 rescued DNA damagehypersensitivity of Δmus-30 strains, demonstrating that the MUS-30-WDR76 interaction is functionally important. DNA damage-sensitivity of Δmus-30 is partially suppressed by deletion of methyl adenine glycosylase-1, a component of the base excision repair machinery (BER); however, the rate of BER is not affected in Δmus-30 strains. We found that MUS-30deficient cells are not defective for DSB repair, and we observed a negative genetic interaction between Δmus-30 and Δmei-3, the Neurospora RAD51 homolog required for homologous recombination. Together, our findings suggest that MUS-30, an LSH/DDM1 homolog, is required to prevent DNA damage arising from toxic base excision repair intermediates. Overall, our study provides important new information about the functions of the LSH/DDM1 family of enzymes. Author Summary Inside cells, eukaryotic DNA exists in a highly packaged structure called chromatin. Chromatin packaging often inhibits enzymes that need to access the genetic information. It is therefore important for cells to regulate chromatin structure so that the genome can PLOS Genetics |
doi:10.1371/journal.pgen.1005790 pmid:26771905 pmcid:PMC4714748 fatcat:v2gofnuhbbbxhhxe3chmutvsuy

Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth

Evelina Y. Basenko, Takahiko Sasaki, Lexiang Ji, Cameron J. Prybol, Rachel M. Burckhardt, Robert J. Schmitz, Zachary A. Lewis
2015 Proceedings of the National Academy of Sciences of the United States of America  
E6346 | www.pnas.org/cgi/doi/10.1073/pnas.1511377112 Basenko et al. E6348 | www.pnas.org/cgi/doi/10.1073/pnas.1511377112Basenko et al.  ...  (A) The y axis shows relative ChIP-seq enrichment across the entire LGVII (x axis; Top) and across a ∼250-kb region (800-1,050 kb; Bottom) for H3K9me3 and H3K27me3 in wild type and for H3K27me3 in the  ... 
doi:10.1073/pnas.1511377112 pmid:26578794 pmcid:PMC4655558 fatcat:5ok5mvjfc5bblf55jlisvhchfe

EuPathDB: the eukaryotic pathogen genomics database resource

Cristina Aurrecoechea, Ana Barreto, Evelina Y. Basenko, John Brestelli, Brian P. Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S. Harb (+18 others)
2016 Nucleic Acids Research  
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are
more » ... with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polyso-mal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data.
doi:10.1093/nar/gkw1105 pmid:27903906 pmcid:PMC5210576 fatcat:gp4twmzt7rh2be7oga6xfszwpi

Growing a circular economy with fungal biotechnology: a white paper

Vera Meyer, Evelina Y. Basenko, J. Philipp Benz, Gerhard H. Braus, Mark X. Caddick, Michael Csukai, Ronald P. de Vries, Drew Endy, Jens C. Frisvad, Nina Gunde-Cimerman, Thomas Haarmann, Yitzhak Hadar (+15 others)
2020 Fungal Biology and Biotechnology  
Fungi have the ability to transform organic materials into a rich and diverse set of useful products and provide distinct opportunities for tackling the urgent challenges before all humans. Fungal biotechnology can advance the transition from our petroleum-based economy into a bio-based circular economy and has the ability to sustainably produce resilient sources of food, feed, chemicals, fuels, textiles, and materials for construction, automotive and transportation industries, for furniture
more » ... beyond. Fungal biotechnology offers solutions for securing, stabilizing and enhancing the food supply for a growing human population, while simultaneously lowering greenhouse gas emissions. Fungal biotechnology has, thus, the potential to make a significant contribution to climate change mitigation and meeting the United Nation's sustainable development goals through the rational improvement of new and established fungal cell factories. The White Paper presented here is the result of the 2nd Think Tank meeting held by the EUROFUNG consortium in Berlin in October 2019. This paper highlights discussions on current opportunities and research challenges in fungal biotechnology and aims to inform scientists, educators, the general public, industrial stakeholders and policymakers about the current fungal biotech revolution.
doi:10.1186/s40694-020-00095-z pmid:32280481 pmcid:PMC7140391 fatcat:3imkffh7bzaedo6hxjxp3eula4

Acknowledgement to Reviewers of Genes in 2019

Genes Editorial Office
2020 Genes  
Y.  ...  Basenko Evert M. van Schothorst Evgeniy S. Balakirev Ewa Jablonska Ewa Niewiadomska Eyal Seroussi Ezequiel Tolosa Fabian Fries Fabio A.  ... 
doi:10.3390/genes11010059 fatcat:h45b66h3trcvrgssnxtkt6fk6y

Recombination Can either Help Maintain Very Short Telomeres or Generate Longer Telomeres in Yeast Cells with Weak Telomerase Activity

Evelina Basenko, Zeki Topcu, Michael J. McEachern
2011 Eukaryotic Cell  
Type I survivors exhibit amplification of subtelomeric YЈ elements and have relatively slower growth and short terminal telomeric tracts (11, 36, 57) .  ...  DNA was digested with BsrBI and was resolved on a 3.2% agarose gel. 1134 BASENKO ET AL. EUKARYOT. CELL the ter1-28C(Taq) mutant, that produced near-normal colonies.  ... 
doi:10.1128/ec.05079-11 pmid:21666075 pmcid:PMC3165439 fatcat:vjqj6egv6netzju34xywu7lbna

Mutant Telomeric Repeats in Yeast Can Disrupt the Negative Regulation of Recombination-Mediated Telomere Maintenance and Create an Alternative Lengthening of Telomeres-Like Phenotype

L. H. Bechard, B. D. Butuner, G. J. Peterson, W. McRae, Z. Topcu, M. J. McEachern
2008 Molecular and Cellular Biology  
We also thank Evelina Basenko for helpful comments on the manuscript and Rolf Kooistra for providing us with the wild-type strain CBS 2359 and the ku80⌬ strain.  ...  Basenko, and M. McEachern, unpublished data).  ...  Type I survivors display amplified subtelomeric YЈ elements and have short terminal tracts of telomeric repeats (42, 75) .  ... 
doi:10.1128/mcb.00423-08 pmid:19029249 pmcid:PMC2630680 fatcat:rtpsndemsfc2xatp4imlo5a5gi

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models [article]

Maureen A. Carey, Gregory L. Medlock, Michał Stolarczyk, William A. Petri, Jennifer L. Guler, Jason A. Papin
2019 bioRxiv   pre-print
Aurrecoechea, Cristina, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Predictions Using EnsembleFBA." PLoS Comput. Biol. 13 (3).  ... 
doi:10.1101/772467 fatcat:hjrasufn35bjlgjhqynkjehqte

Maintenance of Very Long Telomeres by Recombination in the Kluyveromyces lactis stn1-M1 Mutant Involves Extreme Telomeric Turnover, Telomeric Circles, and Concerted Telomeric Amplification

J. Xu, M. J. McEachern
2012 Molecular and Cellular Biology  
We also thank Evelina Basenko and Elizabeth Lucht for critical reading of the manuscript. This work was supported by a grant to M.J.M. from the National Institutes of Health (GM 61645).  ...  Basenko and M. J. McEachern, unpublished data). One possibility to help account for these observations may be that RAD59 is able to promote RTE even in the absence of RAD50 and RAD51.  ...  Type I survivors are characterized by amplification of subtelomeric Y= elements and short telomeric tracts, while type II survivors are characterized by lengthened tracts of telomeric repeats (79) .  ... 
doi:10.1128/mcb.00430-12 pmid:22645309 pmcid:PMC3434524 fatcat:ars5ju2rmvcrzmseqbmok3ozzy

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

Evelina Basenko, Jane Pulman, Achchuthan Shanmugasundram, Omar Harb, Kathryn Crouch, David Starns, Susanne Warrenfeltz, Cristina Aurrecoechea, Christian Stoeckert, Jessica Kissinger, David Roos, Christiane Hertz-Fowler
2018 Journal of Fungi  
A new class of Y/F/WxC effector proteins was reported in haustoria-producing plant pathogens by Godfrey et al. [37] .  ...  A new class of Y/F/WxC effector proteins was reported in haustoria-producing plant pathogens by Godfrey et al. [37] .  ... 
doi:10.3390/jof4010039 pmid:30152809 pmcid:PMC5872342 fatcat:dvrizssofzdw7ic2elcplaviwe