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Research: Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4
- Kate Liddiard,
- Brian Ruis,
- Taylor Takasugi,
- Adam Harvey,
- Kevin E. Ashelford,
- Eric A. Hendrickson,
- and Duncan M. Baird
Genome Res. May 2016 26: 588-600; Published in Advance March 3, 2016, doi:10.1101/gr.200840.115
...of telomere insult and not peculiar to telomerase-expressing cell lines (Fig. 4C). We used comparative mapping to the informative XpYp telomere-adjacent haplotypes in MRC5 cells (Supplemental Fig. 1B; Capper et al. 2007) to establish the involvement of a single allele, consistent with sister chromatid fusion...
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Research: Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- Yongbin Li,
- Xiao Liu,
- Peter Sarkies,
- and Zhongying Zhao
Genome Res. November/December 2022 32: 2015-2027; Published in Advance November 9, 2022, doi:10.1101/gr.277205.122
...Genetic exchange with an outcrossing sister species causes severe -wide dysregulation in a selfing Caenorhabditis nematode Dongying Xie1, Pohao Ye1, Yiming Ma1, Yongbin Li2, Xiao Liu2, Peter Sarkies3 and Zhongying Zhao1,4 1Department of Biology, Hong Kong Baptist University, Hong Kong, China; 2...
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Methods: Establishing glucose- and ABA-regulated transcription networks in Arabidopsis by microarray analysis and promoter classification using a Relevance Vector Machine
- Yunhai Li,
- Kee Khoon Lee,
- Sean Walsh,
- Caroline Smith,
- Sophie Hadingham,
- Karim Sorefan,
- Gavin Cawley,
- and Michael W. Bevan
Genome Res. March 2006 16: 414-427; Published in Advance January 19, 2006, doi:10.1101/gr.4237406
...in stable transgenic lines. The successful application of machine learning algorithms for promoter sequence analysis using Bayesian statistical principles established models of transcriptional pathways regulating glucose- and ABA-mediated gene expression and demonstrated that these methods hold promise...
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Research: The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species
- Eva H. Stukenbrock,
- Thomas Bataillon,
- Julien Y. Dutheil,
- Troels T. Hansen,
- Ruiqiang Li,
- Marcello Zala,
- Bruce A. McDonald,
- Jun Wang,
- and Mikkel H. Schierup
Genome Res. December 2011 21: 2157-2166; Published in Advance October 12, 2011, doi:10.1101/gr.118851.110
...The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species Eva H. Stukenbrock 1 , 5 , 6 , Thomas Bataillon 1 , Julien Y. Dutheil 1 , Troels T...
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Commentary: ‘Why genomes in pieces?’ revisited: Sucking lice do their own thing in mtDNA circle game
- David M. Rand
Genome Res. May 2009 19: 700-702; doi:10.1101/gr.091132.109
...David Rand David M. D Rand D.M. Rand Rand, D.M Rand, David M David Rand David M, Rand Rand David M Rand, DM DavidM Rand David M Rand DM Rand Rand, D 10.1101/gr.091132.109 1088-9051 genome;19/5/700 ‘Why genomes in pieces?’ revisited: Sucking lice do their own thing in mtDNA circle game Commentary...
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Research: Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species
- Phillip A. Morin,
- Frederick I. Archer,
- Andrew D. Foote,
- Julia Vilstrup,
- Eric E. Allen,
- Paul Wade,
- John Durban,
- Kim Parsons,
- Robert Pitman,
- Lewyn Li,
- Pascal Bouffard,
- Sandra C. Abel Nielsen,
- Morten Rasmussen,
- Eske Willerslev,
- M. Thomas P. Gilbert,
- and Timothy Harkins
Genome Res. July 2010 20: 908-916; Published in Advance April 22, 2010, doi:10.1101/gr.102954.109
...) are reciprocally monophyletic and form sister taxa substantially divergent from both open-water type A and all other killer whales. Therefore, we recommend that they be designated as distinct species that have diverged from one another for ;150,000 yr and suggest that further analysis of nuclear sequence data...
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Research: Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease
- Claudio Casola,
- Ugne Zekonyte,
- Andrew D. Phillips,
- David N. Cooper,
- and Matthew W. Hahn
Genome Res. March 2012 22: 429-435; Published in Advance November 16, 2011, doi:10.1101/gr.127738.111
...of orthologous protein sequences, and other structural features (Ramensky et al. 2002; Ng and Henikoff 2003). Given the high number of paralogous gene sequences found in our own and previous studies, we reasoned that many yetundescribed deleteriousmutations responsible for nonsynonymous changes in functional...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...of meiotic crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.Tandem repetitive sequences...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...explain the transcriptional regulation of your GOI, this does not mean that you have to do all of the “wet-laboratory” experiments yourself: Data mining is a crucial step in developing your hypotheses. Proliferation of easily accessible, large-scale, high-throughput studies provides fertile ground...
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Research: Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila
- Michelle Pherson,
- Ziva Misulovin,
- Maria Gause,
- and Dale Dorsett
Genome Res. April 2019 29: 602-612; Published in Advance February 22, 2019, doi:10.1101/gr.243832.118
...associate specifically with gene promoters and transcriptional enhancers, or how sister chromatid cohesion is established. Here, we use -wide chromatin immunoprecipitation in Drosophila cells to show that SA and the Fs(1)h (BRD4) BET domain protein help recruit Nipped-B and cohesin to enhancers and DNA...
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