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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
..., and A3The histone locus in Drosophila melanogaster is present at the 39DE region of Chromosome 2L, bordering the pericentromeric heterochromatin. The highly homogeneous nature of this locus has impeded its resolution to the base pair level. The current reference iso-1 Rel6 has only ∼69 kb (12 units...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...et al. 2016). Tetrahymena possesses a unique nuclear architecture containing a transcriptionally active macronucleus (MAC), and a transcriptionally silent micronucleus (MIC). During sexual reproduction, the new MAC chromosomes undergo ∼200 regulated double-stranded DNA breaks and endoreplication...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
.... The subtelomeric elements, including rDNA, were massively rearranged and involved in breakage–fusion–bridge cycles, translocations, recombinations, and chromosome circularization. These events were established progressively over time and displayed heterogeneity at the subpopulation level. New telomere...
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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...of the sgRNA/Cas9 complex to scan the DNA for target sites.When we analyzed the cleavage efficiencies of sgRNAs used in Drosophila (Ren et al. 2014), we observed a good overlap with the ability of those sgRNAs to adopt the correct structure and having a high cleavage efficiency. Further refinement...
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Method: Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits
- Carlos Ruiz-Arenas,
- Alejandro Cáceres,
- Marcos López,
- Dolors Pelegrí-Sisó,
- Josefa González,
- and Juan R. González
Genome Res. December 2020 30: 1802-1814; Published in Advance November 17, 2020, doi:10.1101/gr.258301.119
...in Drosophila melanogaster and human, and the chromosomes under selective pressure at the lactase locus in humans. We then applied recombClust to the complex human 1q21.1 region, where nonallelic homologous recombination produces deleterious phenotypes. We discovered and validated the presence of two different...
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Method: Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
- Michael P. McGurk and
- Daniel A. Barbash
Genome Res. May 2018 28: 714-725; Published in Advance March 27, 2018, doi:10.1101/gr.231472.117
...-element related array in Drosophila guanche is comprised of elements missing ∼100 nt of terminal sequence (Miller et al. 1992), and all elements in the fixed Bari1 tandem array have incomplete TIRs (Marsano et al. 2003). The terminal inverted repeats at the ends of DNA transposons are endonuclease cut sites...
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Research: Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase
- Ayako Yamanishi,
- Kosuke Yusa,
- Kyoji Horie,
- Masahiro Tokunaga,
- Kohji Kusano,
- Chikara Kokubu,
- and Junji Takeda
Genome Res. September 2013 23: 1462-1473; Published in Advance August 1, 2013, doi:10.1101/gr.152744.112
...repeats (Fig. 5) can also be seen in Drosophila melanogaster Blm mutants (Garcia et al. 2011), suggesting the existence of a common mechanism for DEL formation in a Blm-deficient background. BLM helicase acts to unwind secondary DNA structures at the telomere (Sfeir et al. 2009). The loss of BLM may...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...regions.Meiotic crossovers form via inter-homolog repair of DNA double-strand breaks (DSBs) that are generated by SPO11 topoisomerase-related complexes (Szostak et al. 1983; Keeney et al. 1997; Robert et al. 2016; Vrielynck et al. 2016). Diverse eukaryotes have evidence for recombination hotspots, which...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...crossover could contribute to centromere evolution (Smith 1976). In this influential model, meiotic DNA double-strand breaks (DSBs) are repaired using a nonallelic location on a homolog, with the potential to cause gain and loss of intervening tandem repeats (Smith 1976). However, it is widely documented...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...%). In CC-2931, a Crypton and a previously undescribed type of DNA element have caused 71% of chromosomal rearrangements, whereas in CC-1952, a Dualen LINE is associated with 87% of duplications. Other SMs, notably large duplications in CC-2931, are likely products of various double-strand break repair...
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