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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...synthesis) and synthesis of precursors for macromolecules (amino acids for proteins and nucleoside triphosphates for DNA and RNA synthesis). In some cases, as studied here, recombination is critical for viral DNA replication, which together produce concatemeric DNA essential for viral packaging...
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Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
- Benjamin Davies,
- Gang Zhang,
- Daniela Moralli,
- Samy Alghadban,
- Daniel Biggs,
- Chris Preece,
- Peter Donnelly,
- and Anjali Gupta Hinch
Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
.... The evolutionary turnover of recombination hot spots contributes to speciation in mice. Genes Dev 30: 266–280. doi:10.1101/gad.270009.115 ↵Sugiyama T, Kantake N, Wu Y, Kowalczykowski SC. 2006. Rad52-mediated DNA annealing after Rad51-mediated DNA strand exchange promotes second ssDNA capture. EMBO J 25: 5539...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...-Seq Library Prep Kit FWD 369 following Lexogen`s standard protocol (015UG009V0252). Libraries were prepared with a 370 starting amount of 300 ng and amplified in 14 PCR cycles. Libraries were profiled in a High 371 Sensitivity DNA on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit 372...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...prior to cleaning and concentrating. One DNA sample from each individual was chosen, based on the DNA amount and quality, to be sequenced. Sequencing libraries were produced using the Illumina DNA PCR-free library preparation kit according to the manufacturer's protocol, using an input DNA quantity...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, et al. 2003. Antisense transcripts with rice full-length cDNAs. Genome Biol 5: R5. Ozsolak F, Milos PM. 2011. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12: 87–98. Peisley A, Jo MH, Lin C, Wu B...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
...Biosciences). After clonal expansion, genomic DNA was extracted from each clone using the SimplePrep reagent for DNA (Takara, #9180) and screened for mutations by quantitative PCR (qPCR). Candidate clones were further verified for mutations by Sanger sequencing.RNA interferenceSmall interfering RNA (siRNA...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...enrichment identified in upd tumor samples. Together, these scRNA-seq data support the usage of upd tumor testes in uncovering key characteristics of wild-type stem cells through genomic strategies.Cell-type-specific chromatin landscapes profiled by H3K4me3, H3K27me3, and H3K9me3The high expression...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
...a potential causal mechanism for crossover depletion may involve reduced frequency of interhomolog contacts in transcriptionally active regions. RNA polymerase activity may disrupt interhomolog engagement and thus decrease the stability of recombination intermediates. Further experimental work is needed...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...of the sequencing chromatograms of the PCR products derived from DNA templates confirmed the absence of SNP at the site. The PCR products obtained from cDNA templates were utilized to determine the RNA editing levels of G/(A+G) by assessing the peak heights of base A/G at the editing site. qPCR analysis The cDNA...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...). They are defined as DNA segments with a length of at least 1 kb that share >90% of sequence identity (Bailey et al. 2001, 2002). Their high sequence homology is known to be a driver of nonallelic homologous recombination (NAHR), caused by meiotic misalignment of homologous chromosomes or sister chromatids...

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