Searching journal content for articles similar to Davies et al. 33 (11): 2018.

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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
...@bham.ac.ukAbstractA single guide RNA (sgRNA) directs Cas9 nuclease for gene-specific scission of double-stranded DNA. High Cas9 activity is essential for efficient gene editing to generate gene deletions and gene replacements by homologous recombination. However, cleavage efficiency is below 50...
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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
..., but characterization of their roles in phage lifecycles is limited, and their impact on phage replication is controversial. To address these issues, we have searched for phages whose growth is impacted by the major recombination-promoting helicase-nuclease of Escherichia coli, the RecBCD enzyme. Although no phages...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...conspecific and interspecific variations, and their potential impact on hybrid incompatibility, remains lacking. Here, we present a pan study of populations from both species, revealing that C. nigoni consistently possesses larger s and higher gene counts than C. briggsae. This difference primarily results...
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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
...or exhibit more than a twofold difference in frequency of occurrence relative to the background, suggesting they are not viable candidate motifs for promoting recombination in hotspots.Identification and characterization of the PRDM9 gene in termitesWe searched the M. bellicosus and C. secundus s...
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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
...and is susceptible to splice variant “blindness.” Human cancer is especially rich in variations, including coding region mutations of TF genes; these features can sometimes offer similar insights as knockdown/knockout experiments. The Eukaryotic Promoter Database has the SNP2TFBS subdatabase linking genetic variants...
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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
...understanding of why certain hotspots are favored to form DSBs and crossovers remains undetermined.Meiotic chromosomes adopt a brush-loop conformation characterized by chromatin loops attached to a central axis (Møens and Pearlman 1988). Although recombination hotspots are found within loops, DSB machinery...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...author: ryan.lister@uwa.edu.auAbstractIn plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed...
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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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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...encompassing (1) differential gene expression analysis; (2) characterization of candidate cCREs; and (3) inference of cell type–specific, TF–target gene networks; and (4) integrative analyses linking peaks to genes and associating AD -wide association study (GWAS) loci with cCREs. This enabled prioritization...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...a common G0 founder pair (Fig. 1A). Two G1 females were mated to a single male sibling, yielding two litters of naturally conceived mice. To obtain a matched ART-derived cohort, oocytes from two hormonally superovulated G1 female siblings were harvested and in vitro fertilized with sperm from a second G1...

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