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PNAS Papers on Strawberry Evolution, Cell Cycle Regulators, False-Positive Triplex Gene Editing

Editor's Note: Some of the articles described below are not yet available at the PNAS site but are scheduled to be posted this week.

A team from China, the US, Belgium, and South Africa puts together a pan-genome for the strawberry plant genus Fragaria, describing the evolutionary history of the plants as well as a previously unappreciated species called Fragaria emeiensis Jia J. Lei in the process. With the help of long-read sequencing and de novo assembly, the researchers came up with reference genomes for five Fragaria species before going on to resequence plants from 128 more Fragaria accessions for their subsequent pan-genome, phylogenetic, and strawberry trait association analyses. "We anticipate that these reference genomes and datasets, combined with our phylogenetic estimates of species relationships, is the phylogenomic framework needed to elevate Fragaria as a true model system for evolutionary genomics," they write.

Columbia University researchers report on cell cycle-related roles for the MDM2 ubiquitin ligase and its heterodimeric partner MDMX, known for regulating the tumor suppressor p53, and for a p73 protein from the same family as p53. The team's RNA interference-based gene knockdown experiments suggested that interfering with MDM2, MDMX, a related E3 ligase enzyme, or p73 prompted a cell cycle arrest in cells that either contained tumor-related forms of p53 or were missing the tumor suppressor entirely. Based on these and other findings, the authors proposed a model in which "MDM2 and MDMX, working at least in part as a heterocomplex, may play a p53-independent role in maintaining cell cycle progression by promoting the activity of [cell cycle-related E2F transcription factor] family members as well as p73, making them a potential target of interest in cancers lacking wild-type p53."

A Stanford University and Vera Therapeutics team describes false-positive that can turn up when using digital droplet PCR (ddPCR)-based analyses to assess the effects of triplex gene editing experiments that involve "poly lactic-co-glycolic acid" nanoparticle delivery of chromosome target-binding peptide nucleic acid (PNA) sequences and donor single-strand DNA (ssDNA) template sequences. "Our work here indicates that peptide nucleic acids have an intrinsic capability to aggregate with single-stranded DNA donor templates, which may lead to false positives in PCR-based readouts," the researchers explain. "To mitigate this issue, we have validated several methods including size exclusion, nuclease digestion, and purification columns, which reversed the appearance of false signals."

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