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Volume 21 Issue 3, March 2024

Brighter autonomous bioluminescence

Autonomously glowing Arabidopsis thaliana plants express an improved version of the fungal bioluminescence pathway.

See Shakhova et al.

Image: Tatiana Karataeva, Planta LLC. Cover Design: Thomas Phillips.

Editorial

  • Peer review is at the heart of publishing scientific papers. In this first installment of a two-part Editorial, we explain how we manage the process at Nature Methods.

    Editorial

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This Month

  • In a group interview, early-career researchers in proteomics share how they plan for the future and navigate divides over methods.

    • Vivien Marx
    This Month
  • Brown seaweeds are multicellular eukaryotes that have been evolving independently of animals and plants for more than a billion years. The filamentous brown alga Ectocarpus has been used as a model to understand the biology of these enigmatic organisms and to shed light on a range of major questions, from the molecular basis of complex developmental patterns to the evolution of sex.

    • Susana M. Coelho
    This Month
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Correspondence

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Research Highlights

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Technology Feature

  • Collaborations between researchers and companies can progress swimmingly and teams quickly validate findings and mature methods. All too often, things can’t advance and the ‘Valley of Death’ looms. New ways to collaborate, underpinned by computational muscle, can help.

    • Vivien Marx

    Collection:

    Technology Feature
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News & Views

  • sc-SPORT offers a way to probe RNA structure at the single-cell level. It reveals cell-to-cell heterogeneity in RNA folding.

    • Elizabeth A. Jolley
    • Philip C. Bevilacqua
    News & Views
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Research Briefings

  • We pinpoint PCR artifacts as the primary source of inaccurate quantification in both short- and long-read RNA sequencing, a problem that intensifies with an increase in PCR cycles in both bulk and single-cell sequencing contexts. To overcome this challenge, we engineered a novel unique molecular identifier (UMI) barcode composed of homotrimer nucleotide blocks. This design facilitates accurate quantification of RNA molecules, substantially improving molecular counting.

    Research Briefing
  • Interactions between RNA and RNA-binding proteins (RBPs) define the fate and function of every RNA molecule. We present TREX, or targeted RNase H-mediated extraction of crosslinked RBPs, an efficient and accurate method to unbiasedly reveal the protein interactors of specific regions of RNAs isolated from living cells.

    Research Briefing
  • We developed a prime editing (PE) strategy by incorporating a 5′–3′ exonuclease activity, which enhanced the efficacy and precision of ≥30-nucleotide DNA insertions without a secondary nick. Our optimization of the PE complex revealed that recruiting the exonuclease via an RNA aptamer outperformed direct protein fusions.

    Research Briefing
  • Intrinsically disordered regions of proteins are prevalent across the kingdoms of life; however, biophysical characterization is expensive, requiring specialized expertise and equipment and time-consuming sample preparation. By combining simulations and deep learning, we have developed a method to predict their average ensemble properties directly from sequence.

    Research Briefing
  • We developed Tapioca, an integrative ensemble machine learning-based framework, to accurately predict global protein–protein interaction network dynamics. Tapioca enabled the characterization of host regulation during reactivation from latency of an oncogenic virus. Introducing an interactome homology analysis method, we identified a proviral host factor with broad relevance for herpesviruses.

    Research Briefing
  • We developed a high-content profiling method named vibrational painting (VIBRANT) for single-cell drug response measurements, combining vibrational imaging, multiplexed vibrational probes and machine learning. VIBRANT showed high performance in predicting drug mechanisms of action, discovering novel compounds and assessing drug combinations, demonstrating great promise for phenotypic drug discovery.

    Research Briefing
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Perspectives

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Brief Communications

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Articles

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Resources

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