Molecular Biology

Improved base editing and functional screening in Leishmania via co-expression of the AsCas12a ultra variant, a T7 RNA polymerase, and a cytosine base editor

1. Nicole Herrmann May
2. Anh Cao
3. Annika Schmid
4. Fabian Link
5. Jorge Arias-del-Angel
6. Elisabeth Meiser
7. Tom Beneke

• Curated by eLife

  eLife Assessment

  This important article describes a meticulously-developed improved strategy for generation of functionally null mutants in Leishmania spp. via cytosine base editing, with reduced background toxicity and enhanced efficiency relative to a previously-described method. The authors show use of the strategy in a small-scale loss-of-function screen, providing compelling evidence that large-scale screens will be possible. The newly developed tools will be of great interest to researchers working with Leishmania and beyond.

Reviewed by eLife

Embryological cellular origins and hypoxia-mediated mechanisms in PIK3CA -Driven refractory vascular malformations

1. Sota Torii
2. Keiki Nagaharu
3. Nanako Nakanishi
4. Hidehito Usui
5. Yumiko Hori
6. Katsutoshi Hirose
7. Satoru Toyosawa
8. Eiichi Morii
9. Mitsunaga Narushima
10. Yoshiaki Kubota
11. Osamu Nakagawa
12. Kyoko Imanaka-Yoshida
13. Kazuaki Maruyama

Reviewed by Review Commons

A transcriptional control model for doublesex -dependent sex differentiation in Nasonia wasps

1. Julien Rougeot
2. Filippo Guerra
3. Eveline C. Verhulst

Reviewed by Arcadia Science

Sperm fertility in mice with oligo-astheno-teratozoospermia restored by in vivo injection and electroporation of naked mRNA

1. Charline Vilpreux
2. Guillaume Martinez
3. Paul Fourquin
4. Magali Court
5. Florence Appaix
6. Jean-Luc Duteyrat
7. Maxime Henry
8. Julien Vollaire
9. Camille Ayad
10. Altan Yavuz
11. Lisa De Macedo
12. Geneviève Chevalier
13. Edgar Del Llano
14. Emeline Lambert
15. Sekou Ahmed Conte
16. Zeina Wehbe
17. Elsa Giordani
18. Véronique Josserand
19. Jacques Brocard
20. Coutton Charles
21. Bernard Verrier
22. Pierre F Ray
23. Corinne Loeuillet
24. Christophe Arnoult
25. Jessica Escoffier

• Curated by eLife

  eLife Assessment

  This study reports an approach for restoring sperm motility in mice. The strength lies in in the novelty of the methodology being developed, but the evidence for the success of the method or its mechanism is inadequate. Additional experimental support would be required to support the conclusions of the authors.

Reviewed by eLife

Conformational changes, excess area, and elasticity of the Piezo protein-membrane nanodome from coarse-grained and atomistic simulations

1. Sneha Dixit
2. Frank Noé
3. Thomas R. Weikl

• Curated by eLife

  eLife Assessment

  This work represents an important contribution to our understanding of how membrane energetics influence protein conformation and function in mechano-sensitive channels. Through extensive molecular dynamics simulations and energetic analysis, the study demonstrates how the channel structure is shaped by a balance of protein and membrane-induced forces, effectively reconciling experimental data from different membrane environments. However, while much of the computational data is convincing, some aspects of the energetic analysis and models employed remain incomplete.

Reviewed by eLife

N6-methyladenosine in DNA promotes genome stability

1. Brooke A Conti
2. Leo Novikov
3. Deyan Tong
4. Qing Xiang
5. Savon Vigil
6. Thomas J McLellan
7. Chuong Nguyen
8. Nancy De La Cruz
9. Reshma T Veettil
10. Prashant Pradhan
11. Parag Sahasrabudhe
12. Jason D Arroyo
13. Lei Shang
14. Benjamin R Sabari
15. David J Shields
16. Mariano Oppikofer

• Curated by eLife

  eLife Assessment

  This manuscript reports important findings that the methyltransferase METTL3 is involved in the repair of abasic sites and uracil in DNA, mediating resistance to floxuridine-driven cytotoxicity. The presented evidence is conclusive for the involvement of m6A in DNA involving single cell imaging and mass spectrometry data. The authors present convincing evidence that the m6A signal does not result from bacterial contamination or RNA.

Reviewed by eLife

Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency

1. Zach Hensel

• Curated by eLife

  eLife Assessment

  This short manuscript uses mutation counts in phylogenies of millions of SARS-CoV-2 genomes to show that mutation rates systematically differ between regions that are paired or unpaired in the predicted RNA secondary structure of the viral genome. Such an effect of pairing state is not unexpected, but its systematic demonstration using millions of viral genomes is valuable and convincing.

Reviewed by eLife

PAbFold: Linear Antibody Epitope Prediction using AlphaFold2

1. Jacob DeRoo
2. James S Terry
3. Ning Zhao
4. Timothy J Stasevich
5. Christopher D Snow
6. Brian J Geiss

• Curated by eLife

  eLife Assessment

  In this manuscript, the authors describe a new AlphaFold2 pipeline called PabFold that can represent a useful tool for identifying linear antibody epitopes (B-cell epitopes) for different antigens. This information can be used in the selection of different reagents in competitive ELISA assays which can save time and reduce costs. Because several questions about the work remain, the study is currently incomplete.

Reviewed by eLife

Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome

1. Kira A Cozzolino
2. Lynn Sanford
3. Samuel Hunter
4. Kayla Molison
5. Benjamin Erickson
6. Meaghan CS Courvan
7. Taylor Jones
8. Deepa Ajit
9. Matthew D Galbraith
10. Joaquín M Espinosa
11. David Bentley
12. Mary Ann Allen
13. Robin D Dowell
14. Dylan J Taatjes

• Curated by eLife

  eLife Assessment

  This is an important study providing compelling evidence that the Mediator kinase module mediates an elevated inflammatory response, manifested by heightened cytokine levels, associated with Downs syndrome (DS) via transcriptional changes impacting cell signaling and metabolism that involve mobilization of nuclear receptors by altered lipid metabolites, which has significance for the treatment of DS and other chronic inflammatory conditions. Particular strengths of the study include the combined experimental approaches of transcriptomics, untargeted metabolomics and cytokine screens and the use of sibling matched cell lines (trisomy 21 vs disomy 21) from various donors. Evidence is also provided implicating the Mediator kinase module in controlling mRNA splicing and mitochondrial function that should stimulate new research to elucidate the mechanistic bases for these novel functions.

Reviewed by eLife

Decoding m6Am by simultaneous transcription-start mapping and methylation quantification

1. Jianheng Fox Liu
2. Ben R Hawley
3. Luke S Nicholson
4. Samie R Jaffrey

• Curated by eLife

  eLife Assessment

  This study presents a new quantitative method, CROWN-seq, to map the cap-adjacent RNA modification N6,2'-O-dimethyladenosine (m6Am) with single nucleotide resolution. Using thoughtful controls and well-validated reagents, the authors provide compelling evidence that the method is reliable and reproducible. Additionally, the study provides important evidence that m6Am may increase transcription in modified mRNAs. However, the data only demonstrates a correlation between m6Am and transcriptional regulation rather than causality. Overall, this study is poised to advance m6Am research, being of broad interest to the RNA biology and gene regulation fields.

Reviewed by eLife