eLife

Latest preprint reviews

1. Sensitive remote homology search by local alignment of small positional embeddings from protein language models

   This article has 3 authors:

   1. Sean R Johnson
   2. Meghana Peshwa
   3. Zhiyi Sun

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study addresses the problem of detecting weak similarity between protein sequences, a procedure commonly used to infer homology or assign putative functions to uncharacterized proteins. The authors present a convincing approach that combines recently developed protein language models with well-established methods. The benchmarks provided show that the proposed tool is fast and accurate for remote homology detection, making this paper of general interest to all researchers working in the fields of protein evolution and genome annotation.

   Reviewed by eLife

2. Post-transcriptional splicing can occur in a slow-moving zone around the gene

   This article has 18 authors:

   1. Allison Coté
   2. Aoife O'Farrell
   3. Ian Dardani
   4. Margaret Dunagin
   5. Chris Coté
   6. Yihan Wan
   7. Sareh Bayatpour
   8. Heather L Drexler
   9. Katherine A Alexander
   10. Fei Chen
   11. Asmamaw T Wassie
   12. Rohan Patel
   13. Kenneth Pham
   14. Edward S Boyden
   15. Shelly Berger
   16. Jennifer Phillips-Cremins
   17. L Stirling Churchman
   18. Arjun Raj

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This fundamental study addresses a long-standing mystery in splicing regulation: does splicing occur co- or post-transcriptionally? The authors provide compelling evidence demonstrating that splicing can occur post-transcriptionally at a transcription site proximal zone, changing the way we think about splicing.

   Reviewed by eLife

3. Antigenic strain diversity predicts different biogeographic patterns of maintenance and decline of antimalarial drug resistance

   This article has 3 authors:

   1. Qixin He
   2. John K Chaillet
   3. Frédéric Labbé

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The study is an important advancement to the consideration of antimalarial drug resistance: the authors make use of both modelling results and supporting empirical evidence to demonstrate the role of malaria strain diversity in explaining biogeographic patterns of drug resistance. The theoretical methods and the corresponding results are compelling, with the novel model presented moving beyond existing models to incorporate malaria strain diversity and antigen-specific immunity. This work is likely to be interesting to malaria researchers and others working with antigenically diverse infectious diseases.

   Reviewed by eLife

4. Noncanonical usage of stop codons in ciliates expands proteins with structurally flexible Q-rich motifs

   This article has 8 authors:

   1. Chi-Ning Chuang
   2. Hou-Cheng Liu
   3. Tai-Ting Woo
   4. Ju-Lan Chao
   5. Chiung-Ya Chen
   6. Hisao-Tang Hu
   7. Yi-Ping Hsueh
   8. Ting-Fang Wang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents useful results on glutamine-rich motifs in relation to protein expression and alternative genetic codes. The solid data are based on bioinformatic approaches that are employed to systematically uncover sequence features associated with proteome-wide amino acid distribution and biological processes.

   Reviewed by eLife

5. Articular cartilage corefucosylation regulates tissue resilience in osteoarthritis

   This article has 7 authors:

   1. Kentaro Homan
   2. Tomohiro Onodera
   3. Hisatoshi Hanamatsu
   4. Jun-ichi Furukawa
   5. Daisuke Momma
   6. Masatake Matsuoka
   7. Norimasa Iwasaki

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study sheds light on the pivotal role of alterations in chondrocyte glycan metabolism in two contexts: The onset of cartilage degeneration and early onset of osteoarthritis (OA). The action is through hypertrophic differentiation of chondrocytes, a finding that provides insights into the identification of nascent markers for early-stage OA. The evidence supporting the claims is solid, with the authors clearly demonstrating the role of articular cartilage corefucosylation in the development of OA. The authors' inferences would be further enhanced through future experiments aimed at analyzing the mechanisms underlying the changes in glycometabolism in cartilage.

   Reviewed by eLife

6. A role for JAK2 in mediating cell surface GHR-PRLR interaction

   This article has 7 authors:

   1. Chen Chen
   2. Jing Jiang
   3. Tejeshwar C Rao
   4. Ying Liu
   5. Tatiana T Marquez Lago
   6. Stuart J Frank
   7. André Leier

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study that characterizes a surprising interaction between two different cytokine/hormone receptors using nanoscale resolution (dSTORM) microscopy. The study provides solid evidence that the interaction is ligand-dependent, and is mediated by the receptor-associated intracellular signalling molecule JAK2. While at present limited to growth hormone and prolactin receptors in a limited number of cell lines, there are potentially broad implications for cytokine signalling, as such JAK2-mediated interactions could occur between a range of different cytokines. Moreover, the specific hormone interactions shown in the manuscript may have significant implications for understanding how these hormones can have differential effects in breast cancer, under different conditions.

   Reviewed by eLife

7. Topological stress triggers persistent DNA lesions in ribosomal DNA with ensuing formation of PML-nucleolar compartment

   This article has 12 authors:

   1. Alexandra Urbancokova
   2. Terezie Hornofova
   3. Josef Novak
   4. Sarka Andrs Salajkova
   5. Sona Stemberkova Hubackova
   6. Alena Uvizl
   7. Tereza Buchtova
   8. Martin Mistrik
   9. Brian McStay
   10. Zdenek Hodny
   11. Jiri Bartek
   12. Pavla Vasicova

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study asks how Promyelocytic leukemia protein (PML) becomes associated with the nucleoli of cells (PML Nucleolar Associations, PNAs) upon various genotoxic stimuli. Using immunostaining analysis with induced DNA double-strand breaks (DSBs) in rDNA repeats, the authors provide solid evidence that PNAs are triggered mostly by the inhibition of topoisomerase and RNA polymerase I, which is augmented by homologous recombination but not by the non-homologous end joining double-strand break repair pathway. The findings have potential implications for a better understanding of how DNA damage in ribosomal DNA is repaired for genome stability. This paper is of interest to researchers in the fields of nuclear structure and DNA repair.

   Reviewed by eLife

8. Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction

   This article has 18 authors:

   1. Sara Latini
   2. Veronica Venafra
   3. Giorgia Massacci
   4. Valeria Bica
   5. Simone Graziosi
   6. Giusj Monia Pugliese
   7. Marta Iannuccelli
   8. Filippo Frioni
   9. Gessica Minnella
   10. John Donald Marra
   11. Patrizia Chiusolo
   12. Gerardo Pepe
   13. Manuela Helmer Citterich
   14. Dimitros Mougiakakos
   15. Martin Böttcher
   16. Thomas Fischer
   17. Livia Perfetto
   18. Francesca Sacco

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study could potentially represent a step forward towards personalized medicine by combining cell-based data and a prior-knowledge network to derive Boolean-based predictive logic models to uncover altered protein/signaling networks within cancer cells. The level of evidence supporting the conclusions is solid, as the authors present analyses on independent, real-world data to validate their approach. These findings could be of interest to medical biologists working in the field of cancer, as the work should inform drug development and treatment choices in the field of oncology.

   Reviewed by eLife

9. Sorting of secretory proteins at the trans-Golgi network by human TGN46

   This article has 10 authors:

   1. Pablo Lujan
   2. Carla Garcia-Cabau
   3. Yuichi Wakana
   4. Javier Vera Lillo
   5. Carmen Rodilla-Ramírez
   6. Hideaki Sugiura
   7. Vivek Malhotra
   8. Xavier Salvatella
   9. Maria F Garcia-Parajo
   10. Felix Campelo

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study provides the fundamental insight that TGN46, a single-pass membrane protein, acts as a cargo receptor for proteins at the Trans-Golgi Network. The authors demonstrate that the luminal domain of TGN46 is crucial for the incorporation of the soluble secretory protein PAUF into CARTS, a class of vesicles mediating TGN to surface traffic. The data presented are compelling, yielding a clear model for the sorting of cargos destined for secretion.

   Reviewed by eLife

10. Plasma growth hormone pulses induce male-biased pulsatile chromatin opening and epigenetic regulation in adult mouse liver

    This article has 3 authors:

    1. Andy Rampersaud
    2. Jeannette Connerney
    3. David J Waxman

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This important study offers new and convincing support for the idea that about a third of mouse liver DNAse hypersensitivity sites (DHS) showing male-biased chromatin opening are sex-biased because of the male-specific cyclic action of growth hormone pulses to alter chromatin accessibility, as compared to the relative ineffectiveness of the more static pattern of growth hormone secretion in females. Supporting evidence is found in the impact of hypophysectomy and growth hormone treatment on chromatin accessibility, and the binding of specific transcription factors and epigenetic marks at STAT5-sensitive sites. This work uncovers mechanisms underlying sex differences in liver function and will be of broad interest to endocrinologists and hepatologists.

    Reviewed by eLife