eLife

Latest preprint reviews

1. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells

   This article has 9 authors:

   1. Sarah G Swygert
   2. Dejun Lin
   3. Stephanie Portillo-Ledesma
   4. Po-Yen Lin
   5. Dakota R Hunt
   6. Cheng-Fu Kao
   7. Tamar Schlick
   8. William S Noble
   9. Toshio Tsukiyama

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work characterizes chromatin compaction in quiescent yeast cells and its role in the repression of gene expression. The authors' findings that chromatin compaction via heterogeneous interactions between nucleosomes directly contributes to transcriptional repression provides a useful conceptual paradigm for studies of quiescence in other organisms.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

2. Laminar microcircuitry of visual cortex producing attention-associated electric fields

   This article has 5 authors:

   1. Jacob A Westerberg
   2. Michelle S Schall
   3. Alexander Maier
   4. Geoffrey F Woodman
   5. Jeffrey D Schall

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study recorded brain activity in monkeys to identify the neural mechanisms underlying an attention-related scalp ERP component that is similar to the human N2pc component. Intriguing evidence was provided that the surface potential was at least partly a result of current flows in the feedback-receiving supragranular and infragranular layers of area V4, not the granular layer that receives feedforward inputs. However, it is not entirely clear if these very interesting intracortical effects are the source of the scalp ERP effects.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

3. Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing

   This article has 4 authors:

   1. Yiquan Wang
   2. Ruipeng Lei
   3. Armita Nourmohammad
   4. Nicholas C Wu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper performs a systematic analysis of the fitness landscape of the influenza virus protein neuraminidase (NA). The paper analyzes 864 different combinations of mutations, over six genetic backgrounds. The main findings are that the fitness landscape correlates well across genetic backgrounds, and that natural evolution of neuraminidase seems to select for neutrally charged variants.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

4. Dual signaling via interferon and DNA damage response elicits entrapment by giant PML nuclear bodies

   This article has 12 authors:

   1. Myriam Scherer
   2. Clarissa Read
   3. Gregor Neusser
   4. Christine Kranz
   5. Anna K Kuderna
   6. Regina Müller
   7. Florian Full
   8. Sonja Wörz
   9. Anna Reichel
   10. Eva-Maria Schilling
   11. Paul Walther
   12. Thomas Stamminger

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work has potential broad interest to both virologists and cell biologists interested in the regulatory functions of promyelocytic leukaemia nuclear bodies (PML-NBs). The authors use a combination of imaging techniques to identify PML, the principal scaffolding protein of PML-NBs, to form a variety of different structures in response to viral infection, immune stimulation, and DNA damage. Thestudy identifies PML to restrict the replication of human cytomegalovirus (HCMV) at multiple stages of infection through the formation of alternate PML-scaffold assemblies.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

5. Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development

   This article has 10 authors:

   1. Scott A Rankin
   2. Jeffrey D Steimle
   3. Xinan H Yang
   4. Ariel B Rydeen
   5. Kunal Agarwal
   6. Praneet Chaturvedi
   7. Kohta Ikegami
   8. Michael J Herriges
   9. Ivan P Moskowitz
   10. Aaron M Zorn

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The formation of the cardiopulmonary circuit is a vital terrestrial adaptation, and precise mechanisms defining how the heart and lung co-develop would be interesting to a broad developmental biology audience. In this manuscript, Rankin et al. propose a nuanced model that bridges previous observations regarding the role of Tbx5 and retinoic acid in forming the cardiopulmonary circuit. This manuscript nicely utilizes forward and reverse genetic approaches in Xenopus model system to rigorously study to describe a Tbx5-Aldh1a2- Shh pathway that leads to reciprocal mesoderm-endoderm interactions and co-induction of segmental heart and lung identities.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

6. Behavioral control by depolarized and hyperpolarized states of an integrating neuron

   This article has 2 authors:

   1. Aylesse Sordillo
   2. Cornelia I Bargmann

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The interneuron RIM affects many behaviours in C. elegans. Attempts to understand or manipulate its function have sometimes led to conflicting and difficult to interpret results. Sordillo and Bargmann investigate the role of the RIM in locomotion by manipulating it's signaling properties in multiple ways. The strength of this approach is that targeting multiple biological signaling mechanisms, they are able to conduct a nuanced analysis of RIM's signaling functions that goes beyond simplistic ON/OFF distinctions. They reach two primary conclusions: 1. RIM depolarization extends reversals via synaptic (glutamatergic) and secretory (tyraminergic) signaling; 2. RIM hyperpolarization promotes forward locomotion via electrical signaling through gap junctions. As a result, RIM was shown to act for stabilizing both forward and backward movement, which is important for understanding of C. elegans in general. Also, the implication that interneurons can be multifunctional in this way is intriguing and potentially impactful.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

7. Competitive binding of MatP and topoisomerase IV to the MukB dimerization hinge

   This article has 11 authors:

   1. Gemma L. M. Fisher
   2. Jani R. Bolla
   3. Karthik V. Rajasekar
   4. Jarno Mäkelä
   5. Rachel Baker
   6. Man Zhou
   7. Josh P. Prince
   8. Mathew Stracy
   9. Carol V. Robinson
   10. Lidia K. Arciszewska
   11. David J. Sherratt

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of potential interest to an audience of biochemists, cell biologists, and structural biologists working in the area of chromosome organization and segregation. A wide range of in vitro methods is used to provide compelling biochemical evidence for the interaction of MatP and ParEC at the hinge of MukB, the condensin of Enterobacteria. However, the evidence supporting the significance of these interactions in vivo is less strong, limiting the biological implications of the elegant biochemical findings.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

8. The YTHDF proteins ECT2 and ECT3 bind largely overlapping target sets and influence target mRNA abundance, not alternative polyadenylation

   This article has 8 authors:

   1. Laura Arribas-Hernández
   2. Sarah Rennie
   3. Michael Schon
   4. Carlotta Porcelli
   5. Balaji Enugutti
   6. Robin Andersson
   7. Michael D Nodine
   8. Peter Brodersen

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Post-transcriptional gene regulation mediated by YTH proteins that bind N6-methyladenosine (m6A) in mRNA is a pathway that has emerged of importance in eukaryotic biology. This paper focuses on two evolutionarily close proteins of this family, ETC2 and ETC3 to find redundant, specific and divergent functions. The authors addressed previously contradictory reports regarding the subcellular location of these proteins. The paper is of general interest to scientists within the field of post-transcriptional gene regulation and RNA biology and is not limited to the plant research community. This will advance our understanding of mRNA methylation and its role in plant biology.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

     This manuscript was co-submitted with: https://www.biorxiv.org/content/10.1101/2021.04.18.440342v2

   Reviewed by eLife

9. Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate

   This article has 5 authors:

   1. Thomas Hackl
   2. Sarah Duponchel
   3. Karina Barenhoff
   4. Alexa Weinmann
   5. Matthias G Fischer

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Approaching the search of novel viruses while in an endogenized stage, rather than as free virions, the study by Hackl et al. reveals a large diversity of complete and fragmented virophage genomes - termed EMALEs- scattered throughout the genomes of four strains of the marine protist Cafeteria. Given that the activation of the integrated virophage mavirus during infection by the giant virus, CroV, has been shown to have a protective effect on the Cafeteria population, this study provides a tantalizing window into the traces of virophage-giant virus¬-protist interactions in the marine environment. Given the enormous diversity of virophages and giant viruses that have been found in metagenomes with no known hosts, this study is a step towards deciphering the biology of these viruses.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

   Reviewed by eLife

10. Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2

    This article has 8 authors:

    1. Laura Arribas-Hernández
    2. Sarah Rennie
    3. Tino Köster
    4. Carlotta Porcelli
    5. Martin Lewinski
    6. Dorothee Staiger
    7. Robin Andersson
    8. Peter Brodersen

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Gene regulation triggered by recognising N6-methyladenosine (m6A) by RNA-binding proteins emerged as a fundamental process for development and adaptation in most eukaryotes. This paper is of interest to scientists within the field of post-transcriptional gene regulation and RNA biology. In a deep and thorough analysis, the authors resolved previously contradictory reports of sequence motifs associated with methylation sites in messenger RNAs and shed light on the proteins that recognise this modification.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

      This manuscript was co-submitted with: https://www.biorxiv.org/content/10.1101/2021.08.01.454660v1

    Reviewed by eLife