eLife

Latest preprint reviews

1. Global chromatin mobility induced by a DSB is dictated by chromosomal conformation and defines the HR outcome

   This article has 7 authors:

   1. Fabiola García Fernández
   2. Etienne Almayrac
   3. Ànnia Carré Simon
   4. Renaud Batrin
   5. Yasmine Khalil
   6. Michel Boissac
   7. Emmanuelle Fabre

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study is of relevance to the field of DNA repair. It uses a cleverly designed new recombination assay in yeast to address the impact of DNA break position on global genome mobility. A centromere-proximal DNA double-strand break (DSB) induces an H2A(X) phosphorylation-dependent global mobility that accelerates but is not essential for DSB repair, while a centromere-distal DSB triggers global mobility that is essential for repair and which depends on H2A(X) phosphorylation, Rad9 and Rad51. Together, these data support a model where global genome mobility promotes homologous recombination repair, particularly for centromere-distal DSBs, and help settle some recent controversy in the field.

     (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 #3 agreed to share their name with the authors.)

   Reviewed by eLife

2. Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans

   This article has 10 authors:

   1. Jun Kim
   2. David S Jimenez
   3. Bhavana Ragipani
   4. Bo Zhang
   5. Lena A Street
   6. Maxwell Kramer
   7. Sarah E Albritton
   8. Lara H Winterkorn
   9. Ana K Morao
   10. Sevinc Ercan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is potentially of broad interest to researchers in the chromosome biology field. With specific loading sequences identified, the condensin DC complex studied here provides an elegant system to investigate the in vivo activities of SMC complexes. Combining Hi-C, ChIP-seq and RNA-seq, the authors have a comprehensive suite of assays to probe their questions. However, not all of their major conclusions are currently supported by the data.

     (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

3. Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia

   This article has 8 authors:

   1. Sean Akira Montgomery
   2. Tetsuya Hisanaga
   3. Nan Wang
   4. Elin Axelsson
   5. Svetlana Akimcheva
   6. Milos Sramek
   7. Chang Liu
   8. Frédéric Berger

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Mechanisms for controlling gene dosage and uniparental gene expression vary widely across the eukaryotic tree, with many such mechanisms still unknown. Montgomery et al. describe an epigenetic mechanism used to modulate paternal chromosome gene dosage during the transient diploid state of the primarily haploid plant, Marchantia polymorpha. This fascinating case of genome-wide genomic imprinting will be of broad interest to evolutionary biologists, epigeneticists, and those focused on understanding the context and mechanisms of gene dosage control.

     (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

4. Natural killer (NK) cell-derived extracellular-vesicle shuttled microRNAs control T cell responses

   This article has 13 authors:

   1. Sara G Dosil
   2. Sheila Lopez-Cobo
   3. Ana Rodriguez-Galan
   4. Irene Fernandez-Delgado
   5. Marta Ramirez-Huesca
   6. Paula Milan-Rois
   7. Milagros Castellanos
   8. Alvaro Somoza
   9. Manuel José Gómez
   10. Hugh T Reyburn
   11. Mar Vales-Gomez
   12. Francisco Sánchez Madrid
   13. Lola Fernandez-Messina

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This report identified NK-extracellular-vesicle (NK-EV)-associated microRNAs and characterized them by small RNA next-generation sequencing. They found that NK-EVs promote Th1 polarization and activation of monocyte and monocyte-derived dendritic cells. The findings are potentially important for understanding NK cell function.

     (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

5. SMAD4 and TGFβ are architects of inverse genetic programs during fate determination of antiviral CTLs

   This article has 9 authors:

   1. Karthik Chandiran
   2. Jenny E Suarez-Ramirez
   3. Yinghong Hu
   4. Evan R Jellison
   5. Zeynep Ugur
   6. Jun Siong Low
   7. Bryan McDonald
   8. Susan M Kaech
   9. Linda S Cauley

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors set out to investigate the roles of SMAD4 and TGFbeta in regulating memory CD8 T cell differentiation during viral infection. To achieve their goal, the authors utilized a variety of available tools including, gene expression, mice that lack certain regulatory genes, and different tissue tissue culture approaches. Although the in vitro experiments yielded interesting results that will interest students of T cell immunology/biology, there is an absence of results from in vivo studies that would validate the in vitro observations.

     (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

6. Activation of targetable inflammatory immune signaling is seen in myelodysplastic syndromes with SF3B1 mutations

   This article has 31 authors:

   1. Gaurav S Choudhary
   2. Andrea Pellagatti
   3. Bogos Agianian
   4. Molly A Smith
   5. Tushar D Bhagat
   6. Shanisha Gordon-Mitchell
   7. Srabani Sahu
   8. Sanjay Pandey
   9. Nishi Shah
   10. Srinivas Aluri
   11. Ritesh Aggarwal
   12. Sarah Aminov
   13. Leya Schwartz
   14. Violetta Steeples
   15. Robert N Booher
   16. Murali Ramachandra
   17. Maria Samson
   18. Milagros Carbajal
   19. Kith Pradhan
   20. Teresa V Bowman
   21. Manoj M Pillai
   22. Britta Will
   23. Amittha Wickrema
   24. Aditi Shastri
   25. Robert K Bradley
   26. Robert E Martell
   27. Ulrich G Steidl
   28. Evripidis Gavathiotis
   29. Jacqueline Boultwood
   30. Daniel T Starczynowski
   31. Amit Verma

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is an outstanding manuscript evaluating a mutation commonly seen in AML and MDS in a spliceosome protein called SF3B1. The authors link this spliceosome mutation to altered transcripts and ultimately to cell cycle proteins and differentiation. This paper will be of high interest for oncologists in that it demonstrates that AML and MDS cells with this mutation can be targeted in a precision medicine approach.

     (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

7. HIF-1α induces glycolytic reprograming in tissue-resident alveolar macrophages to promote cell survival during acute lung injury

   This article has 10 authors:

   1. Parker S Woods
   2. Lucas M Kimmig
   3. Kaitlyn A Sun
   4. Angelo Y Meliton
   5. Obada R Shamaa
   6. Yufeng Tian
   7. Rengül Cetin-Atalay
   8. Willard W Sharp
   9. Robert B Hamanaka
   10. Gökhan M Mutlu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study provides important new information regarding the functions and behavior of lung tissue-resident alveolar macrophages in the context of acute lung injury. New data regarding the impact of hypoxia via HIF-1 on biology of these critical cells are provided and importantly suggesting an impact on the outcome of lung injury.

     (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. A model of egocentric to allocentric understanding in mammalian brains

   This article has 8 authors:

   1. Benigno Uria
   2. Borja Ibarz
   3. Andrea Banino
   4. Vinicius Zambaldi
   5. Dharshan Kumaran
   6. Demis Hassabis
   7. Caswell Barry
   8. Charles Blundell

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper presents an artificial neuronal network which, from action and visual inputs, develops representations of space comparable to those found in the navigational system of the brain. They show that the representations developed by this network can be used in novel environments and in a reinforcement learning task. This demonstration of representations in absolute coordinates from agent-centered information is a significant contribution to neuroscientists as well as machine learning.

     (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

9. Whole-brain comparison of rodent and human brains using spatial transcriptomics

   This article has 6 authors:

   1. Antoine Beauchamp
   2. Yohan Yee
   3. Ben C Darwin
   4. Armin Raznahan
   5. Rogier B Mars
   6. Jason P Lerch

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript is of interest to readers interested in how brain gene expression patterns differ between humans and other animals. The authors develop an innovative approach to map correspondences between the gene expression profiles of human and mouse brains, finding that the profiles of sensorimotor areas are more similar than those of transmodal association cortex. This thus contributes to our understanding of the genetic mechanisms that may drive differences in brain organization across species. The study is methodologically sound and the key claims are supported by the data.

     (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

10. High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly

    This article has 15 authors:

    1. Martin H Berryer
    2. Gizem Rizki
    3. Anna Nathanson
    4. Jenny A Klein
    5. Darina Trendafilova
    6. Sara G Susco
    7. Daisy Lam
    8. Angelica Messana
    9. Kristina M Holton
    10. Kyle W Karhohs
    11. Beth A Cimini
    12. Kathleen Pfaff
    13. Anne E Carpenter
    14. Lee L Rubin
    15. Lindy E Barrett

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Berryer et al. report on an automated and quantitative platform to study the number of synaptic inputs formed in networks of human excitatory neurons and astrocytes in vitro. The authors tested the utility of the platform by screening a large collection of small molecules and identified several modulators of synapse density, which were validated in follow-up experiments. The automated platform substantially extends what is currently available, particularly with respect to the automation of the initial analysis steps. The positive hits identified here, the inhibitors of bromodomain and extraterminal (BET) family of gene expression regulators, are important, and will likely contribute to the understanding of the mechanisms of human synapse assembly.

      (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 name with the authors.)

    Reviewed by eLife