eLife

Latest preprint reviews

1. Spatial chromatin accessibility sequencing resolves high-order spatial interactions of epigenomic markers

   This article has 17 authors:

   1. Yeming Xie
   2. Fengying Ruan
   3. Yaning Li
   4. Meng Luo
   5. Chen Zhang
   6. Zhichao Chen
   7. Zhe Xie
   8. Zhe Weng
   9. Weitian Chen
   10. Wenfang Chen
   11. Yitong Fang
   12. Yuxin Sun
   13. Mei Guo
   14. Juan Wang
   15. Shouping Xu
   16. Hongqi Wang
   17. Chong Tang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This paper reports the development of SCA-seq, a new method derived from PORE-C for simultaneously measuring chromatin accessibility, genome 3D and CpG DNA methylation. Most of the conclusions are supported by convincing data. SCA-seq has the potential to become a useful tool to the scientific communities to interrogate genome structure-function relationships.

   Reviewed by eLife

2. Cancers adapt to their mutational load by buffering protein misfolding stress

   This article has 4 authors:

   1. Susanne Tilk
   2. Judith Frydman
   3. Christina Curtis
   4. Dmitri A Petrov

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Tilk and colleagues present a computational analysis of tumor transcriptomes to investigate the hypothesis that the large number of somatic mutations in some tumors is detrimental such that these detrimental effects are mitigated by an up-regulation by pathways and mechanisms that prevent protein misfolding. The authors address this question by fitting a model that explains the log expression of a gene as a linear function of the log number of mutations in the tumor and show that specific categories of genes (proteasome, chaperones, ...) tend to be upregulated in tumors with a large number of somatic mutations. Some of the associations presented could arise through confounding, but overall the authors present solid evidence that mutational load is associated with higher expression of genes involved in mitigation of protein misfolding – an important finding with general implications for our understanding of cancer evolution.

   Reviewed by eLife

3. High-altitude hypoxia exposure inhibits erythrophagocytosis by inducing macrophage ferroptosis in the spleen

   This article has 9 authors:

   1. Wan-ping Yang
   2. Mei-qi Li
   3. Jie Ding
   4. Jia-yan Li
   5. Gang Wu
   6. Bao Liu
   7. Yu-qi Gao
   8. Guo-hua Wang
   9. Qian-qian Luo

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This useful study reports that a week or more of hypoxia exposure in mice increases erythropoiesis and decreases the number of iron-recycling macrophages in the spleen, compromising their capacity for red blood cell phagocytosis – reflected by increased mature erythrocyte retention in the spleen. Compared to an earlier version, the study has been strengthened with mouse experiments under hypobaric hypoxia and complemented by extensive ex vivo analyses. Unfortunately, while some of the evidence is solid, the work as it currently stands only incompletely supports the authors' hypotheses. While the study would benefit from additional experiments that more directly buttress the central claims, it should be of interest to the fields of hemopoiesis and bone marrow biology and possibly also blood cancer.

   Reviewed by eLife

4. A local ATR-dependent checkpoint pathway is activated by a site-specific replication fork block in human cells

   This article has 9 authors:

   1. Sana Ahmed-Seghir
   2. Manisha Jalan
   3. Helen E Grimsley
   4. Aman Sharma
   5. Shyam Twayana
   6. Settapong T Kosiyatrakul
   7. Christopher Thompson
   8. Carl L Schildkraut
   9. Simon N Powell

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript reports important data on the cellular response to a single site-specific replication fork block in human MCF7 cells. Compelling evidence shows the efficacy of the bacterial Tus-Ter system to stall replication forks in human cells. Fork stalling let to lasting ATR-dependent phosphorylation of histone H2AX but not of ATR itself and its downstream targets RPA and CHK1.

   Reviewed by eLife

5. Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids

   This article has 7 authors:

   1. Galina Popova
   2. Hanna Retallack
   3. Chang N Kim
   4. Albert Wang
   5. David Shin
   6. Joseph L DeRisi
   7. Tomasz Nowakowski

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The manuscript represents an important study on the pathogenesis of rubella virus tropism and neuropathology in human microglia-containing human stem cell derived organoids and human fetal brain slices. The strength of evidence is compelling, employing two different human-relevant models. The findings will be of broad interest to virologists and infectious disease experts, as well as neurodevelopmental biologists. The findings could also be of interest to pediatrics and obstetrics clinical colleagues.

   Reviewed by eLife

6. Fetal influence on the human brain through the lifespan

   This article has 14 authors:

   1. Kristine B Walhovd
   2. Stine K Krogsrud
   3. Inge K Amlien
   4. Øystein Sørensen
   5. Yunpeng Wang
   6. Anne Cecilie S Bråthen
   7. Knut Overbye
   8. Jonas Kransberg
   9. Athanasia M Mowinckel
   10. Fredrik Magnussen
   11. Martine Herud
   12. Asta K Håberg
   13. Anders Martin Fjell
   14. Didac Vidal-Pineiro

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study uses multiple large neuroimaging data sets acquired at different points through the lifespan to provide solid evidence that birthweight (BW) is associated with robust and persistent variations in cortical anatomy, but less-substantial influences on cortical change over time. These findings, supported by robust statistical methods, illustrate the long temporal reach of early developmental influences and carry relevance for how we conceptualize, study, and potentially modify such influences more generally. The paper will be of interest to people interested in brain development and aging.

   Reviewed by eLife

7. Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models

   This article has 10 authors:

   1. Rita Sianga-Mete
   2. Penelope Hartnady
   3. Wimbai Caroline Mandikumba
   4. Kayleigh Rutherford
   5. Christopher Brian Currin
   6. Florence Phelanyane
   7. Sabina Stefan
   8. Steven Weaver
   9. Sergei L Kosakovsky Pond
   10. Darren P Martin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study revisits the effects of substitution model selection on phylogenetics by comparing reversible and non-reversible DNA substitution models. The authors provide evidence that 1) non time-reversible models sometimes perform better than general time-reversible models when inferring phylogenetic trees out of simulated viral genome sequence data sets, and that 2) non time-reversible models can fit the real data better than the reversible substitution models commonly used in phylogenetics, a finding consistent with previous work. However, the methods are incomplete in supporting the main conclusion of the manuscript, that is that non time-reversible models should be incorporated in the model selection process for these data sets.

   Reviewed by eLife

8. Context-dependent modification of PFKFB3 in hematopoietic stem cells promotes anaerobic glycolysis and ensures stress hematopoiesis

   This article has 28 authors:

   1. Shintaro Watanuki
   2. Hiroshi Kobayashi
   3. Yuki Sugiura
   4. Masamichi Yamamoto
   5. Daiki Karigane
   6. Kohei Shiroshita
   7. Yuriko Sorimachi
   8. Shinya Fujita
   9. Takayuki Morikawa
   10. Shuhei Koide
   11. Motohiko Oshima
   12. Akira Nishiyama
   13. Koichi Murakami
   14. Miho Haraguchi
   15. Shinpei Tamaki
   16. Takehiro Yamamoto
   17. Tomohiro Yabushita
   18. Yosuke Tanaka
   19. Go Nagamatsu
   20. Hiroaki Honda
   21. Shinichiro Okamoto
   22. Nobuhito Goda
   23. Tomohiko Tamura
   24. Ayako Nakamura-Ishizu
   25. Makoto Suematsu
   26. Atsushi Iwama
   27. Toshio Suda
   28. Keiyo Takubo

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study provides novel strategies to overcome certain limitations when investigating the metabolism of hematopoietic stem cells, mainly due to their low abundance. The study provides compelling evidence suggesting that proliferative hematopoietic stem cells mainly use glycolysis (rather than mitochondrial OXPHOS or TCA cycle) as their primary energy source during emergency hematopoiesis. The article provides direct links between metabolic features and cell proliferation and explores alternative energy sources, and is of great interest to stem cell biologists.

   Reviewed by eLife

9. A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

   This article has 8 authors:

   1. Nicole A Ellis
   2. Kevin S Myers
   3. Jessica Tung
   4. Anne Davidson Ward
   5. Kathryn Johnston
   6. Katherine E Bonnington
   7. Timothy J Donohue
   8. Matthias P Machner

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study uses CRISPRi to silence multiple effectors in the pathogen, Legionella pneumophila. It provides a technique that will allow researchers to address functional redundancy amongst effectors, a problem that has persisted even after decades of study. The methodology used is convincing, and further improvement (such as using multiple guides per gene) can lead to the identification of novel virulence factors.

   Reviewed by eLife

10. Multiple repeat regions within mouse DUX recruit chromatin regulators to facilitate an embryonic gene expression program

    This article has 4 authors:

    1. Christina M. Smith
    2. Edward J. Grow
    3. Sean C. Shadle
    4. Bradley R. Cairns

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This useful study provides a systematic mutational analysis to elucidate mechanisms involved in transcriptional activation by the murine DUX protein, DUX is a master transcription factor regulating mammalian early embryonic gene activation and its human homolog DUX4 is also involved in a muscular disease, fascioscapulohumeral dystrophy (FSHD). The data are solid and the interpretations of the findings are reasonable. The work will be of interest to colleagues studying early embryonic development or FSHD.

    Reviewed by eLife