eLife

Latest preprint reviews

1. FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels

   This article has 7 authors:

   1. Ananya Palo
   2. Talina Mohapatra
   3. Anamika Singh
   4. Shithij Thalakkat
   5. Suryasikha Mohanty
   6. Rajeeb Kumar Swain
   7. Manjusha Dixit

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study by Palo et al proposes that FRG1 functions as a negative regulator of Nonsense-Mediated mRNA decay (NMD) by associating with the exon junction complex (EJC) and destabilizing UPF1 independently of DUX4. The authors present solid evidence to dissect the relationship between FRG1 and DUX4 in NMD. However, the evidence to support the claim that FRG1 is a component of the EJC or the NMD machinery is incomplete.

   Reviewed by eLife

2. Maternal SETDB1 enables development beyond cleavage stages by extinguishing the MERVL-driven 2-cell totipotency transcriptional program in the mouse embryo

   This article has 6 authors:

   1. Tie-Bo Zeng
   2. Zhen Fu
   3. Mary F. Majewski
   4. Ji Liao
   5. Marie Adams
   6. Piroska E. Szabó

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable finding on maternal SETDB1 as a key chromatin repressor that shuts down the 2C gene program and enables normal mouse embryonic development. The evidence supporting the claims of the authors is solid, although the inclusion of a causality test, a mechanistic understanding of SETDB1 targeting, and phenotypic quantification would have greatly strengthened the study. The work will be of broad interest to biologists working on embryonic development, stem cells and gene regulation.

   Reviewed by eLife

3. Cell cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase

   This article has 6 authors:

   1. Linda Choubani
   2. Hisashi Miura
   3. Takako Ichinose
   4. Asami Oji
   5. Rory T Cerbus
   6. Ichiro Hiratani

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript provides valuable insight into how genome organization changes as cells progress through the cell cycle after mitotic exit. The conclusions are supported by solid, rigorous data, and the use of sorted unsynchronized cells rather than cells treated with drugs is a particular strength. Two sharp genome remodeling events are identified at G1-S and to a lesser extent, at S-G2 transitions. A discussion on the limitations of Hi-C and a broader interpretation of results in the context of other mechanistic models would strengthen the overall rigor.

   Reviewed by eLife

4. Jam2 Signaling Functions Downstream of Hand2 To Initiate The Formation Of Organ-Specific Vascular Progenitors In Zebrafish

   This article has 7 authors:

   1. Martyna Griciunaite
   2. Julius Martinkus
   3. Sanjeeva Metikala
   4. Ricardo DeMoya
   5. Suman Gurung
   6. Diandra Rufin Florat
   7. Saulius Sumanas

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study addresses the question of how organ-specific blood vessels form during different stages of development, and how specific genes may regulate these processes. New genetic tools were developed to label distinct endothelial cell populations and track them over time in different mutant backgrounds. The results are solid; however, additional data quantification, lineage tracing, and cell autonomy experiments would further strengthen the conclusions.

   Reviewed by eLife

5. AT-HOOK-MOTIF NUCLEAR LOCALIZED 15 extends plant longevity by binding at poorly accessible, epigenetic mark-depleted chromatin that surrounds transcribed regions

   This article has 3 authors:

   1. Thalia Luden
   2. Jihed Chouaref
   3. Remko Offringa

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents an important study into the molecular function of AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15), a member of the AHL protein family, identifying it as a potential regulator of three-dimensional gene-loop organization within transcribed gene bodies. The authors support this claim with compelling genome-wide evidence, integrating AHL15 binding profiles with transcriptional and chromatin accessibility changes, as well as demonstrating overlap with genes known to form loops across transcribed regions. The evidence supporting the claims of the authors is solid. Collectively, these findings will be of broad interest to biologists seeking to understand the core regulatory mechanisms underlying gene expression.

   Reviewed by eLife

6. Uncoupling the TFIIH Core and Kinase Modules Leads To Misregulated RNA Polymerase II CTD Serine 5 Phosphorylation

   This article has 6 authors:

   1. Gabriela Giordano
   2. Robin Buratowski
   3. Célia Jeronimo
   4. Christian Poitras
   5. François Robert
   6. Stephen Buratowski

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important work demonstrates the role of physically linking the core and CTD kinase modules of TFIIH via separate domains of subunit Tfb3 in confining RNA Polymerase II Serine 5 CTD phosphorylation to promoter regions of transcribed genes in budding yeast. The main findings, resulting from analyses of viable Tfb3 mutants in which the linkage between TFIIH core and kinase modules has been severed, are supported by solid evidence from in vitro and in vivo experiments. There is an intriguing possibility that the Tfb3-mediated connection between core and kinase modules of TFIIH is an evolutionary addition to an ancestral state of physically unconnected enzymes, which could be examined more rigorously with additional evolutionary analyses.

   Reviewed by eLife

7. Energy Landscape Analysis Reveals Thalamic Modulation of Brain State Transitions During Movie Watching

   This article has 9 authors:

   1. Qiuyi Liu
   2. Lili Sun
   3. Xinyi Zhao
   4. Wenbin Qu
   5. Jiaqi Zhou
   6. Ziang Wang
   7. Kaizhou Li
   8. Huiting Lei
   9. Xia Liang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study investigated the dynamics of human cortical network activity with functional magnetic resonance imaging during movie watching and studied the modulation of these dynamics by subcortical areas using an energy landscape mapping method. The authors identified a set of brain states defined at the level of canonical functional networks, quantified how the brain transitions between these states, and related transition probabilities to inter-subject correlations in evoked brain activity. A major emphasis of the work concerns the role of the thalamus, which shows transition-linked activity changes and dynamic connectivity patterns, including differential involvement of parvalbumin- and calbindin-associated thalamic subdivisions. The analytical strategy developed in this study is applicable to other task- and resting-state fMRI data and would be useful for many researchers in the field; however, the evidence supporting the overall conclusions remains incomplete due to limitations associated with fMRI data preprocessing, analysis, and cross-validation.

   Reviewed by eLife

8. Impacts of DNA Methylation on H2A.Z Deposition and Nucleosome Stability

   This article has 4 authors:

   1. Rochelle M Shih
   2. Yasuhiro Arimura
   3. Hide A Konishi
   4. Hironori Funabiki

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides valuable mechanistic insight into the mutually exclusive distributions of the histone variant H2A.Z and DNA methylation by testing two hypotheses: (i) that DNA methylation destabilizes H2A.Z nucleosomes, thereby preventing H2A.Z retention, and (ii) that DNA methylation suppresses H2A.Z deposition by ATP-dependent chromatin remodelling complexes. Through a series of well-designed and carefully executed experiments, findings are presented in support of both hypotheses. However, the evidence in support of either hypothesis is incomplete, so that the proposed mechanisms underlying the enrichment of H2A.Z on unmethylated DNA remain somewhat speculative.

   Reviewed by eLife

9. Identifying tissue states by spatial protein patterns related to chemotherapy response in triple-negative breast cancer

   This article has 11 authors:

   1. Luciana M Luque
   2. Mohammad Asif Khan
   3. Giuseppe Torrisi
   4. Tessa D Green
   5. David Hardman
   6. Claudia Owczarek
   7. Tom A Phillips
   8. Debora S Marks
   9. Maddy Parsons
   10. Chris Sander
   11. Linus J Schumacher

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important work implementing data mining methods on IMC data to discover spatial protein patterns related to the triple-negative breast cancer patients' chemotherapy response. The evidence supporting the claims of the authors is solid, although more detailed methodology clarification and validation are needed. While the accuracy of the methods is not very high, the work shows potential for translational application.

   Reviewed by eLife

10. Molecular and Functional Analysis of Calcium Binding by a Cancer-linked Calreticulin Mutant

    This article has 7 authors:

    1. Ishmael Nii Ayibontey Tagoe
    2. Amanpreet Kaur
    3. Osbourne Quaye
    4. Emmanuel Ayitey Tagoe
    5. Nicole Koropatkin
    6. Leslie S Satin
    7. Malini Raghavan

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study investigates low-affinity Ca2+ binding by WT calreticulin and mutant calreticulin associated with type I myeloproliferative neoplasms, as well as the impact on Ca2+ fluxes in suspension cultures of megakaryocyte-like cells in vitro in response to ER Ca2+ ATPase inhibitors that deplete endoplasmic reticulum (ER) Ca2+ store and open plasma membrane Ca2+ channels through STIM1-Orai interactions. The results are important in that they show that Ca2+ binding by calreticulin and store-operated Ca2+ entry are not fundamentally impacted by the type I deletion mutation in calreticulin, which rules out a direct effect of the calreticulin mutation on its own low-affinity Ca2+ binding and any broad impact on ER Ca2+ regulation. The strength of the data and methods used ranges from solid to convincing, although the use of suspension-based flow cytometric assays to investigate ER Ca2+ levels and Ca2+ entry can be challenged. High-affinity Ca2+ binding sites could be further considered, and possible confounding effects of Abl kinase activity in the megakaryocyte-like cell lines could be offset.

    Reviewed by eLife