eLife

Latest preprint reviews

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. Involuntary feedback responses reflect a representation of partner actions

   This article has 7 authors:

   1. Seth R Sullivan
   2. John H Buggeln
   3. Jan A Calalo
   4. Truc T Ngo
   5. Jennifer A Semrau
   6. Michael J Carter
   7. Joshua GA Cashaback

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study combines a two-person joint hand-reaching paradigm with game-theoretical modeling to examine whether, and how, one's reflexive visuomotor responses are modulated by a partner's control policy and cost structure. The study provides a solid and novel set of behavioral findings suggesting that involuntary visuomotor feedback is indeed modulated in the context of interpersonal coordination. The work will be of interest to cognitive scientists studying the motoric and social aspects of action control.

   Reviewed by eLife

8. Concurrent category-selective neural activity across the ventral occipito-temporal cortex supports a non-hierarchical view of human visual recognition

   This article has 4 authors:

   1. Corentin Jacques
   2. Jacques Jonas
   3. Sophie Colnat-Coulbois
   4. Bruno Rossion

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study addresses a classic debate in visual processing, using a strong method applied to a rare clinical population to evaluate hierarchical models of visual object perception. The paper finds only partial support for the hierarchical model: as expected, neural responses in ventral visual cortex show increased representational selectivity for faces along the posterior-anterior axes, but the onsets of the signals do not show a temporal hierarchy, indicating more parallel processing. The iEEG dataset is impressive, but the evidence for lack of temporal hierarchy is incomplete: essential quality checks need to be performed, and statistical analyses adapted to ensure that the data and analyses would be able to reveal temporal hierarchy if it were present in the data.

   Reviewed by eLife

9. Domain-adaptive matching bridges synthetic and in vivo neural dynamics for neural circuit connectivity inference

   This article has 10 authors:

   1. Kaiwen Sheng
   2. Shanghang Zhang
   3. Shenjian Zhang
   4. Yutao He
   5. Maxime Beau
   6. Peng Qu
   7. Xiaofei Liu
   8. Youhui Zhang
   9. Lei Ma
   10. Kai Du

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This article reports an algorithm for inferring the presence of synaptic connection between neurons based on naturally occurring spiking activity of a neuronal network. One key improvement is to combine self-supervised and synthetic approaches to learn to focus on features that generalize to the conditions of the observed network. This valuable contribution is currently supported by incomplete evidence.

   Reviewed by eLife

10. Improved inference of latent neural states from calcium imaging data

    This article has 4 authors:

    1. Stephen Keeley
    2. David Zoltowski
    3. Adam Charles
    4. Jonathan Pillow

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This valuable study provides a practical computational framework for inferring latent neural states directly from calcium fluorescence recordings, bypassing the traditional need for a separate spike deconvolution step. The evidence supporting the method is solid, featuring rigorous validation across multiple latent variable model families (including HMM, GPFA, and LFADS) using both simulated and experimental data. However, the assessment of the method's generality would be further strengthened by application to a broader range of experimental datasets, such as recordings from different brain regions or using different calcium indicators.

    Reviewed by eLife