eLife

Latest preprint reviews

1. PTBP1 depletion in mature astrocytes reveals distinct splicing alterations without neuronal features

   This article has 5 authors:

   1. Min Zhang
   2. Naoto Kubota
   3. David Nikom
   4. Ayden Arient
   5. Sika Zheng

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study reports important negative results, showing that genetically removing the RNA-binding protein PTBP1 in astrocytes is insufficient to convert them into neurons, thereby challenging previous claims in the field. It also offers a compelling analysis of PTBP1's role in regulating astrocyte-specific splicing. The evidence is strong, as the experiments are technically sound, carefully controlled, and supported by both imaging and transcriptomic analyses.

   Reviewed by eLife

2. Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution

   This article has 4 authors:

   1. Alastair J Tulloch
   2. Ryan Nicholas Delgado
   3. Rinaldo Catta-Preta
   4. Constance L Cepko

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript presents a valuable methodological approach to investigating context-dependent activity of cis-regulatory activity within defined genomic loci. The authors combine a locus-specific massively parallel reporter assay, enabling unbiased and high-coverage profiling of enhancer activity across large genomic regions, with a degenerate reporter assay to identify nucleotides critical for enhancer function. The data supporting the conclusions are solid, highlighted by successful identification and characterization of both previously known and new regulatory elements across multiple developmental stages, cell types, and species. While the approach has inherent limitations in sensitivity, and indirect assignment of regulatory elements to target genes, it provides a flexible platform for nominating candidate cis-regulatory elements across defined loci.

   Reviewed by eLife

3. Formation of task representations and replay in mouse medial prefrontal cortex

   This article has 6 authors:

   1. Hamed Shabani
   2. Hannah Muysers
   3. Yuk-Hoi Yiu
   4. Jonas-Frederic Sauer
   5. Marlene Bartos
   6. Christian Leibold

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study characterizes the evolution of medial prefrontal cortex activity during the learning of an odor-based choice task. The evidence provided is solid, providing quantification of functional classes of cells over the course of learning using the longitudinal calcium recordings in prefrontal cortex, and quantification of prefrontal sequences. However, the experimental design appears to provide limited evidence to support strong conclusions regarding the functional relevance of neural sequences. The study will be of interest to neuroscientists investigating learning and decision-making processes.

   Reviewed by eLife

4. JAX Animal Behavior System (JABS), a genetics-informed, end-to-end advanced behavioral phenotyping platform for the laboratory mouse

   This article has 7 authors:

   1. Anshul Choudhary
   2. Brian Q Geuther
   3. Thomas J Sproule
   4. Glen Beane
   5. Vivek Kohar
   6. Jarek Trapszo
   7. Vivek Kumar

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study presents JABS, an open-source platform that integrates hardware and user-friendly software for standardized mouse behavioral phenotyping. The work has practical implications for improving reproducibility and accessibility in behavioral neuroscience, especially for linking behavior to genetics across diverse mouse strains. The strength of evidence is convincing, with comprehensive validation of the platform's components and enthusiastic reviewer support.

   Reviewed by eLife

5. OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species

   This article has 5 authors:

   1. Kuan-Hao Chao
   2. Alan Mao
   3. Anqi Liu
   4. Steven L Salzberg
   5. Mihaela Pertea

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study introduces a modern and accessible PyTorch reimplementation of the widely used SpliceAI model for splice site prediction. The authors provide convincing evidence that their OpenSpliceAI implementation matches the performance of the original while improving usability and enabling flexible retraining across species. These advances are likely to be of broad interest to the computational genomics community.

   Reviewed by eLife

6. The microtubule-binding protein EML3 is required for mammalian embryonic growth and cerebral cortical development; Eml3 null mice are a model of cobblestone brain malformation

   This article has 10 authors:

   1. Isabelle Carrier
   2. Eduardo Diez
   3. Valerio EC Piscopo
   4. Susanne Bechstedt
   5. Hans van Bokhoven
   6. Myriam Srour
   7. Albert Berghuis
   8. Stefano Stifani
   9. Yojiro Yamanaka
   10. Roderick R McInnes

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study is the first characterization of the phenotype caused by a lack of Eml3 expression in mice. Mutant animals present a disrupted pial basement membrane, leading to focal extrusions from the cerebral cortex, called ectopias. The methodology is convincing and the conclusions are solid, although further investigations on the molecular and cellular mechanisms are required to improve the manuscript. This work would be of interest to neural development biologists and human geneticists working on brain disorders.

   Reviewed by eLife

7. SLC35G3 is a UDP-N-acetylglucosamine transporter for sperm glycoprotein formation and underpins male fertility in mice

   This article has 5 authors:

   1. Daisuke Mashiko
   2. Shingo Tonai
   3. Haruhiko Miyata
   4. Martin M Matzuk
   5. Masahito Ikawa

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study reports the physiological function of a putative transmembrane UDP-N-acetylglucosamine transporter called SLC35G3 in spermatogenesis. The conclusion that SLC35G3 is a new and essential factor for male fertility in mice and probably in humans is supported by convincing data. This study will be of interest to reproductive biologists and physicians working on male infertility.

   Reviewed by eLife

8. A quantitative in vivo CRISPR-imaging platform identifies regulators of hyperplastic and hypertrophic adipose morphology in zebrafish

   This article has 3 authors:

   1. Rebecca Wafer
   2. Panna Tandon
   3. James Minchin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this manuscript, Wafer and Tandon et al. present a thoughtful and well-designed genetic screen for regulators of adipose remodeling using zebrafish as a model system. This work is valuable because it uncovers several genes associated with adipose tissue hyperplastic hypertrophic morphology and diet-induced remodelingthe hat have considerable potential health impact. The rigorous phenotypic analyses and compelling evidence make this work a key resource for the field.

   Reviewed by eLife

9. Allosteric modulation of dimeric GPR3 by ligands in the dimerization interface

   This article has 7 authors:

   1. Zeming Qiu
   2. Wei Wang
   3. Yingying Nie
   4. Junxiang Lin
   5. Beimeng Zhang
   6. Haonan Xing
   7. Sanduo Zheng

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Qiu et al. present multiple dimeric structures of GPR3, which reveal the binding mode of the inverse agonist AF64394. The findings provide important insights into the regulation of GPCR3 and potentially other related orphan GPCRs. The authors present convincing evidence of their claims through thoughtful analysis of their cryo-EM structures, mutagenesis, and cell-based assays. This work will be of interest to GPCR investigators, especially those studying the signaling of orphan receptors.

   Reviewed by eLife

10. ATG2A engages RAB1A and ARFGAP1 positive membranes during autophagosome biogenesis

    This article has 11 authors:

    1. Devin M Fuller
    2. Yumei Wu
    3. Florian Schueder
    4. Burha Rasool
    5. Shanta Nag
    6. Justin L Korfhage
    7. Rolando Garcia-Milian
    8. Katerina D Melnyk
    9. Joerg Bewersdorf
    10. Pietro De Camilli
    11. Thomas J Melia

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study provides important insights into the crosstalk between ATG2A with components of the early secretory pathway. While the mechanisms governing autophagic membrane expansion remain yet to be fully understood, in this study the authors employ an elegant proximity labelling approach and identify two ER-Golgi intermediate compartment (ERGIC)-localized proteins. Through a series of complementary experiments combining microscopy and biochemistry, the authors identify ARFGAP1 and Rab1A as components of early autophagic membranes, which accumulate at the periphery of pre-autophagosomal structures induced by loss of ATG2. The overall study is well executed and the evidence supporting the claims is convincing.

    Reviewed by eLife