1. DNA methylation insulates genic regions from CTCF loops near nuclear speckles

    This article has 6 authors:
    1. Shelby A. Roseman
    2. Allison P. Siegenfeld
    3. Ceejay Lee
    4. Nicholas Z. Lue
    5. Amanda L. Waterbury
    6. Brian B. Liau
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study examines the impact of DNA methylation on CTCF binding in two cancer cell lines. Increased CTCF binding sites are enriched in gene bodies, and associate with nuclear speckles, indicating a potential role in increased transcription. However, the association with nuclear speckles needs to be more diligently demonstrated. Thus the strength of the evidence is considered incomplete. This work would be made more valuable to the community if these claims were buttressed by additional evidence and a deeper discussion of new findings in the light of previous relevant literature. This work will be of interest to the chromosome biology/epigenetics field.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  2. A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

    This article has 4 authors:
    1. Arkadiy K Golov
    2. Alexey A Gavrilov
    3. Noam Kaplan
    4. Sergey V Razin
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Identifying chromatin interactions with high sensitivity and resolution at the genome-wide scale continues to be technically challenging. This study introduces findings based on the improved MNase-based proximity ligation method, MChIP-C, which enables genome-wide measurement of chromatin interactions at single-nucleosome resolution. The evidence presented in this manuscript is convincing, and the technological advancements will be valuable for the study of 3D genome architecture.

    Reviewed by eLife

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  3. Is tumor mutational burden predictive of response to immunotherapy?

    This article has 5 authors:
    1. Carino Gurjao
    2. Dina Tsukrov
    3. Maxim Imakaev
    4. Lovelace J Luquette
    5. Leonid A Mirny
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This useful study examines relationships between tumor mutational burden and the response to immunotherapy, using new data sets along with publicly available data sets. The authors conclude that tumor mutational burden cut-offs are unreliable proxies for predicting the response to therapy, underpinned by solid evidence, but with several caveats and assumptions that leave the central question subject to further inquiry. In summary, this is an interesting study that adds to a growing body of work investigating the particular conditions governing the effectiveness of immunotherapy.

    Reviewed by eLife

    This article has 6 evaluationsAppears in 1 listLatest version Latest activity
  4. Increased inflammatory signature in myeloid cells of non-small cell lung cancer patients with high clonal hematopoiesis burden

    This article has 7 authors:
    1. Hyungtai Sim
    2. Hyun Jung Park
    3. Geun-Ho Park
    4. Yeon Jeong Kim
    5. Woong-Yang Park
    6. Se-Hoon Lee
    7. Murim Choi
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable article represents a significant body of work that addresses some novel aspects of the biology of lung cancer, the overall influence of CHIP and its impacts on responses to therapy. While a high clonal hematopoiesis (CHIP) burden was previously linked with an inflammatory phenotype in other disease settings, the authors demonstrate with solid evidence that this is also true for lung cancer. CHIP is complex and more data will be required to substantiate more evidence with regard perhaps to specific mutations in certain situations and how this might influence therapy choices.

    Reviewed by eLife

    This article has 6 evaluationsAppears in 1 listLatest version Latest activity
  5. Functional characteristics and computational model of abundant hyperactive loci in the human genome

    This article has 2 authors:
    1. Sanjarbek Hudaiberdiev
    2. Ivan Ovcharenko
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study explores the sequence characteristics and conservation of high-occupancy target loci, regions in the human genome such as promoters and enhancers that are bound by a multitude of transcription factors. The computational analyses presented in this study are solid. This study would be a helpful resource for researchers performing ChIP-seq based analyses of transcription factor binding.

    Reviewed by eLife

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  6. Expression of most retrotransposons in human blood correlates with biological aging

    This article has 8 authors:
    1. Yi-Ting Tsai
    2. Nogayhan Seymen
    3. I Richard Thompson
    4. Xinchen Zou
    5. Warisha Mumtaz
    6. Sila Gerlevik
    7. Ghulam J Mufti
    8. Mohammad M Karimi
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      The study by Tsai et al. employed multi-omics approaches, including transcriptomic, methylomic, and single-cell RNA-seq, and provided a solid and comprehensive analysis of the correlation between retrotransposable element (RTE) expression and biological aging in human blood. Their findings highlight the differential roles of RTE families, providing valuable insights for understanding the mechanisms of human aging.

    Reviewed by eLife

    This article has 11 evaluationsAppears in 1 listLatest version Latest activity
  7. High-speed whole-genome sequencing of a Whippet: Rapid chromosome-level assembly and annotation of an extremely fast dog’s genome

    This article has 8 authors:
    1. Marcel Nebenführ
    2. David Prochotta
    3. Alexander Ben Hamadou
    4. Axel Janke
    5. Charlotte Gerheim
    6. Christian Betz
    7. Carola Greve
    8. Hanno Jörn Bolz
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      This Data Release paper presents the genome of the whippet breed of dog. Demonstrating a streamlined laboratory and bioinformatics workflows with PacBio HiFi long-read whole-genome sequencing that enables the generation of a high-quality reference genome within one week. The genome study being a collaboration between an academic biodiversity institute and a medical diagnostic company. The presented method of working and workflow providing examples that can be used for a wide range of future human and non-human genome projects. The final is 2.47 Gbp assembly being of high quality - with a contig N50 of 55 Mbp and a scaffold N50 of 65.7 Mbp. This reference being scaffolded into 39 chromosome-length scaffolds and the annotation resulting in 28,383 transcripts. The results also looked at the Myostatin gene which can be used for breeding purposes, as these heterozygous animals can have an advantage in dog races. The reviewers making the authors clarify this part a little better with additional results. Overall this study demonstrating how rapidly animal genome research can be carried out through close and streamlined time management and collaboration.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
  8. Transcriptomic profiling of Schlemm’s canal cells reveals a lymphatic-biased identity and three major cell states

    This article has 15 authors:
    1. Revathi Balasubramanian
    2. Krishnakumar Kizhatil
    3. Taibo Li
    4. Nicholas Tolman
    5. Aakriti Bhandari
    6. Graham Clark
    7. Violet Bupp-Chickering
    8. Ruth A Kelly
    9. Sally Zhou
    10. John Peregrin
    11. Marina Simón
    12. Christa Montgomery
    13. W Daniel Stamer
    14. Jiang Qian
    15. Simon WM John
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study has characterized the unique expression of Schlemm's canal endothelial cells (SECs) using FACS-sorted specific cell bulk RNA-Seq and scRNA-/snRNA-Seq of mouse SECs. The compelling study identified novel biomarkers for SECs and molecular markers for two inner wall SEC states and outwall SECs in mouse eyes. Significant gene networks and pathways were elucidated for their potential contribution to glaucoma pathogenesis, providing targets for further research in relation to glaucoma.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  9. Interchromosomal segmental duplication drives translocation and loss of P. falciparum histidine-rich protein 3

    This article has 11 authors:
    1. Nicholas J Hathaway
    2. Isaac E Kim
    3. Neeva WernsmanYoung
    4. Sin Ting Hui
    5. Rebecca Crudale
    6. Emily Y Liang
    7. Christian P Nixon
    8. David Giesbrecht
    9. Jonathan J Juliano
    10. Jonathan B Parr
    11. Jeffrey A Bailey
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This work provides important insight into the mechanisms of hrp2 and particularly hrp3 deletion generation. The generation of additional long-read data alongside a new analysis of 19,000 public short-read sequenced genomes makes this the most detailed investigation currently available on this topic, which has high public health importance and also basic biological interest. The revised version of the manuscript provides convincing evidence for the proposed mechanisms.

    Reviewed by eLife

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  10. Genome-wide mapping of native co-localized G4s and R-loops in living cells

    This article has 8 authors:
    1. Ting Liu
    2. Xing Shen
    3. Yijia Ren
    4. Hongyu Lu
    5. Yu Liu
    6. Chong Chen
    7. Lin Yu
    8. Zhihong Xue
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study describes a useful antibody-free method to map both G-quadruplexes and R-loops in vertebrate cells independently of the BG4 and S9.6 antibodies. It also reveals that the helicase Dhx9 can affect the self-renewal and differentiation capacities of mESCs, perhaps by regulating co-localized G4s and R-loops. The datasets provided might constitute a good starting point for future functional studies, and although the strength of the evidence that DHX9 interferes with the ability of mESCs to differentiate by regulating directly the stability of either G4s or R-loops has been improved compared to a previous version, it is still incomplete.

    Reviewed by eLife

    This article has 10 evaluationsAppears in 1 listLatest version Latest activity
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