eLife

Latest preprint reviews

1. Site-specific DNA demethylation during spermatogenesis presets the sites of nucleosome retention in mouse sperm

   This article has 5 authors:

   1. So Maezawa
   2. Masashi Yukawa
   3. Akihiko Sakashita
   4. Artem Barski
   5. Satoshi H Namekawa

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides valuable findings on the role of site-specific DNA methylation changes during spermatogenesis and their contribution to paternal epigenetic inheritance. The study proposes that selective loss of DNA methylation at a subset of promoters is required for nucleosome retention and the establishment of epigenetic states that may influence embryonic gene regulation. The present study's conclusion is mostly supported by solid data.

   Reviewed by eLife

2. A mathematical model clarifies the ABC Score formula used in enhancer-gene prediction

   This article has 3 authors:

   1. Joseph Nasser
   2. Kee-Myoung Nam
   3. Jeremy Gunawardena

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study dissects the mathematical and biological assumptions underlying the commonly used Activity-by-Contact model of enhancer action in transcriptional regulation. The authors provide a convincing mathematical analysis that links this (mostly phenomenological) model to concrete molecular mechanisms of enhancer function. This work provides a strong foundation from which to analyze a broad swath of genome-wide data such as that generated by CRISPRi screens.

   Reviewed by eLife

3. We couldn't get details of this article at this time:
   10.1101/2024.11.18.623660

4. We couldn't get details of this article at this time:
   10.1101/2023.11.29.569072

5. We couldn't get details of this article at this time:
   10.1101/2024.10.22.619585

6. We couldn't get details of this article at this time:
   10.1101/2025.02.07.637179

7. Master control genes in the regeneration of rod photoreceptors from endogenous progenitor cells in zebrafish retina

   This article has 9 authors:

   1. Eyad Shihabeddin
   2. Abirami Santhanam
   3. Stephan Tetenborg
   4. Alexandra L Aronowitz
   5. Haichao Wei
   6. Guoting Qin
   7. Chengzhi Cai
   8. Jiaqian Wu
   9. John O’Brien

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Shihabeddin et al utilized single-cell RNA-Seq analysis of adult P23H zebrafish animals to identify transcription factors (e2fs, Prdm1a, Sp1) expressed selectively in neural progenitors and immature rods, and validated their necessity for regeneration using morphant analysis. The finding is useful, and the evidence is convincing. The deeper mechanistic analysis could further strengthen the current work by (1) distinguishing developmental vs regenerative transcriptional factors, (2) the addition of matched scATAC-Seq data, and (3) integration with single-cell multiome data from developing retina.

   Reviewed by eLife

8. We couldn't get details of this article at this time:
   10.1101/2024.12.09.627541

9. We couldn't get details of this article at this time:
   10.1101/2025.02.03.636224

10. We couldn't get details of this article at this time:
    10.1101/2024.10.01.615270