Genomics

Stranded short nascent strand sequencing reveals the topology of DNA replication origins in Trypanosoma brucei

1. Slavica Stanojcic
2. Bridlin Barckmann
3. Pieter Monsieurs
4. Lucien Crobu
5. Simon George
6. Yvon Sterkers

• Curated by eLife

  eLife Assessment

  The authors attempt to use sequencing of nascent DNA (DNA linked to an RNA primer, "SNS-Seq") to localise DNA replication origins in Trypanosoma brucei, but they analyse the results for only part of the genome. There are also significant discrepancies between their results and those from other origin mapping methods which have not been addressed, meaning that SNS-seq has not been validated for origin mapping in T. brucei. For this reason, the evidence that origins are distributed as the authors claim - and not where previously mapped - is inadequate. This work will be of interest to those studying DNA replication.

Reviewed by eLife

A high-coverage genome from a 200,000-year-old Denisovan

1. Stéphane Peyrégne
2. Diyendo Massilani
3. Yaniv Swiel
4. Michael James Boyle
5. Leonardo N. M. Iasi
6. Arev P. Sümer
7. Alba Bossoms Mesa
8. Cesare de Filippo
9. Bence Viola
10. Elena Essel
11. Sarah Nagel
12. Julia Richter
13. Antje Weihmann
14. Barbara Schellbach
15. Hugo Zeberg
16. Johann Visagie
17. Maxim B. Kozlikin
18. Michael V. Shunkov
19. Anatoly P. Derevianko
20. Kay Prüfer
21. Benjamin M. Peter
22. Matthias Meyer
23. Svante Pääbo
24. Janet Kelso

Reviewed by preLights

Beyond the transcript: chromatin implications in trans-splicing in Trypanosomatids

1. Romina Trinidad Zambrano Siri
2. Paula Beati
3. Lucas Inchausti
4. Pablo Smircich
5. Guillermo Daniel Alonso
6. Josefina Ocampo

Reviewed by Review Commons

Evolutionary remodeling of non-canonical ORF translation in mammals

1. Yue Chang
2. Tianyu Lei
3. Feng Zhou
4. Jiawen Jiang
5. Yu Huang
6. Ziyang Zhu
7. Hong Zhang

• Curated by eLife

  eLife Assessment

  This study presents a large, systematically curated catalog of non-canonical open reading frames (ncORFs) in human and mouse by reanalyzing nearly 400 Ribo-seq datasets using a standardized pipeline; the resulting atlas consolidates ncORF annotations across tissues and provides a valuable reference for understanding non-canonical translation and ORF emergence. The main conclusions are supported by consistent data processing and multiple computational measures of translation and conservation. While the pipeline is transparent and robust, several downstream analyses are descriptive, and some evolutionary interpretations remain correlative; dataset heterogeneity, uneven tissue representation, and limited experimental validation also constrain the strength of a subset of the findings. Overall, the evidence is solid, and the resource will be broadly used by the community.

Reviewed by eLife

RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations

1. Cenny Taslim
2. Yuan Zhang
3. Genevieve C. Kendall
4. Emily R. Theisen

Reviewed by GigaScience

Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature

1. Anastasia Unitt
2. Made Krisna
3. Kasia M Parfitt
4. Keith A Jolley
5. Martin CJ Maiden
6. Odile B Harrison

• Curated by eLife

  eLife Assessment

  This important study introduces the Life Identification Number (LIN) coding system as a powerful and versatile approach for classifying Neisseria gonorrhoeae lineages. The authors show that LIN codes capture both previously defined lineages and their relationships in a way that aligns with the species' phylogenetic structure. The compelling evidence presented, together with its integration into the PubMLST platform, underscores its strong potential to enhance epidemiological surveillance and advance our understanding of gonococcal population biology.

Reviewed by eLife

Nonlinear transcriptional responses to gradual modulation of transcription factor dosage

1. Júlia Domingo
2. Mariia Minaeva
3. John A Morris
4. Samuel Ghatan
5. Marcello Ziosi
6. Neville E Sanjana
7. Tuuli Lappalainen

• Curated by eLife

  eLife Assessment

  This important work develops a new protocol to experimentally perturb target genes across a quantitative range of expression levels in cell lines. The evidence supporting their new perturbation approach is convincing, and we propose that focusing on single modality (activation or inhibition) would be sufficient to draw their conclusions. The study will be of broad interest to scientists in the fields of functional genomics and biotechnology.

Reviewed by eLife

Crossing host boundaries: the evolutionary drivers and correlates of viral host jumps

1. Cedric C.S. Tan
2. Lucy van Dorp
3. Francois Balloux

Reviewed by Rapid Reviews Infectious Diseases

Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites

1. Yatendra Kumar
2. Dipta Sengupta
3. Elias T Friman
4. Robert S Illingworth
5. Manon Soleil
6. Zheng Fan
7. Hua Wang
8. Kristian Helin
9. Matthieu Gerard
10. Wendy A Bickmore

• Curated by eLife

  eLife Assessment

  The reviewers have found that this manuscript is a valuable contribution, and the evidence in support of its conclusions is mostly solid. It provides novel insights and raises interesting possibilities about the functions of an understudied histone modification within the nucleosome core; however, the data are mostly descriptive and correlative, and although this has value, it is not totally persuasive. Short of additional non-genomic experiments, a more detailed analysis of the genomic data and perhaps additional data would strengthen the conclusions. The manuscript crucially needs further antibody validation to raise confidence in the data.

Reviewed by eLife

Conservation of chromatin states and their association with transcription factors in land plants

1. Vikas Shukla
2. Elin Axelsson
3. Tetsuya Hisanaga
4. Jim Haseloff
5. Frédéric Berger
6. Facundo Romani

Reviewed by Review Commons