Genomics

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 Arcadia Science, eLife

Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells

1. Volker Soltys
2. Moritz Peters
3. Dingwen Su
4. Marek Kučka
5. Yingguang Frank Chan

• Curated by eLife

  eLife Assessment

  This study presents a useful methodological advance that better enables the simultaneous measurement of gene expression and chromatin accessibility in individual cells. The evidence supporting the improved detection of gene expression is solid, though the reduced performance in detecting chromatin accessibility represents a limitation. This method will be of interest to those studying transcription and gene regulation.

Reviewed by eLife

Intestinal Receptor of SARS-CoV-2 in Inflamed IBD Tissue Seems Downregulated by HNF4A in Ileum and Upregulated by Interferon Regulating Factors in Colon

1. Bram Verstockt
2. Sare Verstockt
3. Saeed Abdu Rahiman
4. Bo-jun Ke
5. Kaline Arnauts
6. Isabelle Cleynen
7. João Sabino
8. Marc Ferrante
9. Gianluca Matteoli
10. Séverine Vermeire

Reviewed by Rapid Reviews Infectious Diseases, ScreenIT

Genomic and epidemiologic characteristics of SARS-CoV-2 persistent infections in California, January 2021 - July 2023

1. John M. Bell
2. Jesse Elder
3. Rahil Ryder
4. Emily A. Smith
5. Michelle Scribner
6. Sabrina Gilliam
7. Deva Borthwick
8. Megan Crumpler
9. Jacek Skarbinski
10. Christina Morales
11. Debra A. Wadford

Reviewed by Rapid Reviews Infectious Diseases

Viral metagenomics of synanthropic urban bats: a surveillance strategy for uncovering potentially zoonotic viruses

1. Juliana Amorim Conselheiro
2. Filipe Romero Rebello Moreira
3. Gisely Toledo Barone
4. Adriana Araujo Reis-Menezes
5. Adriana Rückert da Rosa
6. Débora Cardoso de Oliveira
7. Bárbara Aparecida Chaves
8. Vanderson de Souza Sampaio
9. Felipe Rocha
10. Marco Antonio Natal Vigilato
11. Rodrigo Guerino Stabeli
12. Rodrigo Fabiano do Carmo Said
13. Gabriel Luz Wallau
14. Paulo Eduardo Brandão
15. Anderson Fernandes de Brito

Reviewed by Rapid Reviews Infectious Diseases

Population structure and antimicrobial resistance of Corynebacterium diphtheriae in Victoria, Australia

1. Lamali Sadeesh Kumar
2. Kylie Hui
3. Janet Strachan
4. Norelle L. Sherry
5. Benjamin P. Howden
6. Sarah L. Baines

Reviewed by Rapid Reviews Infectious Diseases

Autosomal Allelic Inactivation: Variable Replication and Dosage Sensitivity

1. Michael B Heskett
2. Athanasios E Vouzas
3. Brian Johnstone
4. Krister P Freese
5. Phillip A Yates
6. Philip F Copenhaver
7. Paul T Spellman
8. David M Gilbert
9. Mathew J Thayer

• Curated by eLife

  eLife Assessment

  This important study links allelic expression imbalance with replication timing, suggesting a stochastic model for haploinsufficiency in dosage-sensitive disease. The integration of allele-specific RNA-seq and replication timing in clonal systems provides solid evidence for an association between asynchronous replication and allelic imbalance, although the scope and generality of some conclusions require more cautious interpretation. This study will interest epigeneticists and genome regulation researchers studying replication timing and monoallelic expression, as well as developmental biologists and human geneticists concerned with clonal heterogeneity, haploinsufficiency, and variable disease penetrance.

  [Editors' note: this paper was reviewed by Review Commons.]

Reviewed by eLife

Single-nucleus multiple-organ chromatin accessibility mapping in the rat

1. Ronghai Li
2. Yue Yuan
3. Shanshan Duan
4. Qiuting Deng
5. Wen Ma
6. Chang Liu
7. Peng Gao
8. Li Lu
9. Chuanyu Liu

Reviewed by GigaScience

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years

1. Megan A Phillips
2. Robert A Petit
3. Daniel B Weissman
4. Timothy D Read

• Curated by eLife

  eLife Assessment

  Using genome databases, the authors performed solid bioinformatic analyses to trace the genomic history of the clinically relevant Staphylococcus aureus tetracycline resistance plasmid pT181 over the last seven decades. They discovered that this element has transitioned from a multicopy plasmid to a chromosomally integrated element, and the work represents a valuable demonstration of the use of publicly available data to investigate plasmid biology and inform clinical epidemiology. This work will appeal to researchers interested in staphylococcal evolution and plasmid biology.

Reviewed by eLife

Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

1. Jie Lin
2. Yujian Wen
3. Ji Tang
4. Xuecong Zhang
5. Huanlin Zhang
6. Hao Zhu

• Curated by eLife

  eLife Assessment

  This valuable study uses tools of population and functional genomics to examine long non-coding RNAs (lncRNAs) in the context of human evolution. Analyses of computationally predicted human-specific lncRNAs and their genomic targets lead to the development of hypotheses regarding the potential roles of these genetic elements in human biology. Compared to previous versions, the conclusions regarding evolutionary acceleration and adaptation have become more solid by more fully taking data and literature on human/chimpanzee genetics and functional genomics into account.

Reviewed by eLife