Genomics

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

Nuclear genome profiling of two species of Epidendrum (Orchidaceae): genome size, repeatome and ploidy

1. Miguel A. Alcalá-Gaxiola
2. Gerardo A. Salazar
3. Eric Hágsater
4. Mónica A. Flores-Iniestres
5. Lidia I. Cabrera
6. Aldo I. Aviña-Rivera
7. Pedro Mercado-Ruaro
8. Susana Magallon
9. Carolina Granados Mendoza
10. Aleida Núñez-Ruiz
11. Gloria Soldevila
12. Araxi Urrutia
13. Rubi N. Meza-Lázaro

Reviewed by Review Commons

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 Gérard
10. Wendy A Bickmore

• Curated by eLife

  eLife Assessment

  This fundamental study provides the first genome-wide characterization of H3K115 acetylation and identifies a striking and previously unappreciated association of this globular-domain histone modification with fragile nucleosomes at CpG island promoters, active enhancers, and CTCF binding sites. While the work is largely descriptive and correlative in nature the evidence is compelling. The authors present multiple, orthogonal genomic and biochemical analyses that consistently support their central conclusions.

Reviewed by eLife

Expression-Driven Genetic Dependency Reveals Targets for Precision Medicine

1. Abdulkadir Elmas
2. Hillary M. Layden
3. Jacob D. Ellis
4. Luke N. Bartlett
5. Xian Zhao
6. Reika Kawabata-Iwakawa
7. Hideru Obinata
8. Scott W. Hiebert
9. Kuan-lin Huang

Reviewed by GigaScience