Genomics

Trade-offs in modeling context dependency in complex trait genetics

1. Eric Weine
2. Samuel Pattillo Smith
3. Rebecca Kathryn Knowlton
4. Arbel Harpak

• Curated by eLife

  eLife Assessment

  It is known from model organisms that genes' effects on traits are often modulated by environmental variables, but similar gene-by-environment (GxE) interactions have been difficult to detect using statistical analyses of genomic data, e.g., in humans. This study introduces a new framework to estimate gene-by-environment effects, treating it as a bias-variance tradeoff problem. The authors convincingly show that greater statistical power can be achieved in detecting GxE if an underlying model of polygenic GxE is assumed. This polygenic amplification model is a truly novel view with fundamental promise for the detection of GxE in genomic datasets, especially with continued development to detect more complex signals of amplification.

Reviewed by eLife

Genomic evidence for hybridization and introgression between blue peafowl and green peafowl and selection for white plumage

1. Gang Wang
2. Liping Ban
3. Xinye Zhang
4. Xiurong Zhao
5. Xufang Ren
6. Anqi Chen
7. Li Zhang
8. Yan Lu
9. Zhihua Jiang
10. Xiaoyu Zhao
11. Junhui Wen
12. Yalan Zhang
13. Xue Cheng
14. Huie Wang
15. Wenting Dai
16. Yong Liu
17. Zhonghua Ning
18. Lujiang Qu

Reviewed by GigaScience

High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

1. Porter M Hall
2. Lauren A Mayse
3. Lu Bai
4. Marcus B Smolka
5. B Franklin Pugh
6. Michelle D Wang

• Curated by eLife

  eLife Assessment

  The Twin Domain model proposed by Lui and Wang proposing that twin supercoiling domains of DNA emerge during transcription were first described decades ago, but direct experimental evidence has been challenging to obtain. Here, the authors make a fundamental contribution by directly measuring DNA torsion in cells using a photoactivatable intrastrand cross-linker compared to controls. They gather compelling data using this clever method, which provides direct evidence in support of the twin-supercoiled domain model, for torsional effects at transcription start and end sites, and thereby uncover novel features of higher order structure of chromatin in yeast. These data are exciting, and the tools will be of interest to anyone studying chromosome structure and gene regulation.

Reviewed by eLife

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus ) provide evidence of haplotype diversity

1. Temitope Opeyemi Oriowo
2. Ioannis Chrysostomakis
3. Sebastian Martin
4. Sandra Kukowka
5. Thomas Brown
6. Sylke Winkler
7. Eugene W Myers
8. Astrid Böhne
9. Madlen Stange

Reviewed by GigaScience

Discovering root causal genes with high-throughput perturbations

1. Eric V Strobl
2. Eric Gamazon

• Curated by eLife

  eLife Assessment

  This work provides an important framework for understanding the primary causes of disease. While the theoretical results rely on strong assumptions about the underlying causal mechanisms, the authors provide solid empirical evidence that the framework is robust to modest violations of these assumptions.

Reviewed by eLife

Mapping HIV-1 RNA structure, homodimers, long-range interactions and persistent domains by HiCapR

1. Yan Zhang
2. Jingwan Han
3. Xie Dejian
4. Wenlong Shen
5. Ping Li
6. Jian You Lau
7. Jingyun Li
8. Lin Li
9. Grzegorz Kudla
10. Zhihu Zhao

• Curated by eLife

  eLife Assessment

  This manuscript focuses on the identification of RNA crosslinks within the HIV RNA genome under different conditions i.e. in infected cells and in virions using a new method called HiCapR. These cross-links reveal long-range interactions that can be used to determine the structural arrangement of the viral RNA, providing valuable data that show differences in the genomic organization in different conditions. The data analysis, however, is incomplete and based on extensive computational analysis from a limited number of datasets.

Reviewed by eLife

Dark side of the honeymoon: reconstructing the Asian x European rose breeding history through the lens of genomics

1. Thibault Leroy
2. Elise Albert
3. Tatiana Thouroude
4. Sylvie Baudino
5. Jean-Claude Caissard
6. Annie Chastellier
7. Jérôme Chameau
8. Julien Jeauffre
9. Thérèse Loubert
10. Saretta Nindya Paramita
11. Alix Pernet
12. Vanessa Soufflet-Freslon
13. Cristiana Oghina-Pavie
14. Fabrice Foucher
15. Laurence Hibrand-Saint Oyant
16. Jérémy Clotault

Reviewed by Peer Community in Evolutionary Biology

Methylation Clocks Do Not Predict Age or Alzheimer’s Disease Risk Across Genetically Admixed Individuals

1. Sebastián Cruz-González
2. Esther Gu
3. Lissette Gomez
4. Makaela Mews
5. Jeffery M Vance
6. Michael L Cuccaro
7. Mario R Cornejo-Olivas
8. Briseida E Feliciano-Astacio
9. Goldie S Byrd
10. Jonathan L Haines
11. Margaret A Pericak-Vance
12. Anthony J Griswold
13. William S Bush
14. John A Capra

• Curated by eLife

  eLife Assessment

  This valuable study assesses epigenetic clocks across ancestries, including in the context of accelerated aging in Alzheimer's Disease patients. It provides convincing evidence for population differences in age estimation accuracy across a variety of epigenetic clocks, but the degree to which these differences reflect continuous variation in ancestry, and/or are confounded by environmental or power differences is not entirely clear; consequently, the evidence that reduced portability is rooted in genetics is incomplete. Given the accelerating use of epigenetic clocks across fields, this study is nevertheless likely to be of interest to researchers working on human genetic and epigenetic variation or who apply epigenetic clocks to diverse human populations.

Reviewed by eLife

Adenine DNA methylation associated to transcription is widespread across eukaryotes

1. Pedro Romero Charria
2. Cristina Navarrete
3. Vladimir Ovchinnikov
4. Luke A Sarre
5. Victoria Shabardina
6. Elena Casacuberta
7. David Lara-Astiaso
8. Arnau Sebé-Pedrós
9. Alex de Mendoza

Reviewed by preLights

Dynamics and regulatory roles of RNA m6A methylation in unbalanced genomes

1. Shuai Zhang
2. Ruixue Wang
3. Kun Luo
4. Shipeng Gu
5. Xinyu Liu
6. Junhan Wang
7. Ludan Zhang
8. Lin Sun

• Curated by eLife

  eLife Assessment

  This valuable study suggests that the dosage compensation complex and m6A act in a feedback loop in Drosophila melanogaster. The study provides integrated analyses of RNA sequencing and mapping data of the m6A RNA modification in the context of unbalanced genomes, which suggests that m6A modification status may influence H3K16Ac deposition through regulation of the acetyltransferase MOF. However, it is not clear whether this regulation is directly or indirectly related to m6A regulation. The evidence is considered incomplete due to technical concerns, as quantitative assessments were made using non-quantitative methods.

Reviewed by eLife