Genetics

Phylogenetic evidence for asparagine to aspartic acid protein editing of N-glycosylated SARS-CoV-2 viral proteins by NGLY1 deglycosylation/deamidation suggests an unusual vaccination strategy

1. Gary Ruvkun
2. Fei Ji
3. Ruslan I. Sadreyev

Reviewed by ScreenIT

Cre/lox regulated conditional rescue and inactivation with zebrafish UFlip alleles generated by CRISPR-Cas9 targeted integration

1. Fang Liu
2. Sekhar Kambakam
3. Maira P Almeida
4. Zhitao Ming
5. Jordan M Welker
6. Wesley A Wierson
7. Laura E Schultz-Rogers
8. Stephen C Ekker
9. Karl J Clark
10. Jeffrey J Essner
11. Maura McGrail

• Curated by eLife

  Evaluation Summary:

  This technical paper describes a novel strategy for conditional mutagenesis in zebrafish. The method employs the authors' previously reported GeneWeld CRISPR/Cas9 targeted integration strategy to allow target genes to be "turned off" or "turned on" in a tissue-specific manner. Once fully validated, the approach would provide a valuable new addition to the "zebrafish genetic toolkit" that is likely to be widely used for assessing cell- and tissue-specific gene function in this model organism.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Common host variation drives malaria parasite fitness in healthy human red cells

1. Emily R Ebel
2. Frans A Kuypers
3. Carrie Lin
4. Dmitri A Petrov
5. Elizabeth S Egan

• Curated by eLife

  Evaluation Summary:

  This paper investigates the role of common human genetic variation in explaining the relationship between host genetics, red blood cell physiology, and susceptibility to Plasmodium falciparum (the parasite responsible for malaria). It finds evidence that common variants in a small set of red blood cell proteins predict parasite invasion and growth rates. Contrary to hypotheses about ancestry-associated malaria selection, these variants are not more common in African ancestry populations. The approach used to select host factors that impact parasite fitness is pragmatic especially in the context of a small sample size, but the high predictive accuracy (despite moderate within-subject assay replicability) and the uncertain influence of including closely related family members in the analysis, raises some concerns about generalizability beyond the study sample.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias

1. Cory D. Dunn

Reviewed by Review Commons

The genetics of eating behaviors: research in the age of COVID-19

1. Mackenzie E. Hannum
2. Cailu Lin
3. Katherine Bell
4. Aurora Toskala
5. Riley Koch
6. Tharaka Galaniha
7. Alissa Nolden
8. Danielle R Reed
9. Paule Joseph

Reviewed by ScreenIT

Mapping interindividual dynamics of innate immune response at single-cell resolution

1. Natsuhiko Kumasaka
2. Raghd Rostom
3. Ni Huang
4. Krzysztof Polanski
5. Kerstin B. Meyer
6. Sharad Patel
7. Rachel Boyd
8. Celine Gomez
9. Sam N. Barnett
10. Nikolaos I. Panousis
11. Jeremy Schwartzentruber
12. Maya Ghoussaini
13. Paul A. Lyons
14. Fernando J. Calero-Nieto
15. Berthold Göttgens
16. Josephine L. Barnes
17. Kaylee B. Worlock
18. Masahiro Yoshida
19. Marko Z. Nikolić
20. Emily Stephenson
21. Gary Reynolds
22. Muzlifah Haniffa
23. John C. Marioni
24. Oliver Stegle
25. Tzachi Hagai
26. Sarah A. Teichmann

Reviewed by ScreenIT

A sex-specific evolutionary interaction between ADCY9 and CETP

1. Isabel Gamache
2. Marc-André Legault
3. Jean-Christophe Grenier
4. Rocio Sanchez
5. Eric Rhéaume
6. Samira Asgari
7. Amina Barhdadi
8. Yassamin Feroz Zada
9. Holly Trochet
10. Yang Luo
11. Leonid Lecca
12. Megan Murray
13. Soumya Raychaudhuri
14. Jean-Claude Tardif
15. Marie-Pierre Dubé
16. Julie Hussin

• Curated by eLife

  Evaluation Summary:

  This study presents evidence supporting population and sex-specific selection and an epistatic interaction between variants in the genes ADCY9 and CETP of pharmacogenetic importance. The confluence of evidence from population genetics, gene expression, functional experiments, and phenotypic association lends support to the paper's claims beyond what may be achieved by a single analysis. All three reviewers and I agreed that this work is of high interest in medical and population genetics and addresses a challenging topic in an impactful way.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

Regional Variant Analysis of Spike Glycoprotein Mutations of SARS-CoV-2 and Its Implications in COVID-19 Pandemic Control

1. Punnoth Poonkuzhi Naseef
2. Mohamed Saheer Kuruniyan
3. Shyju Ollakkod
4. U.K. Ilyas
5. Muhammed Elayadeth-Meethal

Reviewed by ScreenIT

Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae

1. Fabien Duveau
2. Petra Vande Zande
3. Brian PH Metzger
4. Crisandra J Diaz
5. Elizabeth A Walker
6. Stephen Tryban
7. Mohammad A Siddiq
8. Bing Yang
9. Patricia J Wittkopp

• Curated by eLife

  Evaluation Summary:

  One key question in evolutionary biology is how traits can be affected by spontaneous mutations. This relationship between traits and mutations influences the rate and direction in which traits evolve. Here, the authors map a set of mutations that affect the expression of a focal gene in yeast, and examine their individual effects and locations in the genome and in the regulatory network. The work is rigorous and the results are well presented. The findings will be of great interest for geneticists and evolutionary biologists interested in the evolution of gene expression and of complex traits. Additional analyses and discussions will strengthen the generalization of the conclusions.

Reviewed by eLife

Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation

1. Teresa Romeo Luperchio
2. Leandros Boukas
3. Li Zhang
4. Genay Pilarowski
5. Jenny Jiang
6. Allison Kalinousky
7. Kasper D Hansen
8. Hans T Bjornsson

• Curated by eLife

  Evaluation Summary:

  This manuscript finds common molecular features in the blood of three "Mendelian Disorder of the Epigenetic Machinery" (MDEM) mouse models. These shared features (chromatin accessibility and gene expression) may underlie some of the clinical similarities of these disorders. This work will be of interest to researchers, and to some clinicians studying MDEM and epigenetic variation in mammals. Additional analyses are needed to strengthen the conclusions.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife