Genetics

Interpretable network-guided epistasis detection

1. Diane Duroux
2. Héctor Climente-González
3. Chloé-Agathe Azencott
4. Kristel Van Steen

Reviewed by GigaScience

Gene-set Enrichment with Mathematical Biology (GEMB)

1. Amy L Cochran
2. Kenneth J Nieser
3. Daniel B Forger
4. Sebastian Zöllner
5. Melvin G McInnis

Reviewed by GigaScience

High-throughput phenotyping with deep learning gives insight into the genetic architecture of flowering time in wheat

1. Xu Wang
2. Hong Xuan
3. Byron Evers
4. Sandesh Shrestha
5. Robert Pless
6. Jesse Poland

Reviewed by GigaScience

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication

1. Tobias Moll
2. Valerie Odon
3. Calum Harvey
4. Mark O Collins
5. Andrew Peden
6. John Franklin
7. Emily Graves
8. Jack NG Marshall
9. Cleide dos Santos Souza
10. Sai Zhang
11. Lydia Castelli
12. Guillaume Hautbergue
13. Mimoun Azzouz
14. David Gordon
15. Nevan Krogan
16. Laura Ferraiuolo
17. Michael P Snyder
18. Pamela J Shaw
19. Jan Rehwinkel
20. Johnathan Cooper-Knock

Reviewed by ScreenIT

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

1. Qussai Abbas
2. Alexey Kusakin
3. Kinda Sharrouf
4. Susan Jyakhwo
5. Aleksey S Komissarov

Reviewed by ScreenIT

The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells

1. Dylane Detilleux
2. Peggy Raynaud
3. Berengere Pradet-Balade
4. Dominique Helmlinger

• Curated by eLife

  **Evaluation Summary:
  **
  This manuscript will be of interest to those studying gene transcription and its regulation by co-activator complexes in metazoans. The identification of the large TRAPP subunit shared between two conserved histone modification complexes as a negative regulator of the interferon type I pathway in colorectal cancer cell line provides novel insights into the functions of this TRAPP subunit, which was previously known only for this positive effects on gene transcription.

  (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

Boosting targeted genome editing using the hei-tag

1. Thomas Thumberger
2. Tinatini Tavhelidse-Suck
3. Jose Arturo Gutierrez-Triana
4. Alex Cornean
5. Rebekka Medert
6. Bettina Welz
7. Marc Freichel
8. Joachim Wittbrodt

• Curated by eLife

  Evaluation Summary:

  The authors describe the hei-tag, which, when added to a genome editing enzyme, results in increased editing rates in fish embryos and mammalian cell culture. The hei-tag tool could provide a valuable alternative that can potentially boost genome editing efficiency in different species and systems. The wider applicability of this approach still requires further investigation, since the improvement of editing efficiency is so far supported by experimental data on only a few targets. It would also be important to learn how the authors' design decisions affect activity, especially when benchmarked against current state-of-art genome editing tools.

  (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

Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction

1. Alex Cornean
2. Jakob Gierten
3. Bettina Welz
4. Juan Luis Mateo
5. Thomas Thumberger
6. Joachim Wittbrodt

• Curated by eLife

  Evaluation Summary:

  This is an important study that comprehensively compares the activities of different base editors in both medaka and zebrafish. The authors also provide a web tool for experimental design allowing approximately 30% of known human disease associated nucleotide variants to be modeled in fish with validated editors within days following injection. While other studies have shown similar activities in zebrafish, the authors nicely demonstrate the ability to generate phenotypes using different base editors in both zebrafish and medaka that correlate with specific base changes. This gene editing system coupled with the ability to design gRNAs efficiently with a web interface will likely have a lasting impact on the field.

  (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 #3 agreed to share their name with the authors.)

Reviewed by eLife

Maintenance of copy number variation at the human salivary agglutinin gene ( DMBT1 ) by balancing selection driven by host-microbe interactions

1. Adel F. Alharbi
2. Nongfei Sheng
3. Katie Nicol
4. Nicklas Strömberg
5. Edward J. Hollox

Reviewed by PeerRef

Nuclear hormone receptor NHR-49 acts in parallel with HIF-1 to promote hypoxia adaptation in Caenorhabditis elegans

1. Kelsie RS Doering
2. Xuanjin Cheng
3. Luke Milburn
4. Ramesh Ratnappan
5. Arjumand Ghazi
6. Dana L Miller
7. Stefan Taubert

• Curated by eLife

  Evaluation Summary:

  This study brings new insight into how organisms maintain homeostasis under stress conditions and has implications for our understanding both development and disease. The study provides evidence that NHR-49 protects animals from hypoxia by activating autophagy, and that it acts independently of the well-described canonical HIF-1 hypoxia response. The experiments are well done, and the conclusions from the results are largely appropriate. The impact of this study will be highest in the specific field of hypoxia, with more moderate impact for wider audiences interested in understanding of how biological maintain homeostasis under stress.

  (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