Genetics

Drosophila pVALIUM10 TRiP RNAi lines cause undesired silencing of Gateway-based transgenes

1. Dimitrije Stanković
2. Gábor Csordás
3. Mirka Uhlirova

Reviewed by Review Commons

CIRKO: A chemical-induced reversible gene knockout system for studying gene function in situ

1. Hui Shi
2. Qin Jin
3. Fangbing Chen
4. Zhen Ouyang
5. Shixue Gou
6. Xiaoyi Liu
7. Lei Li
8. Shuangshuang Mu
9. Chengdan Lai
10. Quanjun Zhang
11. Yinghua Ye
12. Kepin Wang
13. Liangxue Lai

• Curated by eLife

  eLife assessment

  Conditional deletion and reactivation of a gene in situ remain challenging, and this study therefore addresses a gap in the genetic tool box. The authors introduce a reversible conditional gene inactivation and reactivation method using sequential expression of recombinases, with doxycycline treatment terminating gene transcription, while doxycycline and tamoxifen addition restore gene expression.

Reviewed by eLife

A Multi-Tissue Comparison and Molecular Characterization of Canine Organoids

1. Christopher Zdyrski
2. Vojtech Gabriel
3. Oscar Ospina
4. Hannah Wickham
5. Dipak K. Sahoo
6. Kimberly Dao
7. Leeann S. Aguilar Meza
8. Abigail Ralston
9. Leila Bedos
10. William Bastian
11. Sydney Honold
12. Pablo Piñeyro
13. Eugene F. Douglass
14. Jonathan P. Mochel
15. Karin Allenspach

• Curated by eLife

  eLife assessment

  Organoids mimic the architecture and function of their cognate organs and have potential as replacements for animal models. Here the authors generated canine organoids from multiple adult tissues, including endometrium, lung, and pancreas, in addition to previously generated organoids from the kidney, bladder, and liver. However more methodological detail and functional characterization are required before this toolbox can be optimally utilized by wider scientific community.

Reviewed by eLife

A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde

1. Romain Laurent
2. Zachary A Szpiech
3. Sergio S da Costa
4. Valentin Thouzeau
5. Cesar A Fortes-Lima
6. Françoise Dessarps-Freichey
7. Laure Lémée
8. José Utgé
9. Noah A Rosenberg
10. Marlyse Baptista
11. Paul Verdu

• Curated by eLife

  Evaluation Summary:

  The authors leverage genotyping data from the islands of Cabo Verde to study its admixture history and to gain insights into the onset of the Trans-Atlantic Slave Trade. They find that patterns of ancestry between the islands are not the same, suggesting diversity in the founding populations of these islands. These results provide a nice example of how ancestry patterns vary across admixed populations due in part to their unique local history and social practices of that time.

  (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 and Reviewer #2 agreed to share their names with the authors.)

Reviewed by eLife

Contrasting effects of Ksr2, an obesity gene, on trabecular bone volume and bone marrow adiposity

1. Gustavo A Gomez
2. Charles H Rundle
3. Weirong Xing
4. Chandrasekhar Kesavan
5. Sheila Pourteymoor
6. Robert E Lewis
7. David R Powell
8. Subburaman Mohan

• Curated by eLife

  eLife Assessment:

  This is a very valuable study that describes the bone phenotype and mechanism of the action of the obesity gene Ksr2. That there is a site-selective bone phenotype is interesting as is the identification of KSR2 as an actionable target.

  (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

Anopheles homing suppression drive candidates exhibit unexpected performance differences in simulations with spatial structure

1. Samuel E Champer
2. Isabel K Kim
3. Andrew G Clark
4. Philipp W Messer
5. Jackson Champer

• Curated by eLife

  Evaluation Summary:

  This is one of the most thorough assessments to date of suppression gene drives against mosquitoes. The models specifically consider the spatial dynamics of gene drives and whether a form of group selection may prevent the drive from eradicating the population, with mosquito ecology parameters. This manuscript will be of interest to those working in the technical development of gene drives, those predicting how such genetically modified insects would spread in the wild, and those evaluating the technology from regulatory and funding standpoints.

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

Reviewed by eLife

Variation in ubiquitin system genes creates substrate-specific effects on proteasomal protein degradation

1. Mahlon A Collins
2. Gemechu Mekonnen
3. Frank Wolfgang Albert

• Curated by eLife

  Evaluation Summary:

  The authors use an elegant experimental design to study genetic variation in the ubiquitin-proteasome degradation system in yeast. They identify a large number of QTLs for naturally occurring variation, and they elucidate the causal variants and likely functional mechanisms of several of these. The paper illustrates an innovative new approach to high-throughput QTL mapping for specific molecular processes and it will be of interest to colleagues aiming to harness natural variation for understanding a range of biological processes.

  (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

Gene interaction perturbation network deciphers a high-resolution taxonomy in colorectal cancer

1. Zaoqu Liu
2. Siyuan Weng
3. Qin Dang
4. Hui Xu
5. Yuqing Ren
6. Chunguang Guo
7. Zhe Xing
8. Zhenqiang Sun
9. Xinwei Han

• Curated by eLife

  Evaluation Summary:

  Liu et al. describes an unsupervised method that clusters colorectal cancer samples based on perturbations to gene interactions. They show that this method strongly suggests 6 distinct clusters of samples and identifies phenotypes associated with the clusters, including survival, drug response, immune phenotype, response to immune checkpoint inhibitors and perturbed pathways. This is an interesting and significant manuscript, which has been well conducted.

  (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

Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus

1. Constance Kleijwegt
2. Florent Bressac
3. Coline Seurre
4. Wilhelm Bouchereau
5. Camille Cohen
6. Pascale Texier
7. Thomas Simonet
8. Laurent Schaeffer
9. Patrick Lomonte
10. Armelle Corpet

• Curated by eLife

  Evaluation Summary:

  In this manuscript, of interest to the fields of animal immunity and epigenetics, the authors investigate the crosstalk between PML Nuclear Bodies and HIRA, a member of the H3.3 histone chaperone complex, during inflammatory stress. This study raises interesting perspectives on how availability of HIRA could be regulated by PML Nuclear Bodies for histone deposition onto interferon-stimulated genes, which in turn, could be relevant for immune-response mediated gene regulation.

  (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

BRCA1/BRC-1 and SMC-5/6 regulate DNA repair pathway engagement during Caenorhabditis elegans meiosis

1. Erik Toraason
2. Alina Salagean
3. David E Almanzar
4. Jordan E Brown
5. Colette M Richter
6. Nicole A Kurhanewicz
7. Ofer Rog
8. Diana E Libuda

• Curated by eLife

  Evaluation Summary:

  DNA double-strand breaks are a major threat to genome stability. In this study, the roles of two DNA repair proteins, Brc-1 and Smc-5, are investigated in C. elegans meiotic cells, to investigate the DSB repair pathways using the homolog or the sister chromatid as template . The results highlight a regulatory role of Brc-1 and Smc-5 as repressors of repair with the sister chromatid. The experiments are generally well executed, and the findings will be of interest to the DNA repair and C. elegans meiosis communities.

  (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 and Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife