Genetics

Mapping of in vivo cleavage sites uncovers a major role for yeast RNase III in regulating protein-coding genes

1. Lee-Ann Notice-Sarpaning
2. Mathieu Catala
3. Catherine Stuart
4. Sherif Abou Elela
5. Ambro van Hoof

• Curated by eLife

  eLife Assessment

  This valuable study expands the inventory of polyadenylated RNAs cleaved by the double-stranded RNA endonuclease Rnt1 in budding yeast, using solid methodology based on high-throughput sequencing. Previous studies had anecdotally discovered mRNA substrates, and this global characterization is comprehensive with multiple complementary controls. This study sets the stage for deeper investigations into the biological function of Rnt1 and substrate cleavage.

Reviewed by eLife

Importance of higher-order epistasis in protein sequence-function relationships

1. Palash Sethi
2. Juannan Zhou

• Curated by eLife

  eLife Assessment

  In this important work, the authors present a new transformer-based neural network designed to isolate and quantify higher-order epistasis in protein sequences. They provide solid evidence that higher-order epistasis can play key roles in protein function. This work will be of interest to the communities interested in modeling biological sequence data and understanding mutational effects.

Reviewed by eLife

Assessing target genes for homing suppression gene drive

1. Xuejiao Xu
2. Jialing Fang
3. Jingheng Chen
4. Jie Yang
5. Xiaozhen Yang
6. Shibo Hou
7. Weitang Sun
8. Jackson Champer

Reviewed by Review Commons

Genetic Modifiers Influencing the Acute and Long-Term Responses to Traumatic Brain Injury in Drosophila

1. Brandon Molina
2. Jesse Jacob Rojas
3. Nadja El-Mecharrafie
4. Eric P Ratliff
5. Marta Lipinski
6. Kim Diane Finley

Reviewed by PREreview

Identifying the genetic basis and molecular mechanisms underlying phenotypic correlation between complex human traits using a gene-based approach

1. Jialiang Gu
2. Chris Fuller
3. Peter Carbonetto
4. Xin He
5. Jiashun Zheng
6. Hao Li

• Curated by eLife

  eLife Assessment

  To evaluate phenotypic correlations between complex traits, this study aimed to measure the genetic overlap of traits by evaluating GWAS signals assisted by eQTL signals. They suggested an improved version of the previous Sherlock to integrate SNP-level signals into gene-level signals. Then they compared 59 human traits to identify known and novel genetic distance relationships. This work is valuable to the field, but still needs substantial improvement because many parts of the paper are incomplete.

Reviewed by eLife

Massively Parallel Polyribosome Profiling Reveals Translation Defects of Human Disease-Relevant UTR Mutations

1. Wei-Ping Li
2. Jia-Ying Su
3. Yu-Chi Chang
4. Hung-Lun Chiang
5. Yun-Lin Wang
6. Ang-Chu Huang
7. Yu-Tung Hsieh
8. Yi-Hsuan Chiang
9. Yen-Ling Ko
10. Bing-Jen Chiang
11. Cheng-Han Yang
12. Yen-Tsung Huang
13. Chien-Ling Lin

• Curated by eLife

  eLife Assessment

  The effort is timely and the paper carries valuable insights into the function of UTR mutations. There are still significant concerns about both the quality of the screen data, and its ability to detect significant changes in translation and their direction. Therefore, the ability of the screen to support the extensive downstream statistical analysis is limited and leaves the paper incomplete.

Reviewed by eLife

A genome-wide MAGIC kit for recombinase-independent mosaic analysis in Drosophila

1. Yifan Shen
2. Ann T Yeung
3. Payton Ditchfield
4. Elizabeth Korn
5. Rhiannon Clements
6. Xinchen Chen
7. Bei Wang
8. Michael Sheen
9. Parker A Jarman
10. Chun Han

• Curated by eLife

  eLife Assessment

  The study showcases a significant and important enhancement of the MAGIC transgenesis method, by extending it genome-wide to all chromosomes. The authors convincingly demonstrate that the MAGIC mosaic clones can be generated for genes from all, including the 4th chromosome. With this toolkit extension, the method is now most likely set to strongly rival the classical FRT/Flp recombination system for gene manipulation in flies.

Reviewed by eLife

Faroese Whole Genomes Provide Insight into Ancestry and Recent Selection

1. Iman Hamid
2. Ólavur Mortensen
3. Alba Refoyo-Martinez
4. Leivur N Lydersen
5. Anne-Katrin Emde
6. Melissa Hendershott
7. Katrin D Apol
8. Guðrið Andorsdóttir
9. Jonas Meisner
10. Kaja A Wasik
11. Fernando Racimo
12. Stephane E Castel
13. Noomi O Gregersen

• Curated by eLife

  eLife Assessment

  This paper presents an analysis of demography and selection from whole-genome sequencing of 40 Faroese, with data that are useful beyond the study region. Much of the analysis is solid, but a more fine-scale analysis of demographic history could have led to more interesting findings. In addition, there are concerns about the selection analyses, given the special nature of the studied population and sampling scheme. Finally, lack of data availability limits the broader value of the paper.

Reviewed by eLife

Inflammation-Induced Alternative Splicing in Human Endothelial Cells Reveals Genetic Mechanisms of Cardiovascular Disease Risk

1. Anna K. Golebiewski
2. Lindsey K. Stolze
3. Valentina D. Vazquez
4. Alhan Mehrabi Yazdi
5. Cecilia M. Careaga
6. Casey E. Romanoski

Reviewed by Arcadia Science

Life-history trade-offs explain local adaptation in Arabidopsis thaliana

1. Benjamin Brachi
2. Danièle L Filiault
3. Rahul Pisupati
4. Tal Dahan-Meir
5. Anna Igolkina
6. Alison Anastasio
7. Mathew S Box
8. Susan Duncan
9. Talia L Karasov
10. Envel Kerdaffrec
11. Laura Merwin
12. Timothy C Morton
13. Viktoria Nizhynska
14. Polina Yu Novikova
15. Fernando Rabanal
16. Takashi Tsuchimatsu
17. Torbjörn Säll
18. Caroline Dean
19. Svante Holm
20. Joy Bergelson
21. Magnus Nordborg

• Curated by eLife

  eLife Assessment

  This manuscript reports a large series of experiments to investigate specific aspects of plant adaptation, leveraging genetic and genomic resources of Arabidopsis thaliana. The study provides convincing evidence for local adaptation in this highly selfing plant. This is an important dataset contributing to the developing understanding of non-linear selection in plants and beyond.

Reviewed by eLife