Molecular Biology

On demand expression control of endogenous genes with DExCon, DExogron and LUXon reveals differential dynamics of Rab11 family members

1. Jakub Gemperle
2. Thomas S Harrison
3. Chloe Flett
4. Antony D Adamson
5. Patrick T Caswell

• Curated by eLife

  Evaluation Summary:

  This work reports a genome editing strategy that enables blocking and tetracycline-controlled re-expression of fluorescently-tagged proteins from endogenous loci. The authors combine this with the photoactivatable tet-on/off system, a knocksideways approach, as well as the auxin-inducible degron system to improve spatial and temporal control of gene expression. They demonstrate the applicability of the methods by studying the localization, function and protein-expression dynamics of the Rab11-family of small GTPases. Using these approaches, the authors discover subtle differences in the localization as well as expression and degradation kinetics of Rab11a/b/Rab25. The work will be of broad interest to molecular and cell biologists.

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

Reviewed by eLife

Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

1. Julia M Flynn
2. Neha Samant
3. Gily Schneider-Nachum
4. David T Barkan
5. Nese Kurt Yilmaz
6. Celia A Schiffer
7. Stephanie A Moquin
8. Dustin Dovala
9. Daniel NA Bolon

• Curated by eLife

  Evaluation Summary:

  The main protease of SARS-CoV-2 (Mpro) is a leading target for drug design due to its conserved and indispensable role in the life cycle. This study used cutting-edge molecular and statistical methods to generate a detailed genotype-phenotype map of this protein, also called a "fitness landscape." This fitness landscape is impressive in its detail and resolution and offers new insight that can be used to potentially generate new anti-viral drugs. This study was original in conception, precise in execution, and impressive in design. In sum, this constitutes a very meaningful addition to scientific literature.

  (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, ScreenIT

SARS-CoV-2 Viral Genes Compromise Survival and Functions of Human Pluripotent Stem Cell-derived Cardiomyocytes via Reducing Cellular ATP Level

1. Juli Liu
2. Yucheng Zhang
3. Shiyong Wu
4. Lei Han
5. Cheng Wang
6. Sheng Liu
7. Ed Simpson
8. Ying Liu
9. Yue Wang
10. Weinian Shou
11. Yunlong Liu
12. Michael Rubart-von der Lohe
13. Jun Wan
14. Lei Yang

Reviewed by ScreenIT

Sialic acid and fucose residues on the SARS-CoV-2 receptor binding domain modulate IgG reactivity

1. Ebba Samuelsson
2. Ekaterina Mirgorodskaya
3. Kristina Nyström
4. Malin Bäckström
5. Jan-Åke Liljeqvist
6. Rickard Nordén

Reviewed by ScreenIT

High activity of an affinity-matured ACE2 decoy against Omicron SARS-CoV-2 and pre-emergent coronaviruses

1. Joshua J. Sims
2. Sharon Lian
3. Rosemary L. Meggersee
4. Aradhana Kasimsetty
5. James M. Wilson

Reviewed by ScreenIT

Application of sequence semantic and integrated cellular geography approach to study biogenesis of exonic circular RNA

1. Rajnish Kumar
2. Tapobrata Lahiri
3. Manoj Kumar Pal

Reviewed by PeerRef

Binary outcomes of enhancer activity underlie stable random monoallelic expression

1. Djem U Kissiov
2. Alexander Ethell
3. Sean Chen
4. Natalie K Wolf
5. Chenyu Zhang
6. Susanna M Dang
7. Yeara Jo
8. Katrine N Madsen
9. Ishan Paranjpe
10. Angus Y Lee
11. Bryan Chim
12. Stefan A Muljo
13. David H Raulet

• Curated by eLife

  Evaluation Summary:

  In this manuscript by Kissiov et al. the authors show that enhancers can play an instructive role in controlling stable random monoallelic expression (RME). In order to do so, they initially focus on a limited set of natural killer (NK) receptor genes that are subject to RME, which they investigate using several in vivo genetic models. Furthermore, they also show that RME can be considerably more prevalent than previously thought and that enhancer strength and/or number might influence the extent of RME for different genes. One remaining question may be whether this model may apply to other gene types than hematopoietic-related genes. Overall, this is a highly relevant manuscript with major implications in gene regulation and enhancer biology and, thus, of broad scientific interest.

  (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

Rvb1/Rvb2 proteins couple transcription and translation during glucose starvation

1. Yang S Chen
2. Wanfu Hou
3. Sharon Tracy
4. Alex T Harvey
5. Vince Harjono
6. Fan Xu
7. James J Moresco
8. John R Yates
9. Brian M Zid

Reviewed by Review Commons

Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region

1. Sandhya Balasubramanian
2. Matteo Andreani
3. Júlia Goncalves Andrade
4. Tannishtha Saha
5. Devakumar Sundaravinayagam
6. Javier Garzón
7. Wenzhu Zhang
8. Oliver Popp
9. Shin-ichiro Hiraga
10. Ali Rahjouei
11. Daniel B Rosen
12. Philipp Mertins
13. Brian T Chait
14. Anne D Donaldson
15. Michela Di Virgilio

• Curated by eLife

  Evaluation Summary:

  RIF1 is a protein of the DNA damage response with key roles on genome integrity: it prevents DSB resection and hence accurate HR repair, whilst protecting stalled forks from degradation under replication stress conditions. The authors' main finding is the identification of 3 residues in RIF1 protein, that can be phosphorylated in ATM/ATR-dependent manner. However, this phosphorylation is dispensable for the ability of RIF1 to limit double-strand break resection, but is required to counteract the degradation of stalled replication intermediates mediated by the DNA2 nuclease. Therefore, the manuscript suggests that the three sites can provide a potential switch between the two functions of RIF1. These findings will spark the interest of readers working in the DNA replication and repair fields. However, the actual mechanism by which blocking RIF1 phosphorylation prevents RIF1 function at replication forks still needs to be determined.

  (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

Sequence-assignment validation in cryo-EM models with checkMySequence

1. Grzegorz Chojnowski

Reviewed by ScreenIT