Molecular Biology

Structure of human PIEZO1 and its slow inactivating channelopathy mutants

1. Yuanyue Shan
2. Xinyi Guo
3. Mengmeng Zhang
4. Meiyu Chen
5. Ying Li
6. Mingfeng Zhang
7. Duanqing Pei

• Curated by eLife

  eLife Assessment

  This is a useful revised manuscript that shows a set of data including the first cryo-EM structures of human PIEZO1 as well as structures of disease-related mutants in complex with the regulatory subunit MDFIC, which generate different inactivation phenotypes. The molecular basis of PIEZO channel inactivation is of great interest due to its association with several pathologies. This manuscript provides some structural insights that may help to ultimately build a molecular picture of PIEZO channel inactivation. While the structures are of use and clear conformational differences can be seen in the presence of the auxiliary subunit MDFIC, the strength of the evidence supporting the conclusions of the paper, especially the proposed role for pore lipids in inactivation, is incomplete.

Reviewed by eLife

Introduction of cytosine-5 DNA methylation sensitizes cells to oxidative damage

1. J. Krwawicz
2. C.J. Sheeba
3. K. Hains
4. T. McMahon
5. Y. Zhang
6. S. Kriaucionis
7. P Sarkies

• Curated by eLife

  eLife Assessment

  This important work advances our understanding of DNA methylation and its consequences for susceptibility to DNA damage. This work presents evidence that DNA methylation can accentuate the genomic damage propagated by DNA damaging agents as well as potentially being an independent source of such damage. The experimental results reported are sound but the evidence presented to support the conclusions drawn is incomplete and other interpretations are possible. The work will be of broad interest to biochemists, cell and genome biologists.

Reviewed by eLife

Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics

1. Jake VanBelzen
2. Bennet Sakelaris
3. Donna G Brickner
4. Nikita Marcou
5. Hermann Riecke
6. Niall M Mangan
7. Jason H Brickner

• Curated by eLife

  eLife Assessment

  This valuable study compares ChIP-seq and ChEC-seq2 techniques to investigate RNA polymerase II (RNAPII) binding patterns in yeast, revealing that ChEC-seq2 captures distinct regulatory events associated with active transcription missed by ChIP-seq. The authors use ChEC-seq2 data to build a stochastic model of RNAPII kinetics, providing convincing new insights into transcription regulation and the role of the nuclear pore complex. The paper highlights the importance of careful methodological comparisons in understanding RNAPII dynamics.

Reviewed by eLife

Streamlining segmentation of cryo-electron tomography datasets with Ais

1. Mart GF Last
2. Leoni Abendstein
3. Lenard M Voortman
4. Thomas H Sharp

• Curated by eLife

  eLife Assessment

  This work describes a new software platform for machine-learning-based segmentation of and particle-picking in cryo-electron tomograms. The program and its corresponding online database of trained models will allow experimentalists to conveniently test different models and share their results with others. The paper provides convincing evidence that the software will be valuable to the community.

Reviewed by eLife

PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking

1. Thomas E Forman
2. Marcin P Sajek
3. Eric D Larson
4. Neelanjan Mukherjee
5. Katherine A Fantauzzo

• Curated by eLife

  eLife Assessment

  This fundamental work provides new mechanistic insight in regulation of PDGF signaling through splicing controls. The evidence is compelling to demonstrate functional involvement of Srsf3, an RNA binding protein to this new and interesting mechanism. The work will be of broad interest to developmental biologists in general and molecular biologists/biochemists in the field of growth factor signaling and RNA processing.

Reviewed by eLife

An ancient competition for the conserved branchpoint sequence influences physiological and evolutionary outcomes in splicing

1. Karen Larissa Pereira de Castro
2. Jose M Abril
3. Kuo-Chieh Liao
4. Haiping Hao
5. John Paul Donohue
6. William K Russell
7. W Samuel Fagg

• Curated by eLife

  eLife Assessment

  This important manuscript provides insights into the competition between Splicing Factor 1 (SF1) and Quaking (QKI) for binding at the ACUAA branch point sequence in a model intron, regulating exon inclusion. The study employs rigorous transcriptomic, proteomic, and reporter assays, with both mammalian cell culture and yeast models. Nevertheless, while the data are convincing, broadening the analysis to additional exons and narrowing the manuscript's title to better align with the experimental scope would strengthen the work.

Reviewed by eLife

Saccharomyces cerevisiae Rev7 promotes non-homologous end-joining by blocking Mre11 nuclease and Rad50’s ATPase activities and homologous recombination

1. Sugith Badugu
2. Kshitiza Mohan Dhyani
3. Manoj Thakur
4. Kalappa Muniyappa

• Curated by eLife

  eLife Assessment

  This manuscript reports important data providing evidence that a 42 amino acid region of Rev7 is necessary and sufficient for interaction with the Rad50-Mre11-Xrs2 complex in budding yeast. The authors conclude that Rev7 inhibits the Rad50 ATPase and the Mre11 nuclease with the exception of ssDNA exonuclease activity. The convincing data largely support the conclusions, although the effect of Rev7 on homologous recombination is less well documented and the observed effect on resection is moderate. Specifically, the result that the Rev7 C-terminal truncation lacking the 42 amino acid region still suppresses homologous recombination is unexpected and unexplained.

Reviewed by eLife

Human immunodeficiency virus-1 induces host genomic R-loops and preferentially integrates its genome near the R-loop regions

1. Kiwon Park
2. Dohoon Lee
3. Jiseok Jeong
4. Sungwon Lee
5. Sun Kim
6. Kwangseog Ahn

• Curated by eLife

  eLife Assessment

  This study presents two main findings regarding HIV-1 genomic integration. The first, based on convincing evidence in primary cell models, is that HIV-1 induces R loop formation, though the viral driver of this process remains undefined. The second, based on model cell systems with limited physiological relevance to HIV-1, is that a portion of HIV-1 genomes integrates in the vicinity of where R loops form. This finding has the potential to offer fundamental insight into HIV-1 integration, but the strength of the presented evidence was viewed as incomplete and needing additional validation by more direct experimental methods in order to understand what the mechanistic relationship between the formation of R loops and HIV-1 integration is.

Reviewed by eLife

Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations

1. Elisa Posani
2. Pavel Janoš
3. Daniel Haack
4. Navtej Toor
5. Massimiliano Bonomi
6. Alessandra Magistrato
7. Giovanni Bussi

Reviewed by PREreview

Genetic stability of Mycobacterium smegmatis under the stress of first-line antitubercular agents

1. Dániel Molnár
2. Éva Viola Surányi
3. Tamás Trombitás
4. Dóra Füzesi
5. Rita Hirmondó
6. Judit Toth

• Curated by eLife

  eLife Assessment

  This useful study reports on the impact of antibiotic pressure on the genomic stability of the mc2155 strain of Mycobacterium smegmatis, a model for Mycobacterium tuberculosis. The findings of the study indicate that exposure to antibiotics did not lead to the development of new adaptive mutations in controlled laboratory environments, challenging the notion that antibiotic resistance arises from drug-induced microevolution. The genomic analysis provides detailed insights into the stability of M. smegmatis following exposure to standard TB treatment antibiotics, and the evidence suggesting that antibiotic pressure does not contribute to the emergence of new adaptive mutations is solid.

Reviewed by eLife