Molecular Biology

Highly efficient generation of isogenic pluripotent stem cell models using prime editing

1. Hanqin Li
2. Oriol Busquets
3. Yogendra Verma
4. Khaja Mohieddin Syed
5. Nitzan Kutnowski
6. Gabriella R Pangilinan
7. Luke A Gilbert
8. Helen S Bateup
9. Donald C Rio
10. Dirk Hockemeyer
11. Frank Soldner

• Curated by eLife

  Evaluation Summary:

  In this manuscript, Li et al directly compare different editing strategies for human pluripotent stem cells. They demonstrate that prime editing is more efficient and precise, compared with double-strand break-based methods. They also confirm the suitability of prime editing for the introduction of different mutations related to Parkinson's disease as a model.

  (This preprint has been reviewed by eLife. We include the joint public review 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

RNA localization mechanisms transcend cell morphology

1. Raeann Goering
2. Ankita Arora
3. Megan C Pockalny
4. J Matthew Taliaferro

• Curated by eLife

  Evaluation Summary:

  Goering and colleagues investigate subcellular RNA localization across different cell types and species. The major insight is that there may be general mechanisms and specifically conserved proteins that regulate RNA localization in diverse cell types and morphologies. This manuscript will be of interest to those studying gene expression and how its regulation occurs within the cell.

  (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.)

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Validation of scRNA-seq by scRT-ddPCR using the example of ErbB2 in MCF7 cells

1. Tobias Lange
2. Tobias Groß
3. Ábris Jeney
4. Julia Scherzinger
5. Elly Sinkala
6. Christoph Niemöller
7. Stefan Zimmermann
8. Peter Koltay
9. Felix von Stetten
10. Roland Zengerle
11. Csaba Jeney

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Disruption of Smarce1, a component of the SWI/SNF chromatin remodeling complex, decreases nucleosome stability in mouse embryonic stem cells and impairs differentiation

1. Katsunobu Kashiwagi
2. Junko Yoshida
3. Hiroshi Kimura
4. Kyoji Horie

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ATP induced conformational change of axonemal outer dynein arms studied by cryo-electron tomography

1. Noemi Zimmermann
2. Akira Noga
3. Jagan Mohan Obbineni
4. Takashi Ishikawa

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The ADAM17 sheddase complex regulator iTAP/Frmd8 modulates inflammation and tumor growth

1. Marina Badenes
2. Emma Burbridge
3. Ioanna Oikonomidi
4. Abdulbasit Amin
5. Érika de Carvalho
6. Lindsay Kosack
7. Camila Mariano
8. Pedro Domingos
9. Pedro Faísca
10. Colin Adrain

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The establishment of variant surface glycoprotein monoallelic expression revealed by single-cell RNA-seq of Trypanosoma brucei in the tsetse fly salivary glands

1. Sebastian Hutchinson
2. Sophie Foulon
3. Aline Crouzols
4. Roberta Menafra
5. Brice Rotureau
6. Andrew D. Griffiths
7. Philippe Bastin

• Curated by eLife

  Evaluation Summary:

  All reviewers think the study will be really valuable for the field, especially after re-writing to include a detailed comparison with results that were previously published. We all appreciate the clear identification of a gamete sub-population, and also thought that the discovery of low activation of all VSG expression sites was intriguing and will be of considerable interest to those in 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. The reviewers all agreed to share their names with the authors.)

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Antisense non-coding transcription represses the PHO5 model gene at the level of promoter chromatin structure

1. Ana Novačić
2. Dario Menéndez
3. Jurica Ljubas
4. Slobodan Barbarić
5. Françoise Stutz
6. Julien Soudet
7. Igor Stuparević

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Multiple UBX proteins reduce the ubiquitin threshold of the mammalian p97-UFD1-NPL4 unfoldase

1. Ryo Fujisawa
2. Cristian Polo Rivera
3. Karim PM Labib

• Curated by eLife

  Evaluation Summary:

  This paper describes a biochemical analysis of the roles of Ub chain length on Ub-dependent segregase activity of yeast and human p97 and the role of UBX proteins on the disassembly of the CMG replicative helicase complex. The human p97 complex does not segregate substrates with shorter ubiquitin chains as efficiently as does the yeast complex but the human complex can be enhanced in vitro by 3 UBX proteins - FAF1, FAF2, and UBXN7. Cellular studies indicate a partial role for FAF1 and UBXN7 in cells. The paper would be strengthened by additional mechanistic understanding of how the UBX domain functions in activation of segregase activity and the contribution of this pathway in cells.

  (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.)

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The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5

1. Ryota Miyashita
2. Atsuya Nishiyama
3. Weihua Qin
4. Yoshie Chiba
5. Satomi Kori
6. Norie Kato
7. Chieko Konishi
8. Soichiro Kumamoto
9. Hiroko Kozuka-Hata
10. Masaaki Oyama
11. Yoshitaka Kawasoe
12. Toshiki Tsurimoto
13. Tatsuro S Takahashi
14. Heinrich Leonhardt
15. Kyohei Arita
16. Makoto Nakanishi

• Curated by eLife

  Evaluation Summary:

  DNA methylation inheritance through the UHRF1-DNMT1 signaling axis is becoming increasingly appreciated as a ubiquitin-regulated process. This study builds on the observation that UHRF1 multi mono-ubiquitinates the PCNA-associated protein PAF15, and that, similarly to H3 substrates, these mono-ubiquitin sites are bound by DNMT1 and may contribute to its S-phase chromatin association. The authors focus on players involved in ubiquitin removal and PAF15 release from chromatin and they identify the deubiquitinase USP7 and the DNA replication regulator ATAD5 as important to this termination process. While manipulation of these factors using Xenopus egg extracts shows quite striking effects on DNMT1 chromatin association, effects on DNA methylation are minimal and this brings to question the importance and potential impact of the pathway involving PAF15. In addition, how the findings from Xenopus egg extracts translate to regulation of DNA methylation maintenance in mammalian cells is currently unclear.

  (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