Molecular Biology

Mechanistic and thermodynamic characterization of antivirals targeting druggable pocket of SARS-CoV-2 nucleocapsid

1. Preeti Dhaka
2. Ankur Singh
3. Shweta Choudhary
4. Rama Krishna Peddinti
5. Pravindra Kumar
6. Gaurav Kumar Sharma
7. Shailly Tomar

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Potential role of KRAB-ZFP binding and transcriptional states on DNA methylation of retroelements in human male germ cells

1. Kei Fukuda
2. Yoshinori Makino
3. Satoru Kaneko
4. Chikako Shimura
5. Yuki Okada
6. Kenji Ichiyanagi
7. Yoichi Shinkai

• Curated by eLife

  Evaluation Summary:

  The majority, but not all retrotransposons undergo massive reprogramming of their methylation states during germ cell development. This manuscript tests the contribution of binding motifs for KRAB-Zinc Finger Proteins (KZFPs) and the position of retrotransposons relative to genes to explain the variable methylation dynamics of different retrotransposon families, namely L1, SVA and LTR12, as well as potential inter-individual variation during male germ cell development in humans, using an integrative analyses of available sequencing datasets. By bringing insights into the complex regulation of retrotransposons, this study could be of particular interest to the epigenetics community. Some additional analyses would strengthen the inferences made.

  (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

Intragenomic rearrangements in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses

1. Roberto Patarca
2. William A. Haseltine

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Predicted binding interface between coronavirus nsp3 and nsp4

1. Zach Hensel

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Proteomic Analysis of Human Milk Reveals Nutritional and Immune Benefits in the Colostrum from Mothers with COVID-19

1. Juanjuan Guo
2. Minjie Tan
3. Jing Zhu
4. Ye Tian
5. Huanyu Liu
6. Fan Luo
7. Jianbin Wang
8. Yanyi Huang
9. Yuanzhen Zhang
10. Yuexin Yang
11. Guanbo Wang

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Mouse models of COVID-19 recapitulate inflammatory pathways rather than gene expression

1. Cameron R. Bishop
2. Troy Dumenil
3. Daniel J. Rawle
4. Thuy T. Le
5. Kexin Yan
6. Bing Tang
7. Gunter Hartel
8. Andreas Suhrbier

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Multi-omic rejuvenation of human cells by maturation phase transient reprogramming

1. Diljeet Gill
2. Aled Parry
3. Fátima Santos
4. Hanneke Okkenhaug
5. Christopher D Todd
6. Irene Hernando-Herraez
7. Thomas M Stubbs
8. Inês Milagre
9. Wolf Reik

• Curated by eLife

  Evaluation Summary:

  This study describes a novel "maturation phase transient reprogramming" (MPTR) method to restore the epigenome of cells to a more youthful state. The authors demonstrate the effectiveness of the method to reverse several age-related changes including remodeling of the transcriptome. The method appears to peform favorably compared to other transient reprogramming protocols, and the study will be of interest to developmental biologists as well as researchers that study ageing.

  (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

Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions

1. Joy S. Xiang
2. Jasmine R. Mueller
3. En-Ching Luo
4. Brian A. Yee
5. Danielle Schafer
6. Jonathan C. Schmok
7. Frederick E. Tan
8. Katherine Rothamel
9. Rachael N. McVicar
10. Elizabeth M. Kwong
11. Krysten L. Jones
12. Hsuan-Lin Her
13. Chun-Yuan Chen
14. Anthony Q. Vu
15. Wenhao Jin
16. Samuel S. Park
17. Phuong Le
18. Kristopher W. Brannan
19. Eric R. Kofman
20. Yanhua Li
21. Alexandra T. Tankka
22. Kevin D. Dong
23. Yan Song
24. Aaron F. Carlin
25. Eric L. Van Nostrand
26. Sandra L. Leibel
27. Gene W. Yeo

Reviewed by ScreenIT

Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection

1. Joseph W. Guarnieri
2. Joseph M. Dybas
3. Hossein Fazelinia
4. Man S. Kim
5. Justin Frere
6. Yuanchao Zhang
7. Yentli Soto Albrecht
8. Deborah G. Murdock
9. Alessia Angelin
10. Larry N. Singh
11. Scott L. Weiss
12. Sonja M. Best
13. Marie T. Lott
14. Henry Cope
15. Viktorija Zaksas
16. Amanda Saravia-Butler
17. Cem Meydan
18. Jonathan Foox
19. Christopher Mozsary
20. Yared H. Kidane
21. Waldemar Priebe
22. Mark R. Emmett
23. Robert Meller
24. Urminder Singh
25. Yaron Bram
26. Benjamin R. tenOever
27. Mark T. Heise
28. Nathaniel J. Moorman
29. Emily A. Madden
30. Sharon A. Taft-Benz
31. Elizabeth J. Anderson
32. Wes A. Sanders
33. Rebekah J. Dickmander
34. Victoria K. Baxter
35. Stephen B. Baylin
36. Eve Syrkin Wurtele
37. Pedro M. Moraes-Vieira
38. Deanne Taylor
39. Christopher E. Mason
40. Jonathan C. Schisler
41. Robert E. Schwartz
42. Afshin Beheshti
43. Douglas C. Wallace

Reviewed by ScreenIT

Genomic characterization of SARS-CoV-2 from Islamabad, Pakistan by Rapid Nanopore sequencing

1. Nazish Badar
2. Aamer Ikram
3. Muhammad Salman
4. Massab Umair
5. Zaira Rehman
6. Abdul Ahad
7. Hamza Ahmed Mirza
8. Masroor Alam
9. Nayab mehmood
10. Uzma Bashir

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