Genomics

Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity

1. Hamit Izgi
2. Dingding Han
3. Ulas Isildak
4. Shuyun Huang
5. Ece Kocabiyik
6. Philipp Khaitovich
7. Mehmet Somel
8. Handan Melike Dönertaş

• Curated by eLife

  Evaluation Summary:

  This study describes work measuring transcriptional changes through development and later aging. The authors broadly conclude that the transcriptomes of several tissues diverge during development, but re-converge during aging, a pattern that they term "divergence convergence", or DiCo. The trajectories the authors have identified could provide a powerful lens through which to improve our understanding of the basic biology of aging. This paper will be of interest to the aging community, especially to researchers interested in age-dependent gene expression changes and their consequences.

  (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

Evaluation of an optimized protocol and Illumina ARTIC V4 primer pool for sequencing of SARS-CoV-2 using COVIDSeq™ and DRAGEN™ COVID Lineage App workflow

1. Cyndi R. Clark
2. Matthew T. Hardison
3. Holly N. Houdeshell
4. Alec C. Vest
5. Darcy A. Whitlock
6. Dylan D. Skola
7. Jeffrey S. Koble
8. Michael Oberholzer
9. Gary P. Schroth

Reviewed by ScreenIT

Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant

1. Wentai Ma
2. Jing Yang
3. Haoyi Fu
4. Chao Su
5. Caixia Yu
6. Qihui Wang
7. Ana Tereza Ribeiro de Vasconcelos
8. Georgii A. Bazykin
9. Yiming Bao
10. Mingkun Li

Reviewed by ScreenIT

The Geometry of ATG-Walks of the Omicron SARS CoV-2 Virus RNAs

1. Guennadi A. Kouzaev

Reviewed by ScreenIT

Environmentally sensitive hotspots in the methylome of the early human embryo

1. Matt J Silver
2. Ayden Saffari
3. Noah J Kessler
4. Gririraj R Chandak
5. Caroline HD Fall
6. Prachand Issarapu
7. Akshay Dedaniya
8. Modupeh Betts
9. Sophie E Moore
10. Michael N Routledge
11. Zdenko Herceg
12. Cyrille Cuenin
13. Maria Derakhshan
14. Philip T James
15. David Monk
16. Andrew M Prentice

• Curated by eLife

  Evaluation Summary:

  This manuscript will be of interest to researchers interested in the influence of prenatal exposures on infant health. The authors investigate the impact of the season of conception on child DNA methylation levels in two independent cohorts from the Gambia and identify a set of CpGs that are tightly regulated during development. The data support the main conclusions of the manuscript, but some of the analyses could be improved (i.e. possible presence of residual confounding). There is also limited evidence for the functional importance of the observed associations.

  (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

High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors

1. Mingrui Duan
2. Smitha Sivapragasam
3. Jacob S Antony
4. Jenna Ulibarri
5. John M Hinz
6. Gregory MK Poon
7. John J Wyrick
8. Peng Mao

• Curated by eLife

  Evaluation Summary:

  This manuscript will be of interest for researchers interested in DNA repair and transcriptional regulation. The authors provide a series of well-executed and designed high-resolution sequencing data demonstrating that transcription factor (TF) binding perturbs alkylation base damage formation as well as inhibits its repair via base excision repair (BER) at TF binding sites. Moreover, they demonstrate differences between nucleotide excision repair and BER at TF binding sites that are consistent with the different repair mechanism of these two pathways. These results should have an important and timely impact on 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. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Evolution of binding preferences among whole-genome duplicated transcription factors

1. Tamar Gera
2. Felix Jonas
3. Roye More
4. Naama Barkai

• Curated by eLife

  Evaluation Summary:

  The authors applied original approaches to explore the evolution of transcription factors following duplication and subsequent divergence among duplicates. This paper should generate broad interest among evolutionary biologists as it addresses the long-standing question of how newly evolved transcription factors acquire new binding specificity. By combining genome editing with high-precision DNA binding profiling, this study provides extensive in vivo data showing how the binding profiles of transcription factor paralog pairs diverge.

  (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

Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing

1. Jayashree Kumar
2. Lela Lackey
3. Justin M Waldern
4. Abhishek Dey
5. Anthony M Mustoe
6. Kevin M Weeks
7. David H Mathews
8. Alain Laederach

• Curated by eLife

  Evaluation Summary:

  This manuscript will be of interest to biologists who study RNA structure-function relationships in a broad range of systems, splicing researchers, and RNA structure bioinformaticians. An integrative analysis of RNA structure probing, model-based RNA folding energetics, cryo-EM data, and protein binding sequence motifs serves as the basis for a comprehensive, accurate, and robust framework for predictive models of splicing dynamics in a well-studied system. The modeling is leveraged by in silico mutagenesis that reveals novel insights into the mechanisms and tradeoffs that underlie the impact of disease-associated mutations on alternative splicing.

  (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

Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant

1. Kanika Bansal
2. Sanjeet Kumar

Reviewed by ScreenIT

Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies

1. Masaud Shah
2. Hyun Goo Woo

Reviewed by ScreenIT