Genomics

Identification of autosomal cis expression quantitative trait methylation (cis eQTMs) in children’s blood

1. Carlos Ruiz-Arenas
2. Carles Hernandez-Ferrer
3. Marta Vives-Usano
4. Sergi Marí
5. Ines Quintela
6. Dan Mason
7. Solène Cadiou
8. Maribel Casas
9. Sandra Andrusaityte
10. Kristine Bjerve Gutzkow
11. Marina Vafeiadi
12. John Wright
13. Johanna Lepeule
14. Regina Grazuleviciene
15. Leda Chatzi
16. Ángel Carracedo
17. Xavier Estivill
18. Eulàlia Marti
19. Geòrgia Escaramís
20. Martine Vrijheid
21. Juan R González
22. Mariona Bustamante

• Curated by eLife

  Evaluation Summary:

  This manuscript reports for the first time associations between DNA methylation and gene expression in blood samples from 832 children. These associations are important for understanding the regulation of genes in the genome. The importance of this study is underlined by two surprising results: a minority of these associations are also observed in adult blood samples, and only half of the associations were with the nearest gene. These findings are critical for understanding the biological effects of DNA methylation changes caused by exposures and phenotypes.

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

Reviewed by eLife

Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads

1. Florian V De Rop
2. Joy N Ismail
3. Carmen Bravo González-Blas
4. Gert J Hulselmans
5. Christopher Campbell Flerin
6. Jasper Janssens
7. Koen Theunis
8. Valerie M Christiaens
9. Jasper Wouters
10. Gabriele Marcassa
11. Joris de Wit
12. Suresh Poovathingal
13. Stein Aerts

• Curated by eLife

  Evaluation Summary:

  This paper introduces a flexible microfluidics-based single-cell genomics technology that expands and improves over existing custom droplet-based scRNA-seq protocols (inDrops and Drop-seq) in important ways: better data quality, simplified workflow, high cell recovery, and flexibility towards other single-cell applications, as exemplified by HyDrop-based single-cell ATAC-seq. Its flexibility should allow the research community to develop and implement new and custom workflows on this platform, including single-cell multi-omics technologies.

  (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

Endogenous pancreatic microRNAs differentially target the Delta, Omicron, and Wuhan SARS-CoV-2 genomes to upregulate the Diabetes-associated genes

1. Bhavya Bhavya
2. Ekta Pathak
3. Rajeev Mishra

Reviewed by ScreenIT

Genetic loci and metabolic states associated with murine epigenetic aging

1. Khyobeni Mozhui
2. Ake T Lu
3. Caesar Z Li
4. Amin Haghani
5. Jose Vladimir Sandoval-Sierra
6. Yibo Wu
7. Robert W Williams
8. Steve Horvath

• Curated by eLife

  Evaluation Summary:

  In this manuscript, Mozhui and colleagues used several epigenetic predictors, of which most come from other manuscript that have not yet been peer reviewed, to test how they differ between genetically diverse mice from the BXD family (by looking at metabolic traits and lifespan). They also identified several quantitative trait loci for the different predictors, using linkage analysis, which could shed some light on the underlying biology of epigenetic mouse ageing. One of the question that remains is how generalizable (some of) the findings are given that the follow-up analyses were only done using liver tissue.

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

Reviewed by eLife

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