Genomics

Systematic identification of oscillatory gene expression in single cell types

1. Alexis Weinreb
2. Manasa Basavaraju
3. Marc Hammarlund
4. Maxwell G. Heiman

Reviewed by Review Commons

Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells

1. Volker Soltys
2. Moritz A Peters
3. Dingwen Su
4. Marek Kucka
5. Yingguang Frank Chan

• Curated by eLife

  eLife Assessment

  This study presents a useful methodological advance that better enables the simultaneous measurement of gene expression and chromatin accessibility in individual cells. The evidence supporting the improved detection of gene expression is solid. The method has the potential to be more broadly impactful if it were expanded to include orthogonal validation strategies. This method will be of interest to those studying transcription and gene regulation.

Reviewed by eLife

Methylation clocks fail to generalize across genetically admixed individuals

1. Sebastián Cruz-Gonzalez
2. Ogechukwu Okpala
3. Esther Gu
4. Lissette Gomez
5. Makaela Mews
6. Jeffery M Vance
7. Michael L Cuccaro
8. Mario R Cornejo-Olivas
9. Briseida E Feliciano-Astacio
10. Goldie S Byrd
11. Jonathan Haines
12. Margaret A Pericak-Vance
13. Anthony J Griswold
14. William S Bush
15. John A Capra

• Curated by eLife

  eLife Assessment

  This important study assesses the portability of epigenetic clocks across ancestries, including in the context of accelerated aging in Alzheimer's Disease patients. It provides convincing evidence for population differences in age estimation accuracy across a variety of epigenetic clocks, driven in large part by continuous variation in ancestry. Given the accelerating use of epigenetic clocks across fields, this study is likely to be of interest to researchers working on human genetic and epigenetic variation or who apply epigenetic clocks to diverse human populations.

Reviewed by eLife

Autosomal allelic inactivation at loci with variable replication timing and dosage sensitivity

1. Michael B Heskett
2. Athanasios E Vouzas
3. Brian Johnstone
4. Krister P Freese
5. Phillip A Yates
6. Philip F Copenhaver
7. Paul T Spellman
8. David M Gilbert
9. Mathew J Thayer

• Curated by eLife

  eLife Assessment

  This important study links allelic expression imbalance with replication timing, suggesting a stochastic model for haploinsufficiency in dosage-sensitive disease. The integration of allele-specific RNA-seq and replication timing in clonal systems provides solid evidence for an association between asynchronous replication and allelic imbalance, although the scope and generality should be addressed in future work. This study will interest epigeneticists and genome regulation researchers studying replication timing and monoallelic expression, as well as developmental biologists and human geneticists concerned with clonal heterogeneity, haploinsufficiency, and variable disease penetrance.

  [Editors' note: this paper was reviewed by Review Commons.]

Reviewed by eLife

Crossing host boundaries: the evolutionary drivers and correlates of viral host jumps

1. Cedric C.S. Tan
2. Lucy van Dorp
3. Francois Balloux

Reviewed by Rapid Reviews Infectious Diseases

Genome reorganization and its functional impact during breast cancer progression

1. Kathleen S Metz Reed
2. Andrew Fritz
3. Haley Greenyer
4. Kerstin Heselmeyer-Haddad
5. Seth Frietze
6. Janet Stein
7. Gary Stein
8. Tom Misteli

• Curated by eLife

  eLife Assessment

  The study by Reed et al. provides fundamental findings defining the topological changes that occur during tumorigenesis. These compelling findings enhance the understanding of stable long-range connections among genes that reprogram cancer-related functions.

Reviewed by eLife

Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis

1. Simone Daniela Rencken
2. Georgi Tushev
3. David Hain
4. Elena Ciirdaeva
5. Oleg Simakov
6. Gilles Laurent

• Curated by eLife

  eLife Assessment

  This manuscript reports a high-quality genome assembly of the European cuttlefish, Sepia officinalis, a representative species of the Cephalopod lineage. This solid work relies on current best practices in genome sequencing and assembly, combining PacBio HiFi long reads and Hi-C chromatin conformation capture, and on state-of-the-art comparative genomic analyses, including chromosome number evolution and analyses of expanded gene families. The resulting genome will be a valuable resource for researchers interested in cuttlefish biology and comparative genomics in general.

Reviewed by eLife

Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules

1. Alexandre Pellan Cheng
2. Itai Rusinek
3. Aaron Sossin
4. Adam J. Widman
5. Eti Meiri
6. Gat Krieger
7. Ori Hirschberg
8. Doron Shem Tov
9. Shlomit Gilad
10. Ariel Jaimovich
11. Omer Barad
12. Sammantha Avaylon
13. Srinivas Rajagopalan
14. Abigail G. Thress
15. Catherine Potenski
16. Tamara Prieto
17. Dennis J. Yuan
18. Rob Furatero
19. Alexi Runnels
20. Benjamin M. Costa
21. Jonathan E. Shoag
22. Majd Al Assaad
23. Michael Sigouros
24. Jyothi Manohar
25. Abigail King
26. David Wilkes
27. John Otilano
28. Murtaza S. Malbari
29. Olivier Elemento
30. Juan Miguel Mosquera
31. Nasser K. Altorki
32. Ashish Saxena
33. Margaret K. Callahan
34. Nicolas Robine
35. Soren Germer
36. Gilad D. Evrony
37. Bishoy M. Faltas
38. Dan-Avi Landau

Reviewed by PREreview

MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes

1. Thomas C Mathers
2. Michael Paulini
3. Cibele G Sotero-Caio
4. Jonathan M D Wood

Reviewed by GigaScience

Sex Chromosome Turnover and Structural Interspecific Genome Divergence Shapes Meiotic Outcomes in Hybridizing Cobitis

1. S. A. Schlebusch
2. V. Trifonov
3. Z. Halenková
4. M. Klianitskaya
5. D. Dedukh
6. A. Ruiz Herrera
7. L. Álvarez González
8. G. Pujol Infantes
9. E. Hřibová
10. L. Andjel
11. O. Bartoš
12. P. Pajer
13. T. Tichopád
14. D. Kulik
15. J. Kotusz
16. M. Kaštánková Doležálková
17. A. Bohne
18. A. Marta
19. P. Horna
20. R. Reifová
21. Y. Guiguen
22. J. Pačes
23. K. Janko

Reviewed by GigaScience