Genomics

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

Autosomal Allelic Inactivation: Variable Replication 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

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

1. Simone 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. Catherine Potenski
15. Tamara Prieto
16. Dennis J. Yuan
17. Rob Furatero
18. Alexi Runnels
19. Benjamin M. Costa
20. Jonathan E. Shoag
21. Majd Al Assaad
22. Michael Sigouros
23. Jyothi Manohar
24. Abigail King
25. David Wilkes
26. John Otilano
27. Murtaza S. Malbari
28. Olivier Elemento
29. Juan Miguel Mosquera
30. Nasser K. Altorki
31. Ashish Saxena
32. Margaret K. Callahan
33. Nicolas Robine
34. Soren Germer
35. Gilad D. Evrony
36. Bishoy M. Faltas
37. Dan-Avi Landau

Reviewed by PREreview

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

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

Reviewed by GigaScience

Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

1. Hanna Liao
2. Sanjay Kottapalli
3. Yuqi Huang
4. Matthew Chaw
5. Jase Gehring
6. Olivia Waltner
7. Melissa Phung-Rojas
8. Riza M Daza
9. Frederick A Matsen
10. Cole Trapnell
11. Jay Shendure
12. Sanjay Srivatsan

• Curated by eLife

  eLife Assessment

  This important technical study introduces SCOPE, an optics-free spatial reconstruction method based on bidirectional sender and receiver oligonucleotides on barcoded hydrogel beads. By sequencing proximity-encoded chimeric molecules, the authors computationally reconstruct 2D and 3D spatial information at an impressive scale. The technical demonstrations in synthetic bead systems are convincing and establish proof-of-principle that large spatial domains can be reconstructed without microscopy. The methodological advance is clear and the scale is impressive. Direct validation in biological samples would help clarify what additional limitations on applicability may exist. This work will be of interest to those working on spatial mapping.

Reviewed by eLife

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

Stranded short nascent strand sequencing reveals the topology of DNA replication origins in Trypanosoma brucei

1. Slavica Stanojcic
2. Bridlin Barckmann
3. Pieter Monsieurs
4. Lucien Crobu
5. Simon George
6. Yvon Sterkers

• Curated by eLife

  eLife Assessment

  The authors adapt sequencing of nascent DNA (DNA linked to an RNA primer, "SNS-Seq") to map DNA replication origins in Trypanosoma brucei. The main impact of this work is reporting a new set of putative origins, which do not overlap with previously reported origins, but which appear to overlap with previously mapped DNA-RNA hybrid (R-loops). Thus, these valuable findings open up new avenues for further investigation into the mechanistic basis for firing of replication forks in this organism. However, the supporting evidence remains incomplete and would benefit from orthogonal validation. This work will be of interest to those studying DNA replication and epigenetic regulation of fork origins.

Reviewed by eLife

The CLAMP GA-binding transcription factor regulates heat stress-induced transcriptional repression

1. Joseph Aguilera
2. Jingyue Duan
3. Kaitlyn Cortez
4. Rachel S Lee
5. Angelica Aragon
6. Mukulika Ray
7. Erica Larschan

• Curated by eLife

  eLife Assessment

  This important study presents evidence that the Chromatin-linked adaptor for MSL complex proteins (CLAMP) GA-binding transcription factor (TF) regulates ~75% of HS-induced repression in Drosophila and suggests that CLAMP is the first known transcription factor to induce heat-stress-mediated repression of gene expression. While mechanistic details remain to be sorted out, this manuscript provides convincing evidence that novel pathways involving the CLAMP transcription factor repress gene expression during heat shock stress.

Reviewed by eLife

Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development

1. Vivek Bhardwaj
2. Alberto Griffa
3. Helena Viñas Gaza
4. Peter Zeller
5. Alexander van Oudenaarden

• Curated by eLife

  eLife Assessment

  In this valuable study, the authors examine transcription and chromatin dynamics during early zebrafish development by simultaneously profiling histone modifications and full-length transcriptomes in thousands of single cells, providing solid analysis that chromatin and transcriptional states are initially weakly correlated in early embryonic cells and become progressively more aligned as differentiation proceeds. The work also supports a model in which promoter-anchored cis-spreading of H3K27me3 contributes to stable gene silencing during development. Future functional perturbations and orthogonal validations will be needed to determine the causal contribution of Polycomb spreading to fate commitment. Overall, the dataset and accompanying analyses provide a robust resource and a quantitative framework for studying chromatin-transcription relationships during vertebrate embryogenesis.

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

Reviewed by eLife, Review Commons