Genomics

Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome

1. Wenliang Wang
2. Manoj Hariharan
3. Wubin Ding
4. Anna Bartlett
5. Cesar Barragan
6. Rosa Castanon
7. Vince Rothenberg
8. Haili Song
9. Joseph Nery
10. Andrew Aldridge
11. Jordan Altshul
12. Mia Kenworthy
13. Hanqing Liu
14. Wei Tian
15. Jingtian Zhou
16. Qiurui Zeng
17. Huaming Chen
18. Bei Wei
19. Irem B. Gündüz
20. Todd Norell
21. Timothy J Broderick
22. Micah T. McClain
23. Lisa L. Satterwhite
24. Thomas W. Burke
25. Elizabeth A. Petzold
26. Xiling Shen
27. Christopher W. Woods
28. Vance G. Fowler
29. Felicia Ruffin
30. Parinya Panuwet
31. Dana B. Barr
32. Jennifer L. Beare
33. Anthony K. Smith
34. Rachel R. Spurbeck
35. Sindhu Vangeti
36. Irene Ramos
37. German Nudelman
38. Stuart C. Sealfon
39. Flora Castellino
40. Anna Maria Walley
41. Thomas Evans
42. Fabian Müller
43. William J. Greenleaf
44. Joseph R. Ecker

Reviewed by Rapid Reviews Infectious Diseases

Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

1. Hewei Liang
2. Yuanqiang Zou
3. Mengmeng Wang
4. Tongyuan Hu
5. Haoyu Wang
6. Wenxin He
7. Yanmei Ju
8. Ruijin Guo
9. Junyi Chen
10. Fei Guo
11. Tao Zeng
12. Yuliang Dong
13. Yuning Zhang
14. Bo Wang
15. Chuanyu Liu
16. Xin Jin
17. Wenwei Zhang
18. Xun Xu
19. Liang Xiao

• Curated by GigaByte

  Editors Assessment:

  With the recent official launch of BGI’s new CycloneSEQ sequencing platform that delivers long-reads using novel nanpores, this paper presents benchmarking data and validation studies comparing short, long-rea data from other platforms and hybrid assemblies. This study tests the performance of the new platform in sequencing diverse microbial genomes, presenting raw and processed data to enable others to scrutinise and verify the work. Being openly peer-reviewed, and having scripts and protocols also shared for the first time helps provide transparency in this benchmarking process to increase trust in this new technology. On top of benchmarking typed strains, the technology also was tested with complex microbial communities. Yielding complete metagenome-assembled genomes (MAGs) which were not achieved by short- or long-read assemblies alone. By directly reading DNA molecules without fragmentation, the study demonstrating CycloneSEQ delivers long-read data with impressive length and accuracy, unlocking gaps that short-read technologies alone cannot bridge. Future work is expanding to real samples, with and fine-tuning the balance between short-read and long-read data for even faster, higher-quality assemblies.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Single-cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location

1. Joyner Cruz
2. Willam Y Sun
3. Alexandra Verbeke
4. Iswar K Hariharan

• Curated by eLife

  eLife Assessment

  This important study uses standard single-cell RNA-seq analyses combined with methods from the social sciences to assess heterogeneity in gene expression in Drosophila imaginal wing disc cells treated with 4000 rads of ionizing radiation. The use of this methodology from social sciences is novel in Drosophila. A cell cycle based clustering approach allows them to identify a subpopulation of cells that is disproportionately responsible for much of the radiation-induced gene expression. Their convincing analyses reveal genes that are expressed regionally after irradiation, including ligands and transcription factors that have been associated with regeneration, as well as others whose roles in response to irradiation are unknown. This paper would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

Reviewed by eLife

Convergent evolution of epigenome recruited DNA repair across the Tree of Life

1. J Grey Monroe
2. Chaehee Lee
3. Daniela Quiroz
4. Mariele Lensink
5. Satoyo Oya
6. Matthew Davis
7. Evan Long
8. Kevin A Bird
9. Alice Pierce
10. Kehan Zhao
11. Daniel Runcie

• Curated by eLife

  eLife Assessment

  This paper describes the study of the evolution of the N-terminal domain of the MSH6 mismatch repair protein in regard to the presence or absence of histone reader domains. While the presence of the histone reader domains was previously known, the phylogenetic analysis of these domains performed here establishing their insertion through convergent evolution is important, definitively done, and establishes an interesting feature of the MSH6 family of proteins. The work is convincing but the presentation of the structural features of MSH6 could be improved.

Reviewed by eLife

Genome modeling and design across all domains of life with Evo 2

1. Garyk Brixi
2. Matthew G. Durrant
3. Jerome Ku
4. Michael Poli
5. Greg Brockman
6. Daniel Chang
7. Gabriel A. Gonzalez
8. Samuel H. King
9. David B. Li
10. Aditi T. Merchant
11. Mohsen Naghipourfar
12. Eric Nguyen
13. Chiara Ricci-Tam
14. David W. Romero
15. Gwanggyu Sun
16. Ali Taghibakshi
17. Anton Vorontsov
18. Brandon Yang
19. Myra Deng
20. Liv Gorton
21. Nam Nguyen
22. Nicholas K. Wang
23. Etowah Adams
24. Stephen A. Baccus
25. Steven Dillmann
26. Stefano Ermon
27. Daniel Guo
28. Rajesh Ilango
29. Ken Janik
30. Amy X. Lu
31. Reshma Mehta
32. Mohammad R.K. Mofrad
33. Madelena Y. Ng
34. Jaspreet Pannu
35. Christopher Ré
36. Jonathan C. Schmok
37. John St. John
38. Jeremy Sullivan
39. Kevin Zhu
40. Greg Zynda
41. Daniel Balsam
42. Patrick Collison
43. Anthony B. Costa
44. Tina Hernandez-Boussard
45. Eric Ho
46. Ming-Yu Liu
47. Thomas McGrath
48. Kimberly Powell
49. Dave P. Burke
50. Hani Goodarzi
51. Patrick D. Hsu
52. Brian L. Hie

Reviewed by Arcadia Science, Life Science Editors Foundation

DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A

1. Ioannis Kafetzopoulos
2. Francesca Taglini
3. Hazel Davidson-Smith
4. Duncan Sproul

Reviewed by Review Commons

Genome assembly and annotation of Acropora pulchra from Mo’orea French Polynesia

1. Trinity Conn
2. Jill Ashey
3. Ross Cunning
4. Hollie M. Putnam

• Curated by GigaByte

  Editors Assessment:

  Acropora pulchra is a species small polyped stony corals in the family Acroporidae from the the Indo-Pacific. This Data Release is the first study in stony corals to present the DNA methylome in tandem with a high-quality genome assembled utilizing PacBio long-read HiFi sequencing. Sequencing an A. pulchra specimen from Mo’orea, French Polynesia. From this single molecule sequencing data DNA methylation data was also called and quantified, and additional short-read Illumina RNASeq data was used for gene annotation. This producing an assembly size is 518 Mbp, with 174 scaffolds, and a scaffold N50 of 17 Mbp, and 40,518 protein-coding genes called. Peer review requested some improved benchmarking, and it is impressive to see from the results that the genome assembly represents the most complete and contiguous stony coral genome assembly to date. As an important indicator species and this data will hopefully serve as a resource to the coral and wider scientific community. Further quantification of the genome-wide methylation is needed aid the study epigenetics of non-model organisms, and specifically future analyses on methylation in coral.

  *This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individual C. elegans neurons

1. Alec Barrett
2. Erdem Varol
3. Alexis Weinreb
4. Seth R Taylor
5. Rebecca M McWhirter
6. Cyril Cros
7. Berta Vidal
8. Manasa Basaravaju
9. Abigail Poff
10. John A Tipps
11. Maryam Majeed
12. Chen Wang
13. Emily A Bayer
14. Molly Reilly
15. Eviatar Yemini
16. HaoSheng Sun
17. Oliver Hobert
18. David M Miller
19. Marc Hammarlund

• Curated by eLife

  eLife Assessment

  This valuable paper provides refined gene expression datasets for 52 neuron classes in C. elegans using a new method that takes advantage of the complementary strengths of bulk sequencing of flow-sorted cells and single-cell sequencing. In general, support for the paper's findings is convincing. However, more rigorous consideration of some of the method's statistical assumptions and validation of the predicted gene sets would improve the work.

Reviewed by eLife

Single-cell RNA-seq reveals trans-sialidase-like superfamily gene expression heterogeneity in Trypanosoma cruzi populations

1. Lucas Inchausti
2. Lucía Bilbao
3. Vanina A Campo
4. Joaquín Garat
5. José Sotelo-Silveira
6. Gabriel Rinaldi
7. Virginia M Howick
8. María Ana Duhagon
9. Javier G De Gaudenzi
10. Pablo Smircich

• Curated by eLife

  eLife Assessment

  This important study utilizes single-cell RNA sequencing to reveal the heterogeneity of trans-sialidase-like superfamily gene expression in Trypanosoma cruzi populations. The approach is highly convincing, as it successfully assigns cells to specific developmental forms and highlights the variability in surface protein expression among trypomastigotes. However, while the findings are solid and contribute to the understanding of immune evasion mechanisms, the study would benefit from a more detailed exploration of the regulatory factors governing trans-sialidase expression. Strengthening this aspect would further enhance its impact on researchers studying T. cruzi pathogenesis and host-parasite interactions.

Reviewed by eLife

Pyruvate and related energetic metabolites modulate resilience against high genetic risk for glaucoma

1. Keva Li
2. Nicholas Tolman
3. Ayellet V Segrè
4. Kelsey V Stuart
5. Oana A Zeleznik
6. Neeru A Vallabh
7. Kuang Hu
8. Nazlee Zebardast
9. Akiko Hanyuda
10. Yoshihiko Raita
11. Christa Montgomery
12. Chi Zhang
13. Pirro G Hysi
14. Ron Do
15. Anthony P Khawaja
16. Janey L Wiggs
17. Jae H Kang
18. Simon WM John
19. Louis R Pasquale
20. UK Biobank Eye and Vision Consortium

• Curated by eLife

  eLife Assessment

  This study presents a valuable finding on the importance of the plasma metabolome in glaucoma risk prediction. The evidence supporting the claims of the authors is solid and the work offers insights for the design of protective therapeutic strategies for glaucoma. The authors have addressed the concerns of the reviewers and reported on the limitations of the study.

Reviewed by eLife