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 and convincing evidence defining the topological changes that occur during tumorigenesis. The findings enhance the understanding of stable long-range connections among genes that reprogram cancer-related functions. Nevertheless, performing additional experiments is recommended.

Reviewed by eLife

OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species

1. Kuan-Hao Chao
2. Alan Mao
3. Anqi Liu
4. Steven L Salzberg
5. Mihaela Pertea

• Curated by eLife

  eLife Assessment

  This valuable study introduces a modern and accessible PyTorch reimplementation of the widely used SpliceAI model for splice site prediction. The authors provide convincing evidence that their OpenSpliceAI implementation matches the performance of the original while improving usability and enabling flexible retraining across species. These advances are likely to be of broad interest to the computational genomics community.

Reviewed by eLife

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associations

1. Luke J Dillard
2. Gina M Calabrese
3. Larry D Mesner
4. Charles R Farber

• Curated by eLife

  eLife Assessment

  This is a well-done study that provides compelling data from a diverse set of approaches from single cell transcriptome data and network analysis from genetically diverse mouse cells to identify novel driver genes underlying human GWAS associations. The authors present solid evidence that network analysis of scRNA-seq data from genetically diverse mouse bone-marrow derived stromal cells can be informative for identifying human BMD GWAS driver genes. Their approach should be broadly useful and applicable to other GWAS studies.

Reviewed by eLife

Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature

1. Anastasia Unitt
2. Made Krisna
3. Kasia M Parfitt
4. Keith A Jolley
5. Martin CJ Maiden
6. Odile B Harrison

• Curated by eLife

  eLife Assessment

  This important study introduces the Life Identification Number (LIN) coding system as a powerful and versatile approach for classifying Neisseria gonorrhoeae lineages. The authors show that LIN codes capture both previously defined lineages and their relationships in a way that aligns with the species' phylogenetic structure. The compelling evidence presented, together with its integration into the PubMLST platform, underscores its strong potential to enhance epidemiological surveillance and advance our understanding of gonococcal population biology.

Reviewed by eLife

Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR

1. Feroz Akhtar
2. Joselin Hernandez Ruiz
3. Ya-Guang Liu
4. Roy G Resendez
5. Denis Feliers
6. Liza D Morales
7. Alvaro Diaz-Badillo
8. Donna M Lehman
9. Rector Arya
10. Juan Carlos Lopez-Alvarenga
11. John Blangero
12. Ravindranath Duggirala
13. Srinivas Mummidi

• Curated by eLife

  eLife Assessment

  CCL2 is a chemokine with immune cell chemoattractant properties, and it appears to play a role in several chronic inflammatory diseases. The RNA-binding protein HuR controls the stability and translation of CCL2 mRNA. This paper presents convincing evidence that a relatively common genetic variant tied to several disease phenotypes affects the interaction between the mRNA of CCL2 and the RNA-binding protein HuR. While the experiments cannot definitively distinguish between effects on RNA transcription and stability, CCL2 is thought to be relevant for leukocyte migration in various conditions, including chronic inflammation and cancer, and the study presents important findings that may be relevant to a broad audience.

Reviewed by eLife

Telomere-to-telomere African wild rice ( Oryza longistaminata ) reference genome reveals segmental and structural variation

1. Xuanmin Guang
2. Jingnan Yang
3. Shilai Zhang
4. Fei Guo
5. Linzhou Li
6. Xiaoping Lian
7. Tao Zeng
8. Chongyang Cai
9. Fushu Liu
10. Zhihao Li
11. Yangzi Hu
12. Dongming Fang
13. Weiming He
14. Sunil Kumar Sahu
15. Wangsheng Li
16. Haorong Lu
17. Yuxiang Li
18. Huan Liu
19. Xun Xu
20. Ying Gu
21. Fengyi Hu
22. Yuliang Dong
23. Tong Wei

Reviewed by GigaScience

A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps

1. Hardip R. Patel
2. Kirat Alreja
3. Andre L.M. Reis
4. J King Chang
5. Zahra A. Chew
6. Hyungtaek Jung
7. Jillian M. Hammond
8. Ira W. Deveson
9. Aurora Ruiz-Herrera
10. Laia Marin-Gual
11. Clare E. Holleley
12. Xiuwen Zhang
13. Nicholas C. Lister
14. Sarah Whiteley
15. Lei Xiong
16. Duminda S.B. Dissanayake
17. Paul D. Waters
18. Arthur Georges

Reviewed by GigaScience

Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity

1. Khund Sayeed
2. Sreeja Parameswaran
3. Matthew J Beucler
4. Lee E Edsall
5. Andrew VonHandorf
6. Audrey Crowther
7. Omer A Donmez
8. Matthew R Hass
9. Scott Richards
10. Carmy R Forney
11. Hayley K Hesse
12. Sydney H Jones
13. Katelyn A Dunn
14. Jay Wright
15. Merrin Man Long Leong
16. Laura A Murray-Nerger
17. Vijay Yechoor
18. Ben E Gewurz
19. Kenneth M Kaufman
20. John B Harley
21. Bo Zhao
22. William E Miller
23. Leah C Kottyan
24. Matthew T Weirauch

• Curated by eLife

  eLife Assessment

  This interesting study presents important information on how human cytomegalovirus (HCMV) infection disrupts the activity of the TEAD1 transcription factor, leading to widespread chromatin alterations. The strength of evidence in revised manuscript is convincing, and includes additional functional data teasing out how TEAD1-driven chromatin changes might influence HCMV replication. This work will be of interest to the virology, chromosome biology and transcriptional co-regulation fields.

Reviewed by eLife

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

1. Qunfei Guo
2. Youliang Pan
3. Wei Dai
4. Fei Guo
5. Tao Zeng
6. Wanyi Chen
7. Yaping Mi
8. Yanshu Zhang
9. Shuaizhen Shi
10. Wei Jiang
11. Huimin Cai
12. Beiying Wu
13. Yang Zhou
14. Ying Wang
15. Chentao Yang
16. Xiao Shi
17. Xu Yan
18. Junyi Chen
19. Chongyang Cai
20. Jingnan Yang
21. Xun Xu
22. Ying Gu
23. Yuliang Dong
24. Qiye Li

Reviewed by GigaScience

Single-cell multi-omic analysis reveals principles of transcription-chromatin interaction during embryogenesis

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

Reviewed by Review Commons