Genomics

The RNA-binding protein HuR modulates the expression of the disease-linked CCL2 rs1024611G-rs13900T haplotype

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

DNA methylation insulates genic regions from CTCF loops near nuclear speckles

1. Shelby A Roseman
2. Allison P Siegenfeld
3. Ceejay Lee
4. Nicholas Z Lue
5. Amanda L Waterbury
6. Brian B Liau

• Curated by eLife

  eLife Assessment

  This valuable study tested the impact of DNA methylation on CTCF binding in two cancer cell lines. Increased CTCF binding sites are enriched in gene bodies, and associate with nuclear speckles, indicating a role in increased transcription. In the revised work, the inferred association with nuclear speckles has been supported with more solid data. These results will be of interest to the epigenetics field.

Reviewed by eLife

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

1. Oscar Aramburu
2. Belén Gómez-Pardo
3. Paula Rodríguez-Villamayor
4. Andrés Blanco-Hortas
5. Jesús Lamas
6. Pooran Dewari
7. Diego Perojil-Morata
8. Pierre Boudinot
9. Daniel J Macqueen
10. Carmen Bouza
11. Paulino Martínez

Reviewed by GigaScience

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. The data are based on current best practices for sequencing and genome assembly, including PacBio HiFi long reads and Hi-C chromatin conformation capture; the analysis is currently in parts incomplete, as further analyses are required to confirm the correct chromosome number. This genome will be a useful resource for the community of researchers interested in cuttlefish biology and comparative genomics in general.

Reviewed by eLife

Extensive modulation of a conserved cis -regulatory code across 589 grass species

1. Charles O. Hale
2. Sheng-Kai Hsu
3. Jingjing Zhai
4. Aimee J. Schulz
5. Taylor Aubuchon-Elder
6. Germano Costa-Neto
7. Allen Gelfond
8. Mohamed El-Walid
9. Matthew Hufford
10. Elizabeth A. Kellogg
11. Thuy La
12. Alexandre P. Marand
13. Arun S. Seetharam
14. Armin Scheben
15. Michelle Stitzer
16. Travis Wrightsman
17. M. Cinta Romay
18. Edward S. Buckler

Reviewed by PREreview

Gene expression variation across genetically identical individuals predicts reproductive traits

1. Amy K Webster
2. John H Willis
3. Erik Johnson
4. Peter Sarkies
5. Patrick C Phillips

• Curated by eLife

  eLife Assessment

  This important study addresses the role of non-genetic factors in individual differences in phenotype. Using C. elegans, the study finds that non-genetic differences in gene expression, partly influenced by the environment, correlate with individual differences in two reproductive traits. This supports the use of gene expression data as a key intermediate for understanding complex traits. The clever study design makes for compelling evidence.

Reviewed by eLife