Genomics

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

Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles

1. Eugenie C Yen
2. James D Gilbert
3. Alice Balard
4. Albert Taxonera
5. Kirsten Fairweather
6. Heather L Ford
7. Doko-Miles J Thorburn
8. Stephen J Rossiter
9. José M Martín-Durán
10. Christophe Eizaguirre

Reviewed by GigaScience

Chromosome-level reference genome for the medically important Arabian horned viper ( Cerastes gasperettii )

1. Gabriel Mochales-Riaño
2. Samuel R Hirst
3. Adrián Talavera
4. Bernat Burriel-Carranza
5. Viviana Pagone
6. Maria Estarellas
7. Theo Busschau
8. Stéphane Boissinot
9. Michael P Hogan
10. Jordi Tena-Garcés
11. Davinia Pla
12. Juan J Calvete
13. Johannes Els
14. Mark J Margres
15. Salvador Carranza

Reviewed by GigaScience

Genome-wide Chromosome-specific Aneuploidy Engineering and Phenotypic Characterization with CRISPR-Taiji

1. Hugang Feng
2. Daqi Deng
3. Rashmi Dahiya
4. Libin Wang
5. Jingkun Zeng
6. Benjy Jek Yang Tan
7. Fiona Byrne
8. Scott T. C. Shepherd
9. Jiahao Wang
10. Sarah C. Johnson
11. Alison Harrod
12. Karen A. Lane
13. Annika Fendler
14. Anne-Laure Cattin
15. Zayd Tippu
16. Meilun Nie
17. Yiming Zhao
18. Ruijia Wang
19. Wei Ai
20. Omar Bouricha
21. Taja Barber
22. Yuliia Dovga
23. Yihan Xu
24. Weiming Shen
25. Zhen Sun
26. Hongye Wang
27. Jiufei Zhu
28. Yimeng Xu
29. Liani G. Devito
30. Lyn Healy
31. Eugénie S. Lim
32. Samuel M. O’Toole
33. Scott Akker
34. William M. Drake
35. Haojie Jin
36. Jessica A. Downs
37. Sarah E. McClelland
38. John F. X. Diffley
39. Peter Ly
40. Samra Turajlic

Reviewed by PREreview