Genomics

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

Systematic analysis of transcription factor combinatorial binding uncovers TEAD1 as an antagonist of tissue-specific transcription factors in human organogenesis

1. Araceli Garcia-Mora
2. Joshua Mallen
3. Peyman Zarrineh
4. Neil Hanley
5. Dave Gerrard
6. Nicoletta Bobola

• Curated by eLife

  eLife Assessment

  This important study presents a pipeline for discovering cooperative transcription factor (TF) interactions that regulate development, and applies this pipeline in a systematic investigation of TF co-regulation in 11 human embryonic tissues. The authors provide overall solid bioinformatics and experimental support for their findings: although they make a convincing argument for the role of TEAD factors as co-repressors of regulatory activity with tissue-specific TFs, other aspects of the study would benefit from additional validation. This work would be of interest to cell biologists focused on development or on discovery of TF relationships.

Reviewed by eLife

The first near-complete genome assembly of pig: enabling more accurate genetic research

1. Caiyun Cao
2. Jian Miao
3. Qinqin Xie
4. Jiabao Sun
5. Hong Cheng
6. Zhenyang Zhang
7. Fen Wu
8. Shuang Liu
9. Xiaowei Ye
10. Zhe Zhang
11. Qishan Wang
12. Yuchun Pan
13. Zhen Wang

Reviewed by GigaScience

Genome organization by SATB1 binding to base-unpairing regions (BURs) provides a scaffold for SATB1-regulated gene expression

1. Yoshinori Kohwi
2. Xianrong Wong
3. Mari Grange
4. Thomas Sexton
5. Hunter W Richards
6. Yohko Kitagawa
7. Shimon Sakaguchi
8. Ya-Chen Liang
9. Cheng-Ming Chuong
10. Vladimir A Botchkarev
11. Ichiro Taniuchi
12. Karen L Reddy
13. Terumi Kohwi-Shigematsu

• Curated by eLife

  eLife Assessment

  This is a very important study in which the authors have modified ChIP-seq and 4C-seq with a urea step, which drastically changes the pattern of chromatin interactions observed for SATB1, but not other proteins (including CTCF). The study highlights that the urea protocols provide a complementary view of protein-chromatin interactions for some proteins, which can uncover previously hidden, functionally significant layers of chromatin organization. If applied more widely, these protocols may significantly further our understanding of chromatin organization. The study's findings are supported by a wealth of controls, making the evidence compelling.

Reviewed by eLife