Genomics

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

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

  Complex traits are influenced by genes and the environment, but especially the latter is difficult to pin down. This important study uses C. elegans to demonstrate 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, which is further strengthened by experimental confirmation that identified differentially expressed genes indeed influence these traits.

Reviewed by eLife

Exploiting functional regions in the viral RNA genome as druggable entities

1. Dehua Luo
2. Yingge Zheng
3. Zhiyuan Huang
4. Zi Wen
5. Lijun Guo
6. Yingxiang Deng
7. Qingling Li
8. Yuqing Bai
9. Shozeb Haider
10. Dengguo Wei

• Curated by eLife

  eLife Assessment

  The study presents a fundamental advance in antiviral RNA research by adapting SHAPE-Map to chart the secondary structure of the Porcine Epidemic Diarrhoea Virus (PEDV) genome in infected cells and pinpointing structurally conserved, accessible RNA elements as therapeutic targets. A broad, well-documented integration of biochemical probing, computational analysis, and functional validation provides convincing evidence that these regions are both biologically relevant and druggable. Beyond PEDV, the work offers a generalizable framework for RNA-guided antiviral discovery that will interest researchers in RNA therapeutics and viral genome biology.

Reviewed by eLife

Chromosome-level genome assemblies of five Sinocyclocheilus species

1. Chao Bian
2. Ruihan Li
3. Yuqian Ouyang
4. Junxing Yang
5. Xidong Mu
6. Qiong Shi

• Curated by GigaByte

  **Editors Assessment: ** Sinocyclocheilus are a genus of freshwater cavefish fish that are endemic to the Karst regions of Southwest China. Having diverse traits in morphology, behavior, and physiology typical of cavefish, that make them interesting models for studying cave adaptation and phylogenetic evolution. The manuscript assembled chromosomal-level genomes of five Sinocyclocheilus species, and conducted allotetraploid origin analysis on these species. Assembling S. grahami (the golden-line barbel), using PacBio and Hi-C sequencing technologies, a final chromosome-level genome assembly was 1.6 Gb in size with a contig N50 of 738.5 kb and a scaffold N50 of 30.7 Mb. With 93.1% of the assembled genome sequences and 93.8% of the predicted genes anchored onto 48 chromosomes. Subsequently the authors conducted a homologous comparison to obtain chromosome-level genome assemblies for four other Sinocyclocheilus species: S. maitianheensis, S. rhinocerous, S. anshuiensis, and S. Anophthalmus. With over 82% of the genome sequences anchored on these constructed chromosomes. Peer review provided clarification on the assembly strategy and provided more benchmarking. This data having the potential to contribute to species conservation and the exploitation of potential economic and ecological values of diverse Sinocyclocheilus members.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

1. Yered Pita-Juarez
2. Dimitra Karagkouni
3. Nikolaos Kalavros
4. Johannes C. Melms
5. Sebastian Niezen
6. Toni M. Delorey
7. Adam L Essene
8. Olga R. Brook
9. Deepti Pant
10. Disha Skelton-Badlani
11. Pourya Naderi
12. Pinzhu Huang
13. Liuliu Pan
14. Tyler Hether
15. Tallulah S. Andrews
16. Carly G.K. Ziegler
17. Jason Reeves
18. Andriy Myloserdnyy
19. Rachel Chen
20. Andy Nam
21. Stefan Phelan
22. Yan Liang
23. Amit Dipak Amin
24. Jana Biermann
25. Hanina Hibshoosh
26. Molly Veregge
27. Zachary Kramer
28. Christopher Jacobs
29. Yusuf Yalcin
30. Devan Phillips
31. Michal Slyper
32. Ayshwarya Subramanian
33. Orr Ashenberg
34. Zohar Bloom-Ackermann
35. Victoria M. Tran
36. James Gomez
37. Alexander Sturm
38. Shuting Zhang
39. Stephen J. Fleming
40. Sarah Warren
41. Joseph Beechem
42. Deborah Hung
43. Mehrtash Babadi
44. Robert F. Padera
45. Sonya A. MacParland
46. Gary D. Bader
47. Nasser Imad
48. Isaac H. Solomon
49. Eric Miller
50. Stefan Riedel
51. Caroline B.M. Porter
52. Alexandra-Chloé Villani
53. Linus T.-Y. Tsai
54. Winston Hide
55. Gyongyi Szabo
56. Jonathan Hecht
57. Orit Rozenblatt-Rosen
58. Alex K. Shalek
59. Benjamin Izar
60. Aviv Regev
61. Yury Popov
62. Z. Gordon Jiang
63. Ioannis S. Vlachos

Reviewed by Rapid Reviews Infectious Diseases

Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2

1. Hisato Kobayashi
2. Tatsushi Igaki
3. Soichiro Kumamoto
4. Keisuke Tanaka
5. Tomoya Takashima
6. So I Nagaoka
7. Shunsuke Suzuki
8. Masaaki Hayashi
9. Marilyn B Renfree
10. Manabu Kawahara
11. Shun Saito
12. Toshihiro Kobayashi
13. Hiroshi Nagashima
14. Hitomi Matsunari
15. Kazuaki Nakano
16. Ayuko Uchikura
17. Hiroshi Kiyonari
18. Mari Kaneko
19. Hiroo Imai
20. Kazuhiko Nakabayashi
21. Matthew C Lorincz
22. Kazuki Kurimoto

• Curated by eLife

  eLife Assessment

  The authors analyses describe a novel mechanism by which a retrotransposon-derived LTR may be involved in genomic imprinting and demonstrate imprinting of the ZDBF2 locus in rabbits and Rhesus macaques using allele-specific expression analysis. This imprinting of the ZDBF2 locus correlates with transcription of GPR1-AS orthologs. The accompanying genomic analysis is very well executed allowing for the conclusions reached in the manuscript. The revisions made at the request of the reviewers in this important manuscript strengthen the evidence from the genomic analyses, and as a result, the evidence is now convincing and will be informative to the genomics and developmental biology communities.

Reviewed by eLife

OTX2 controls chromatin accessibility to direct somatic versus germline differentiation

1. Elisa Barbieri
2. Ian Chambers

Reviewed by Review Commons

Transcription can be sufficient, but is not necessary, to advance replication timing

1. Athanasios E. Vouzas
2. Takayo Sasaki
3. Juan Carlos Rivera-Mulia
4. Jesse L. Turner
5. Amber N. Brown
6. Karen E. Alexander
7. Laura Brueckner
8. Bas van Steensel
9. David M. Gilbert

Reviewed by Review Commons

A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

1. Jingzhong Xie
2. Qiaoling Luo
3. Limin Wang
4. Dan Qiu
5. Caihong Zhao
6. Jinghuang Hu
7. Jing Zhang
8. Xinyu Zhao
9. Zhaogen Chen
10. Yibo Wang
11. Yang Yu
12. Mengzhen Luo
13. Haoyuan Song
14. Yuexuan Hou
15. Zhimeng Zhang
16. Mou Yin
17. Haojie Wang
18. Xuanzhao Li
19. Xiaomeng Fu
20. Bei Xiao
21. Yahui Li
22. Jiajie Wu
23. Wenxuan Liu
24. Yanpeng Wang
25. Mo Zhu
26. Yanming Zhang
27. Alisdair R. Fernie
28. Wei Wang
29. Hongjie Li
30. Fei He

Reviewed by PREreview

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