Genomics

Chromosome-Specific Aneuploidy Engineering via dCas9-Induced Centromeric Chromatin Relaxation

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. Yimeng Xu
25. Liani G. Devito
26. Lyn Healy
27. Zhen Sun
28. Weiming Shen
29. Hongye Wang
30. Eugénie S. Lim
31. Samuel M. O’Toole
32. Scott Akker
33. William M. Drake
34. Haojie Jin
35. Jessica A. Downs
36. Sarah E. McClelland
37. John F. X. Diffley
38. Peter Ly
39. 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

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. Mark Gregory
24. Shanshan He
25. Michael Patrick
26. Tushar Rane
27. Aster Wardhani
28. Amit Dipak Amin
29. Jana Biermann
30. Hanina Hibshoosh
31. Molly Veregge
32. Zachary Kramer
33. Christopher Jacobs
34. Yusuf Yalcin
35. Devan Phillips
36. Michal Slyper
37. Ayshwarya Subramanian
38. Orr Ashenberg
39. Zohar Bloom-Ackermann
40. Victoria M. Tran
41. James Gomez
42. Alexander Sturm
43. Shuting Zhang
44. Stephen J. Fleming
45. Sarah Warren
46. Joseph Beechem
47. Deborah Hung
48. Mehrtash Babadi
49. Robert F. Padera
50. Sonya A. MacParland
51. Gary D. Bader
52. Nasser Imad
53. Isaac H. Solomon
54. Eric Miller
55. Stefan Riedel
56. Caroline B. M. Porter
57. Alexandra-Chloé Villani
58. Linus T.-Y. Tsai
59. Winston Hide
60. Gyongyi Szabo
61. Jonathan Hecht
62. Orit Rozenblatt-Rosen
63. Alex K. Shalek
64. Benjamin Izar
65. Aviv Regev
66. Yury V. Popov
67. Z. Gordon Jiang
68. 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 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