Genomics

Regulation of chromatin architecture by transcription factor binding

1. Stephanie Portillo-Ledesma
2. Suckwoo Chung
3. Jill Hoffman
4. Tamar Schlick

• Curated by eLife

  eLife assessment

  In this important study, chromatin is simulated as a polymer at the scale of genes, and the 3D organization of chromatin is analyzed at nucleosome resolution. There is convincing evidence for the emergence of chromatin microdomains due to the action of transcription factors, based on the simulation incorporating well-known biophysical properties of DNA, of nucleosomes, of linker histones, and of the transcription factor pair Myc:Max, as well as considering how the 3D organization of chromatin results from bending and looping of DNA. The work greatly improves our understanding of how the joint action of transcription factors and chromatin features affects chromatin structure and accessibility, which is of interest to anyone studying gene regulation.

Reviewed by eLife

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

1. Arkadiy K. Golov
2. Alexey A. Gavrilov
3. Noam Kaplan
4. Sergey V. Razin

• Curated by eLife

  eLife assessment

  Identifying chromatin interactions with high sensitivity and resolution remains technically challenging using genome-wide approaches. This study presents findings using the refined MNase-based proximity ligation method called MChIP-C, which allows for the measurement of chromatin interactions at single-nucleosome resolution on a genome-wide scale. Overall, the evidence in this manuscript is solid, and the technological advances will be valuable for the study of 3D genome structure.

Reviewed by eLife

Nucleosome conformation dictates the histone code

1. Matthew R Marunde
2. Harrison A Fuchs
3. Jonathan M Burg
4. Irina K Popova
5. Anup Vaidya
6. Nathan W Hall
7. Ellen N Weinzapfel
8. Matthew J Meiners
9. Rachel Watson
10. Zachary B Gillespie
11. Hailey F Taylor
12. Laylo Mukhsinova
13. Ugochi C Onuoha
14. Sarah A Howard
15. Katherine Novitzky
16. Eileen T McAnarney
17. Krzysztof Krajewski
18. Martis W Cowles
19. Marcus A Cheek
20. Zu-Wen Sun
21. Bryan J Venters
22. Michael-C Keogh
23. Catherine A Musselman

• Curated by eLife

  eLife assessment

  The manuscript investigates how the tandem reader domains in BPTF co-recognize two types of modifications present on histone tails, H3K4me3 and H3 acetylation. The authors interpret their results in the context of the conformational restriction of histone tails due to interactions with nucleosomal DNA. The findings contribute new insights into how the nucleosomal context regulates the recognition of multiple histone modifications by tandem reader domains and should be of interest to the broader chromatin field.

Reviewed by eLife

The landscape of tolerated genetic variation in humans and primates

1. Hong Gao
2. Tobias Hamp
3. Jeffrey Ede
4. Joshua G. Schraiber
5. Jeremy McRae
6. Moriel Singer-Berk
7. Yanshen Yang
8. Anastasia S. D. Dietrich
9. Petko P. Fiziev
10. Lukas F. K. Kuderna
11. Laksshman Sundaram
12. Yibing Wu
13. Aashish Adhikari
14. Yair Field
15. Chen Chen
16. Serafim Batzoglou
17. Francois Aguet
18. Gabrielle Lemire
19. Rebecca Reimers
20. Daniel Balick
21. Mareike C. Janiak
22. Martin Kuhlwilm
23. Joseph D. Orkin
24. Shivakumara Manu
25. Alejandro Valenzuela
26. Juraj Bergman
27. Marjolaine Rousselle
28. Felipe Ennes Silva
29. Lidia Agueda
30. Julie Blanc
31. Marta Gut
32. Dorien de Vries
33. Ian Goodhead
34. R. Alan Harris
35. Muthuswamy Raveendran
36. Axel Jensen
37. Idriss S. Chuma
38. Julie E. Horvath
39. Christina Hvilsom
40. David Juan
41. Peter Frandsen
42. Fabiano R. de Melo
43. Fabrício Bertuol
44. Hazel Byrne
45. Iracilda Sampaio
46. Izeni Farias
47. João Valsecchi do Amaral
48. Mariluce Messias
49. Maria N. F. da Silva
50. Mihir Trivedi
51. Rogerio Rossi
52. Tomas Hrbek
53. Nicole Andriaholinirina
54. Clément J. Rabarivola
55. Alphonse Zaramody
56. Clifford J. Jolly
57. Jane Phillips-Conroy
58. Gregory Wilkerson
59. Christian Abee
60. Joe H. Simmons
61. Eduardo Fernandez-Duque
62. Sree Kanthaswamy
63. Fekadu Shiferaw
64. Dongdong Wu
65. Long Zhou
66. Yong Shao
67. Guojie Zhang
68. Julius D. Keyyu
69. Sascha Knauf
70. Minh D. Le
71. Esther Lizano
72. Stefan Merker
73. Arcadi Navarro
74. Thomas Bataillon
75. Tilo Nadler
76. Chiea Chuen Khor
77. Jessica Lee
78. Patrick Tan
79. Weng Khong Lim
80. Andrew C. Kitchener
81. Dietmar Zinner
82. Ivo Gut
83. Amanda Melin
84. Katerina Guschanski
85. Mikkel Heide Schierup
86. Robin M. D. Beck
87. Govindhaswamy Umapathy
88. Christian Roos
89. Jean P. Boubli
90. Monkol Lek
91. Shamil Sunyaev
92. Anne O’Donnell-Luria
93. Heidi L. Rehm
94. Jinbo Xu
95. Jeffrey Rogers
96. Tomas Marques-Bonet
97. Kyle Kai-How Farh

Reviewed by Arcadia Science

Plasma growth hormone pulses induce male-biased pulsatile chromatin opening and epigenetic regulation in adult mouse liver

1. Andy Rampersaud
2. Jeannette Connerney
3. David J Waxman

• Curated by eLife

  eLife assessment

  This important study offers new and convincing support for the idea that about a third of mouse liver DNAse hypersensitivity sites (DHS) showing male-biased chromatin opening are sex-biased because of the male-specific cyclic action of growth hormone pulses to alter chromatin accessibility, as compared to the relative ineffectiveness of the more static pattern of growth hormone secretion in females. Supporting evidence is found in the impact of hypophysectomy and growth hormone treatment on chromatin accessibility, and the binding of specific transcription factors and epigenetic marks at STAT5-sensitive sites. This work uncovers mechanisms underlying sex differences in liver function and will be of broad interest to endocrinologists and hepatologists.

Reviewed by eLife

Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice

1. Elizaveta V Bashkirova
2. Nell Klimpert
3. Kevin Monahan
4. Christine E Campbell
5. Jason Osinski
6. Longzhi Tan
7. Ira Schieren
8. Ariel Pourmorady
9. Beka Stecky
10. Gilad Barnea
11. Xiaoliang Sunney Xie
12. Ishmail Abdus-Saboor
13. Benjamin M Shykind
14. Bianca J Marlin
15. Richard M Gronostajski
16. Alexander Fleischmann
17. Stavros Lomvardas

• Curated by eLife

  eLife assessment

  This is an important paper that revises the canonical model of how olfactory sensory neurons choose which odor receptor to express. The data presented in the paper are convincing and the model proposed is provocative and likely to enable future work.

Reviewed by eLife

A reference assembly for the legume cover crop hairy vetch (Vicia villosa)

1. Tyson Fuller
2. Derek M. Bickhart
3. Lisa M. Koch
4. Lisa Kissing Kucek
5. Shahjahan Ali
6. Haley Mangelson
7. Maria J. Monteros
8. Timothy Hernandez
9. Timothy P. L. Smith
10. Heathcliffe Riday
11. Michael L. Sullivan

• Curated by GigaByte

  Editors Assessment:

  The hairy vetch Vicia villosa is an annual legume widely used as a cover crop due to its ability to withstand harsh winters. Here a new a 2.03GB reference-quality genome is presented, assembled from PacBio HiFi long-sequence reads and Hi-C scaffolding. After adding some more methodological details and long-terminal repeat (LTR) assembly index (LAI) analysis the assembly quality and metrics look quite convincing as a chromosome-scale assembly. This resource hopefully providing the foundation for a genetic improvement program for this important cover crop and forage species.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics

1. Andrew J. C. Russell
2. Jackson A. Weir
3. Naeem M. Nadaf
4. Matthew Shabet
5. Vipin Kumar
6. Sandeep Kambhampati
7. Ruth Raichur
8. Giovanni J. Marrero
9. Sophia Liu
10. Karol S. Balderrama
11. Charles R. Vanderburg
12. Vignesh Shanmugam
13. Luyi Tian
14. Catherine J. Wu
15. Charles H. Yoon
16. Evan Z. Macosko
17. Fei Chen

Reviewed by PREreview

DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes

1. Akihiro Kuno
2. Yoshihisa Ikeda
3. Shinya Ayabe
4. Kanako Kato
5. Kotaro Sakamoto
6. Sayaka R. Suzuki
7. Kento Morimoto
8. Arata Wakimoto
9. Natsuki Mikami
10. Miyuki Ishida
11. Natsumi Iki
12. Yuko Hamada
13. Megumi Takemura
14. Yoko Daitoku
15. Yoko Tanimoto
16. Tra Thi Huong Dinh
17. Kazuya Murata
18. Michito Hamada
19. Masafumi Muratani
20. Atsushi Yoshiki
21. Fumihiro Sugiyama
22. Satoru Takahashi
23. Seiya Mizuno

Reviewed by Review Commons

The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer

1. Johannes Engelken
2. Matthias Altmeyer
3. Renty B. Franklin

Reviewed by PREreview