Genomics

  1. A Pooled Cell Painting CRISPR Screening Platform Enables de novo Inference of Gene Function by Self-supervised Deep Learning

    1. Srinivasan Sivanandan
    2. Bobby Leitmann
    3. Eric Lubeck
    4. Mohammad Muneeb Sultan
    5. Panagiotis Stanitsas
    6. Navpreet Ranu
    7. Alexis Ewer
    8. Jordan E. Mancuso
    9. Zachary F Phillips
    10. Albert Kim
    11. John W. Bisognano
    12. John Cesarek
    13. Fiorella Ruggiu
    14. David Feldman
    15. Daphne Koller
    16. Eilon Sharon
    17. Ajamete Kaykas
    18. Max R. Salick
    19. Ci Chu

    Reviewed by Arcadia Science

    11 evaluationsAppears in 1 listLatest version Latest activity

  2. Characterization of caffeine response regulatory variants in vascular endothelial cells

    1. Carly Boye
    2. Cynthia A Kalita
    3. Anthony S Findley
    4. Adnan Alazizi
    5. Julong Wei
    6. Xiaoquan Wen
    7. Roger Pique-Regi
    8. Francesca Luca

    • Curated by eLife

      eLife assessment

      This important study combines disease-associated genetic variation with a massively parallel reporter assay and different cellular perturbations to identify context-specific genetic regulatory effects. The methods and analyses are solid and the proposed functional variants will be helpful for experimental and quantitative geneticists studying a wide range of complex traits.

    Reviewed by eLife

    4 evaluationsAppears in 1 listLatest version Latest activity

  3. Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells

    1. Silvia Liu
    2. Yan-Ping Yu
    3. Bao-Guo Ren
    4. Tuval Ben-Yehezkel
    5. Caroline Obert
    6. Mat Smith
    7. Wenjia Wang
    8. Alina Ostrowska
    9. Alejandro Soto-Gutierrez
    10. Jian-Hua Luo

    • Curated by eLife

      eLife assessment

      The authors pair single-cell sequencing technology with the LoopSeq synthetic long-read method to examine samples of hepatocellular carcinoma and benign liver, with the goal of identifying mutations and fusion transcripts specific to cancer cells. The authors present a valuable resource and the overall support for the major claims is solid.

    Reviewed by eLife

    8 evaluationsAppears in 1 listLatest version Latest activity

  4. 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

    7 evaluationsAppears in 1 listLatest version Latest activity

  5. 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

    3 evaluationsAppears in 1 listLatest version Latest activity

  6. 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

    3 evaluationsAppears in 1 listLatest version Latest activity

  7. 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

    7 evaluationsAppears in 1 listLatest version Latest activity

  8. 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

    9 evaluationsAppears in 1 listLatest version Latest activity

  9. 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

    2 evaluationsAppears in 2 listsLatest version Latest activity

  10. 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

    1 evaluationAppears in 1 listLatest version Latest activity
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