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

    This article has 22 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  2. OTX2 controls chromatin accessibility to direct somatic versus germline differentiation

    This article has 2 authors:
    1. Elisa Barbieri
    2. Ian Chambers

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  3. Transcription can be sufficient, but is not necessary, to advance replication timing

    This article has 9 authors:
    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

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. A biGWAS strategy reveals the genetic architecture of the interaction between wheat and Blumeria graminis f. sp. tritici

    This article has 30 authors:
    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

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  5. Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome

    This article has 44 authors:
    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

    This article has 2 evaluationsAppears in 1 listLatest version Latest activity
  6. Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

    This article has 19 authors:
    1. Hewei Liang
    2. Yuanqiang Zou
    3. Mengmeng Wang
    4. Tongyuan Hu
    5. Haoyu Wang
    6. Wenxin He
    7. Yanmei Ju
    8. Ruijin Guo
    9. Junyi Chen
    10. Fei Guo
    11. Tao Zeng
    12. Yuliang Dong
    13. Yuning Zhang
    14. Bo Wang
    15. Chuanyu Liu
    16. Xin Jin
    17. Wenwei Zhang
    18. Xun Xu
    19. Liang Xiao
    This article has been curated by 1 group:
    • Curated by GigaByte

      Editors Assessment:

      With the recent official launch of BGI’s new CycloneSEQ sequencing platform that delivers long-reads using novel nanpores, this paper presents benchmarking data and validation studies comparing short, long-rea data from other platforms and hybrid assemblies. This study tests the performance of the new platform in sequencing diverse microbial genomes, presenting raw and processed data to enable others to scrutinise and verify the work. Being openly peer-reviewed, and having scripts and protocols also shared for the first time helps provide transparency in this benchmarking process to increase trust in this new technology. On top of benchmarking typed strains, the technology also was tested with complex microbial communities. Yielding complete metagenome-assembled genomes (MAGs) which were not achieved by short- or long-read assemblies alone. By directly reading DNA molecules without fragmentation, the study demonstrating CycloneSEQ delivers long-read data with impressive length and accuracy, unlocking gaps that short-read technologies alone cannot bridge. Future work is expanding to real samples, with and fine-tuning the balance between short-read and long-read data for even faster, higher-quality assemblies.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte

    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  7. Single-cell transcriptomics of X-ray irradiated Drosophila wing discs reveals heterogeneity related to cell-cycle status and cell location

    This article has 4 authors:
    1. Joyner Cruz
    2. Willam Y Sun
    3. Alexandra Verbeke
    4. Iswar K Hariharan
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study uses standard single-cell RNA-seq analyses combined with methods from the social sciences to assess heterogeneity in gene expression in Drosophila imaginal wing disc cells treated with 4000 rads of ionizing radiation. The use of this methodology from social sciences is novel in Drosophila. A cell cycle based clustering approach allows them to identify a subpopulation of cells that is disproportionately responsible for much of the radiation-induced gene expression. Their convincing analyses reveal genes that are expressed regionally after irradiation, including ligands and transcription factors that have been associated with regeneration, as well as others whose roles in response to irradiation are unknown. This paper would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  8. Convergent evolution of epigenome recruited DNA repair across the Tree of Life

    This article has 11 authors:
    1. J Grey Monroe
    2. Chaehee Lee
    3. Daniela Quiroz
    4. Mariele Lensink
    5. Satoyo Oya
    6. Matthew Davis
    7. Evan Long
    8. Kevin A Bird
    9. Alice Pierce
    10. Kehan Zhao
    11. Daniel Runcie
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This paper describes the study of the evolution of the N-terminal domain of the MSH6 mismatch repair protein in regard to the presence or absence of histone reader domains. While the presence of the histone reader domains was previously known, the phylogenetic analysis of these domains performed here establishing their insertion through convergent evolution is important, definitively done, and establishes an interesting feature of the MSH6 family of proteins. The work is convincing but the presentation of the structural features of MSH6 could be improved.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  9. Genome modeling and design across all domains of life with Evo 2

    This article has 52 authors:
    1. Garyk Brixi
    2. Matthew G. Durrant
    3. Jerome Ku
    4. Michael Poli
    5. Greg Brockman
    6. Daniel Chang
    7. Gabriel A. Gonzalez
    8. Samuel H. King
    9. David B. Li
    10. Aditi T. Merchant
    11. Mohsen Naghipourfar
    12. Eric Nguyen
    13. Chiara Ricci-Tam
    14. David W. Romero
    15. Gwanggyu Sun
    16. Ali Taghibakshi
    17. Anton Vorontsov
    18. Brandon Yang
    19. Myra Deng
    20. Liv Gorton
    21. Nam Nguyen
    22. Nicholas K. Wang
    23. Etowah Adams
    24. Stephen A. Baccus
    25. Steven Dillmann
    26. Stefano Ermon
    27. Daniel Guo
    28. Rajesh Ilango
    29. Ken Janik
    30. Amy X. Lu
    31. Reshma Mehta
    32. Mohammad R.K. Mofrad
    33. Madelena Y. Ng
    34. Jaspreet Pannu
    35. Christopher Ré
    36. Jonathan C. Schmok
    37. John St. John
    38. Jeremy Sullivan
    39. Kevin Zhu
    40. Greg Zynda
    41. Daniel Balsam
    42. Patrick Collison
    43. Anthony B. Costa
    44. Tina Hernandez-Boussard
    45. Eric Ho
    46. Ming-Yu Liu
    47. Thomas McGrath
    48. Kimberly Powell
    49. Dave P. Burke
    50. Hani Goodarzi
    51. Patrick D. Hsu
    52. Brian L. Hie

    Reviewed by Arcadia Science, Life Science Editors Foundation

    This article has 6 evaluationsAppears in 2 listsLatest version Latest activity
  10. DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A

    This article has 4 authors:
    1. Ioannis Kafetzopoulos
    2. Francesca Taglini
    3. Hazel Davidson-Smith
    4. Duncan Sproul

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
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