1. DNA methylation insulates genic regions from CTCF loops near nuclear speckles

    This article has 6 authors:
    1. Shelby A Roseman
    2. Allison P Siegenfeld
    3. Ceejay Lee
    4. Nicholas Z Lue
    5. Amanda L Waterbury
    6. Brian B Liau
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study tested the impact of DNA methylation on CTCF binding in two cancer cell lines. Increased CTCF binding sites are enriched in gene bodies, and associate with nuclear speckles, indicating a role in increased transcription. In the revised work, the inferred association with nuclear speckles has been supported with more solid data. These results will be of interest to the epigenetics field.

    Reviewed by eLife

    This article has 6 evaluationsAppears in 1 listLatest version Latest activity
  2. Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

    This article has 11 authors:
    1. Oscar Aramburu
    2. Belén Gómez-Pardo
    3. Paula Rodríguez-Villamayor
    4. Andrés Blanco-Hortas
    5. Jesús Lamas
    6. Pooran Dewari
    7. Diego Perojil-Morata
    8. Pierre Boudinot
    9. Daniel J. Macqueen
    10. Carmen Bouza
    11. Paulino Martínez

    Reviewed by GigaScience

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  3. Chromosome-scale genome assembly of the European common cuttlefish Sepia officinalis

    This article has 6 authors:
    1. Simone Rencken
    2. Georgi Tushev
    3. David Hain
    4. Elena Ciirdaeva
    5. Oleg Simakov
    6. Gilles Laurent
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript reports a high-quality genome assembly of the European cuttlefish, Sepia officinalis, a representative species of the Cephalopod lineage. The data are based on current best practices for sequencing and genome assembly, including PacBio HiFi long reads and Hi-C chromatin conformation capture; the analysis is currently in parts incomplete, as further analyses are required to confirm the correct chromosome number. This genome will be a useful resource for the community of researchers interested in cuttlefish biology and comparative genomics in general.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. Extensive modulation of a conserved cis -regulatory code across 589 grass species

    This article has 18 authors:
    1. Charles O. Hale
    2. Sheng-Kai Hsu
    3. Jingjing Zhai
    4. Aimee J. Schulz
    5. Taylor Aubuchon-Elder
    6. Germano Costa-Neto
    7. Allen Gelfond
    8. Mohamed El-Walid
    9. Matthew Hufford
    10. Elizabeth A. Kellogg
    11. Thuy La
    12. Alexandre P. Marand
    13. Arun S. Seetharam
    14. Armin Scheben
    15. Michelle Stitzer
    16. Travis Wrightsman
    17. M. Cinta Romay
    18. Edward S. Buckler

    Reviewed by PREreview

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  5. Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

    This article has 6 authors:
    1. Jie Lin
    2. Yujian Wen
    3. Ji Tang
    4. Xuecong Zhang
    5. Huanlin Zhang
    6. Hao Zhu
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study uses tools of population and functional genomics to examine long non-coding RNAs (lncRNAs) in the context of human evolution. Analyses of computationally predicted human-specific lncRNAs and their genomic targets lead to the development of hypotheses regarding the potential roles of these genetic elements in human biology. The conclusions regarding evolutionary acceleration and adaptation, however, only incompletely take data and literature on human/chimpanzee genetics and functional genomics into account.

    Reviewed by eLife

    This article has 11 evaluationsAppears in 1 listLatest version Latest activity
  6. Gene expression variation across genetically identical individuals predicts reproductive traits

    This article has 5 authors:
    1. Amy K Webster
    2. John H Willis
    3. Erik Johnson
    4. Peter Sarkies
    5. Patrick C Phillips
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study addresses the role of non-genetic factors in individual differences in phenotype. Using C. elegans, the study finds 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.

    Reviewed by eLife

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  7. Chromosome-level genome assembly and methylome profile enables insights for the conservation of endangered loggerhead sea turtles

    This article has 10 authors:
    1. Eugenie C. Yen
    2. James D. Gilbert
    3. Alice Balard
    4. Albert Taxonera
    5. Kirsten Fairweather
    6. Heather L. Ford
    7. Doko-Miles J. Thorburn
    8. Stephen J. Rossiter
    9. José M. Martín-Durán
    10. Christophe Eizaguirre

    Reviewed by GigaScience

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  8. Chromosome-level reference genome for the medically important Arabian horned viper ( Cerastes gasperettii )

    This article has 15 authors:
    1. Gabriel Mochales-Riaño
    2. Samuel R. Hirst
    3. Adrián Talavera
    4. Bernat Burriel-Carranza
    5. Viviana Pagone
    6. Maria Estarellas
    7. Theo Busschau
    8. Stéphane Boissinot
    9. Michael P. Hogan
    10. Jordi Tena-Garcés
    11. Davinia Pla
    12. Juan J. Calvete
    13. Johannes Els
    14. Mark J. Margres
    15. Salvador Carranza

    Reviewed by GigaScience

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  9. Chromosome-Specific Aneuploidy Engineering via dCas9-Induced Centromeric Chromatin Relaxation

    This article has 39 authors:
    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

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  10. Systematic analysis of transcription factor combinatorial binding uncovers TEAD1 as an antagonist of tissue-specific transcription factors in human organogenesis

    This article has 6 authors:
    1. Araceli Garcia-Mora
    2. Joshua Mallen
    3. Peyman Zarrineh
    4. Neil Hanley
    5. Dave Gerrard
    6. Nicoletta Bobola
    This article has been curated by 1 group:
    • 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

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
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