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Showing 1–17 of 17 results
Advanced filters: Author: Michael Tolstorukov Clear advanced filters

  • Changes in chromatin structure impact gene expression programs by modulating accessibility to the transcription machinery. Here, West et al. explore differences in nucleosome occupancy between mammalian pluripotent and somatic cells and uncover regulatory regions likely to play key roles in determining cell identity.

    • Jason A. West
    • April Cook
    • Robert E. Kingston
    ResearchOpen Access
    Nature Communications
    Volume: 5, P: 1-12

  • Enhancer of zeste homolog 2 (EZH2) has been implicated as a driver of disease progression and resistance to hormonal therapies. Here, the authors focus on EZH2 in two subtypes of advanced prostate cancer and report how it modulates the bivalent genes thereby leading to forward differentiation after being targeted in neuroendocrine prostate cancer.

    • Varadha Balaji Venkadakrishnan
    • Adam G. Presser
    • Himisha Beltran
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-15

  • Nucleosome positioning and chromatin accessibility are important contributors to the regulation of gene expression. Here the authors describe a method that allows the simultaneous measurement of nucleosome occupancy and chromatin accessibility in the same assay, revealing new features of chromatin organization linked to gene regulation.

    • Jakub Mieczkowski
    • April Cook
    • Michael Y. Tolstorukov
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-11

  • Duplaquet, Li et al. identify and characterize KDM6A as an epigenetic regulator that impacts chromatin accessibility to modulate ASCL1-to-NEUROD1 subtype switching in small cell lung cancer.

    • Leslie Duplaquet
    • Yixiang Li
    • Matthew G. Oser
    Research
    Nature Cell Biology
    Volume: 25, P: 1346-1358

  • The authors characterize a previously undescribed function of Snf5 that involves interaction with the transcription factor Gli1 and downregulation of its activity via chromatin remodeling. Snf5 is shown to restrict Hedgehog (Hh) signaling in normal development and cancer. Hh inhibition emerges as a potential therapeutic strategy for malignant rhabdoid tumors in which Snf5 is commonly lost.

    • Zainab Jagani
    • E Lorena Mora-Blanco
    • Marion Dorsch
    Research
    Nature Medicine
    Volume: 16, P: 1429-1433

  • Fusion genes have been proposed as a potential mechanism of resistance to EGFR tyrosine kinase inhibitors (TKIs) in lung cancer. Here, the authors identify gene fusions that are associated with resistance to EGFR TKIs in non-small cell lung cancers, and test how these fusions impact the response to EGFR TKIs in vitro.

    • Yoshihisa Kobayashi
    • Geoffrey R. Oxnard
    • Pasi A. Jänne
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-14

  • As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study presents a genome-wide chromatin landscape of the fruitfly, based on 18 histone modifications. Nine prevalent chromatin states are described. Integrating these analyses with other data types reveals individual characteristics of different genomic elements. The work provides a resource of unprecedented scale for future experimental investigations.

    • Peter V. Kharchenko
    • Artyom A. Alekseyenko
    • Peter J. Park
    Research
    Nature
    Volume: 471, P: 480-485

  • LSD1 inhibition blocks the neuroendocrine phenotype of some small cell lung cancers (SCLCs). Here, a genome-wide CRISPR/Cas9 LSD1 inhibitor resistance screen identifies the mRNA-binding protein ZFP36L1 as a gene repressed by LSD1 that when restored inhibits SCLC neuroendocrine differentiation.

    • Hsiao-Yun Chen
    • Yavuz T. Durmaz
    • Matthew G. Oser
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-22

  • Efforts to integrate computational tools for variant effect prediction into the process of clinical decision-making are in progress. However, for such efforts to succeed and help to provide more informed clinical decisions, it is necessary to enhance transparency and address the current limitations of computational predictors.

    • Rachel Karchin
    • Predrag Radivojac
    • Dmitriy Sonkin
    Comments & Opinion
    Nature Genetics
    Volume: 56, P: 1324-1326

  • The textile industry is one of the largest polluters. Here the authors show that polyethylene is a sustainable alternative textile with water wicking and fast-drying performance. The fabrication of polyethylene fabrics is compatible with standard equipment and could be dry-coloured, further reducing water consumption.

    • Matteo Alberghini
    • Seongdon Hong
    • Svetlana V. Boriskina
    Research
    Nature Sustainability
    Volume: 4, P: 715-724

  • A large collection of new modENCODE and ENCODE genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human are analysed; this reveals many conserved features of chromatin organization among the three organisms, as well as notable differences in the composition and locations of repressive chromatin.

    • Joshua W. K. Ho
    • Youngsook L. Jung
    • Peter J. Park
    ResearchOpen Access
    Nature
    Volume: 512, P: 449-452

  • A dataset of SNPs and indels from the human genome has now been compared to nucleosome occupancy profiles. Indels tend to be less represented around regions occupied by nucleosomes, whereas SNPs are enriched around nucleosomes in bulk but depleted relative to covalently modified histones, giving insight into genome organization and its possible link to variation.

    • Michael Y Tolstorukov
    • Natalia Volfovsky
    • Peter J Park
    Research
    Nature Structural & Molecular Biology
    Volume: 18, P: 510-515

  • Critical considerations in the design and analysis of ChIP-seq experiments include how to align sequenced tags to the genome, how to detect binding sites and how to estimate the number of tags needed to confidently determine where a protein binds DNA. Using data set for three transcription factors, Kharchenko et al. address these considerations by comparing three novel algorithms with published computational methods.

    • Peter V Kharchenko
    • Michael Y Tolstorukov
    • Peter J Park
    Research
    Nature Biotechnology
    Volume: 26, P: 1351-1359

  • Charles Roberts, Peter Park, Bradley Bernstein and colleagues examine the consequences of SMARCB1 loss on enhancer landscapes in human rhabdoid tumors. They show that SMARCB1 is essential for the integrity and abundance of SWI/SNF complexes and facilitates their targeting to appropriate enhancers.

    • Xiaofeng Wang
    • Ryan S Lee
    • Charles W M Roberts
    Research
    Nature Genetics
    Volume: 49, P: 289-295