A deformation energy model reveals sequence-dependent property of nucleosome positioning View Full Text


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Article Info

DATE

2021-01-16

AUTHORS

Guoqing Liu, Hongyu Zhao, Hu Meng, Yongqiang Xing, Lu Cai

ABSTRACT

We present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference. In addition, we also revealed that remodelers, SNF2 and RSC8, are likely to act in chromatin remodeling by binding to broad nucleosome-depleted regions that are intrinsically favorable for nucleosome positioning. Our data support the important role of position-dependent physical properties of DNA in nucleosome positioning. More... »

PAGES

27-40

References to SciGraph publications

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  • 2011-10-07. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast in BMC GENOMICS
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  • 2019-08-05. Opposing chromatin remodelers control transcription initiation frequency and start site selection in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2016-04-07. A deformation energy-based model for predicting nucleosome dyads and occupancy in SCIENTIFIC REPORTS
  • 2012-06-03. A base pair resolution map of nucleosome positions in yeast in NATURE
  • 2013-03-05. Determinants of nucleosome positioning in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2010-10-16. Prediction of nucleosome DNA formation potential and nucleosome positioning using increment of diversity combined with quadratic discriminant analysis in CHROMOSOME RESEARCH
  • 2016-05-06. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility in NATURE COMMUNICATIONS
  • 2014-04-16. Chromatin as dynamic 10-nm fibers in CHROMOSOMA
  • 2011-05-22. Determinants of nucleosome organization in primary human cells in NATURE
  • 2018-06-11. The implication of DNA bending energy for nucleosome positioning and sliding in SCIENTIFIC REPORTS
  • 2008-12-17. The DNA-encoded nucleosome organization of a eukaryotic genome in NATURE
  • 2006-07-19. A genomic code for nucleosome positioning in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00412-020-00750-9

    DOI

    http://dx.doi.org/10.1007/s00412-020-00750-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1134622566

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/33452566


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