Sequence features accurately predict genome-wide MeCP2 binding in vivo

H. Tomas Rube, Wooje Lee, Miroslav Hejna, Huaiyang Chen, Dag H. Yasui, John F. Hess, Janine M LaSalle, Jun S. Song, Qizhi Gong

Research output: Contribution to journalArticle

25 Scopus citations


Methyl-CpG binding protein 2 (MeCP2) is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood. Using high-resolution MeCP2-binding data, we show that DNA sequence features alone can predict binding with 88% accuracy. Integrating MeCP2 binding and DNA methylation in a probabilistic graphical model, we demonstrate that previously reported genome-wide association with methylation is in part due to MeCP2"™ s affinity to GC-rich chromatin, a result replicated using published data. Furthermore, MeCP2 co-localizes with nucleosomes. Finally, MeCP2 binding downstream of promoters correlates with increased expression in Mecp2-deficient neurons.

Original languageEnglish (US)
Article number11025
JournalNature Communications
StatePublished - Mar 24 2016

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)
  • Physics and Astronomy(all)

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    Rube, H. T., Lee, W., Hejna, M., Chen, H., Yasui, D. H., Hess, J. F., LaSalle, J. M., Song, J. S., & Gong, Q. (2016). Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nature Communications, 7, [11025].