Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 109, Issue 33, Pages 13296-13301Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1211172109
Keywords
epigenetics; heterochromatin; methylation
Categories
Funding
- National Institutes of Health [HD55391, NS046789]
- Howard Hughes Medical Institute
- Eunice Kennedy Shriver National Institute of Child Health and Human Development Fellowship [F32HD072627]
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A central goal of chromatin biology is to reveal how posttranslational histone marks modulate gene expression; however, relatively little is known about the spatial or temporal dynamics of these marks. We previously showed that a dynamic model of histone mark nucleation, propagation, and turnover fits the mean enrichment profiles from 99% of noncentromeric histone H3 lysine 9 trimethylation (H3K9me3) domains in mouse embryonic stem cells without the need for boundary or insulator elements. Here we report the full details of this inherently bounded model of histone modification dynamics and describe several dynamic features of the model using H3K9me3 as a paradigm. By analyzing the kinetic and structural constraints that drive formation of inherently bounded domains, we find that such domains are optimized when the rates of marking and turnover are comparable. Additionally, we find that to establish such domains, propagation of the histone marks must occur primarily through local contacts.
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