DOI: 10.5061/dryad.5d926
title: Data from: Epigenetic memory via concordant DNA methylation is inversely correlated to developmental potential of mammalian cells

description: In storing and transmitting epigenetic information, organisms must balance
 the need to maintain information about past conditions with the capacity
 to respond to information in their current and future environments. Some
 of this information is encoded by DNA methylation, which can be
 transmitted with variable fidelity from parent to daughter strand. High
 fidelity confers strong pattern matching between the strands of individual
 DNA molecules and thus pattern stability over rounds of DNA replication;
 lower fidelity confers reduced pattern matching, and thus greater
 flexibility. Here, we present a new conceptual framework, Ratio of
 Concordance Preference (RCP), that uses double-stranded methylation data
 to quantify the flexibility and stability of the system that gave rise to
 a given set of patterns. We find that differentiated mammalian cells
 operate with high DNA methylation stability, consistent with earlier
 reports. Stem cells in culture and in embryos, in contrast, operate with
 reduced, albeit significant, methylation stability. We conclude that
 preference for concordant DNA methylation is a consistent mode of
 information transfer, and thus provides epigenetic stability across cell
 divisions, even in stem cells and those undergoing developmental
 transitions. Broader application of our RCP framework will permit
 comparison of epigenetic-information systems across cells, developmental
 stages, and organisms whose methylation machineries differ substantially
 or are not yet well understood.
description: FMR1 locus, Fibroblast
 cell line established from individual with fragile X syndrome,
 double-stranded DNA methylation patternsBatchstamp- and
 barcode-authenticated, double-stranded DNA sequence sets collected from
 the human loci indicated, using hairpin-bisulfite PCR.FMR1_FX_Fibroblast_sequences.htmlFMR1, IMR90 Fibroblast cell line, double-stranded DNA methylation patternsFMR1_IMR90Fibroblast_dense_sequences.htmlLine 1 locus, FSH iPS, Differentiated, double-stranded DNA methylation patternsL1_FSH_iPS_Diff_sequences.htmlLine 1, FSH iPS, Undifferentiated, double-stranded DNA methylation patternsL1_FSH_iPS_Undiff_sequences.htmlLine 1, a Fibroblast cell line established from an individual with fragile X syndromeL1_FX_Fibroblast_sequences.htmlLine 1, Fragile X iPS1, double-stranded DNA methylation patternsL1_FX_iPS1_sequences.htmlLine 1, Fragile X iPS2, double-stranded DNA methylation patternsL1_FX_iPS2_sequences.htmlLine 1, H9p37 (long), Differentiated, double-stranded DNA methylation patternsL1_H9p37_long_Diff_sequences.htmlLine 1, H9p37 (long), Undifferentiated, double-stranded DNA methylation patternsL1_H9p37_long_Undiff_sequences.htmlLine 1, H9p37 (short), Differentiated, double-stranded DNA methylation patternsL1_H9p37_short_Diff_sequences.htmlLine 1, H9p37 (short), Undifferentiated, double-stranded DNA methylation patternsL1_H9p37_short_Undiff_sequences.htmlLine 1, H9p81, Undifferentiated, double-stranded DNA methylation patternsL1_H9p81_Undiff_sequences.htmlLine 1, IMR90 Fibroblast, double-stranded DNA methylation patternsL1_IMR90_Fibroblast_sequences.htmlLine 1, IMR90 iPS, double-stranded DNA methylation patternsL1_IMR90_iPS_sequences.htmlLine 1, H9p81, Differentiated, double-stranded DNA methylation patternsL1_H9p81_Diff_sequences.html