PT - JOURNAL ARTICLE AU - Minseung Choi AU - Diane P. Genereux AU - Jamie Goodson AU - Haneen Al-Azzawi AU - Shannon Q. Allain AU - Noah Simon AU - Stan Palasek AU - Carol B. Ware AU - Chris Cavanaugh AU - Daniel G. Miller AU - Winslow C. Johnson AU - Kevin D. Sinclair AU - Reinhard Stöger AU - Charles D. Laird TI - Epigenetic Memory <em>via</em> Concordant DNA Methylation Persists in Mammalian Toti- and Pluripotent Stem Cells AID - 10.1101/072488 DP - 2017 Jan 01 TA - bioRxiv PG - 072488 4099 - http://biorxiv.org/content/early/2017/06/28/072488.short 4100 - http://biorxiv.org/content/early/2017/06/28/072488.full AB - 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. • We are interested in the strategies that various cell types, organisms, and species use to achieve balance between flexibility and stability. 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 confirm previous observations that differentiated cells in mammals operate with high DNA methylation stability. 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.