Linking genome to epigenome

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Guo‐Cheng Yuan

Published Online: Feb 17 2012

DOI: 10.1002/wsbm.1165

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Recent epigenomic studies have identified significant differences between developmental stages and cell types. While the importance of epigenetic regulation has been increasingly recognized, it remains unclear how the global epigenetic patterns are established and maintained. Here I review a number of recent studies with the emphasis on the role of the genomic sequence in shaping the epigenetic landscape. These studies strongly suggest that the sequence information is important not just for controlling target specificity but for orchestrating the diversity of epigenetic patterns among different cell types. The epigenome is maintained by the complex network of a large number of interactions. Integrative approaches are needed to gain insights into these networks. WIREs Syst Biol Med 2012. doi: 10.1002/wsbm.1165

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Figure 1.

A model for the role of the genomic sequence in guiding genome‐wide epigenetic patterns. (a) The intrinsic association between an epigenetic mark and a genome locus is sequence‐dependent and can be quantified by a propensity score. (b) An epigenetic mark (represented by the stars) is constitutively recruited to regions with high propensity scores, mediated by interaction with general factors (represented by the ovals) that target distinct sequence features. These features are usually degenerative and are the main determinants of the propensity scores. On the opposite end, this mark is excluded from regions with low propensity score. In the middle range, the epigenetic pattern is highly variable among different cell types. Occupancy can be enhanced or inhibited because of interactions with many cell type specific factors (represented by other shapes).

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Philip Benfey

Is intrigued by one of the key questions in developmental biology: how cells acquire their identities. This is an important question in human development, where stem cells divide and differentiate into skin, muscle, fat etc. It is equally central to plant development, where most organs and cells are formed from stem cell populations known as meristems. The Benfey lab addresses this question using a combination of genetics, molecular biology, and genomics to identify and characterize the genes that regulate formation of the root in the plant model system, Arabidopsis thaliana. The choice of the root as a model was based on the simplicity of its organization and its stereotyped developmental program.

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Article Title	Linking genome to epigenome
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Linking genome to epigenome

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