Much epigenetic information is thought to be encoded in the identity and localization of potentially heritable chemical modifications to histone protein that package the genome, to which modification-contingent binding partners bind, thereby transducing downstream functional consequences. The fundamental repeating unit of chromatin, the nucleosome core particle, is a two-fold symmetric octamer of histone proteins enshrouded by two superhelical turns of DNA. This architecture places the two copies of each core histone in defined positions each projecting unstructured tails from the core of the structure to that are subject to dense posttranslational modification. For a given modification, is there meaningful information encoded by having two distinct modifiable sites per fundamental repeating unit of chromatin? There are hints that variation at this level is highly regulated, yet little is known about this scale of chromatin modifications owing to lack of tools that can measure these properties. We have developed a breakthrough calibrated ChIP technology that permits us to query this level of nucleosome sub-structure detail for the first time.
In Aim 1 we will directly quantify the symmetry of histone modifications within nucleosomes with our calibrated ChIP method, then probe the function of this newly measurable chromatin property. Given that the unit of recognition for binding partners entire nucleosome and flanking DNA, as opposed to merely the tails, precisely how variation at this level spatially manifests is likely tobe an important element of discrimination. To this end, we have recently developed biochemical evidence that nucleosomal binding partners discriminate as a function of mark-symmetry. We seek to understand the mechanistic properties of this unprecedented level of recognition, both in its biophysical details and its functional consequences for cells and organisms.
In Aim 2 we will define the molecular nature of bivalent domains-the seeming apposition of canonically activating and repressive histone modifications decorating critical developmental genes in pluripotent cells-- using calibrated sequential ChIP experiments calibrated with an exhaustive set of internal standards. We will then examine their biogenesis and predictive power as barriers to differentiation. We expect that the results of this study will illuminate the general principlesof sub-nucleosomal mark recognition and function, forming a compelling argument that this relatively un-explored level of chromatin modification is important for genome management.

Public Health Relevance

Present technology permits only crude measurement of relative amounts of chromatin marks and histone variants at a given place in the genome or quantification of their global levels, but fine-grained detail about the arrangements and patterns of these marks in the fundamental repeating structure of chromatin is lacking. We have devised a new method to probe this largely unstudied level of chromatin structure and will use it to drive a more quantitative maps of the epigenetic landscape. These maps should provide fundamental insight into the epigenetic regulation of transcription and gene control in stem cells and their differentiation; follow-on experiments will probe the mechanisms by which these modification patterns act, as well as their biogenesis and functional importance.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics A Study Section (MGA)
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Carter, Anthony D
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University of Chicago
Schools of Medicine
United States
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Shah, Rohan N; Grzybowski, Adrian T; Cornett, Evan M et al. (2018) Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies. Mol Cell 72:162-177.e7
Chen, Zhonglei; Notti, Ryan Q; Ueberheide, Beatrix et al. (2018) Quantitative and Structural Assessment of Histone Methyllysine Analogue Engagement by Cognate Binding Proteins Reveals Affinity Decrements Relative to Those of Native Counterparts. Biochemistry 57:300-304
Werner, Michael S; Sullivan, Matthew A; Shah, Rohan N et al. (2017) Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription. Nat Struct Mol Biol 24:596-603