Functional Analysis of Epigenetic Complexes

Massachusetts General Hospital, Boston MA

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Abstract

ABSTRACT Research in our laboratory focuses on the mechanisms used by complexes required for transcriptional ‘memory’ during development. Development of complex large organisms requires that master regulatory genes that specify a certain cell lineage be maintained in an ’on’ state throughout the lifetime of an animal and that master regulatory genes that are inappropriate for expression in that lineage be maintained in an ‘off’ state. This proposal is primarily focused on Polycomb-Group complexes, especially Polycomb Repressive Complex 1 (PRC1), which are key to maintaining the repressed state. The Polycomb-Group (PcG) of genes was initially identified in 1947 by Pam Lewis using Drosophila genetic screens. It was subsequently found to be conserved in vertebrates and to be essential for developmental patterning. In humans, paralogs of the fly PcG proteins are frequently found in families of complexes. The PRC1 family of complexes contains over 100 members with overlapping but distinct compositions. These are subdivided into two large sub-families: The non-canonical PRC1 family ubiquitylates histone H2A on lysine 119, the canonical PRC1 family compacts chromatin locally, forms long-range interactions in the genome, and is found in condensates called ‘Polycomb bodies’ both in vitro and in vivo. This proposal focuses on functions of the core protein components of canonical PRC1 (cPRC1). The two defining members of the cPRC1 family are one of the CBX proteins (usually CBX2, 4, 7 or 8) and either PHC1 or PHC2. These proteins are known to be involved in phase separation into condensates, local compaction (CBX2,4,8) and long-range interactions (both PHC proteins.) cPRC1 complexes also contain a PCGF paralog and either RING1A or RING1B. We propose to study the function of canonical PRC1 paralogs using four approaches: The first set of experiments examines the ability of CBX and PHC proteins to generate condensates when mixed with nucleosomal arrays in a purified in vitro system. We will use TIRF microscopy in a protocol that allows visualization and quantification of single nucleosomal arrays, single cPRC1 complexes or sub-complexes, and the condensates that form containing both arrays and PRC1. Dynamics of the condensates will be examined in real time, precise stoichiometries will be measured, and properties will be compared between cPRC1 complexes with different compositions. This will determine the contributions of different CBX and PHC proteins to condensate behavior. The ability of these condensates to interfere with mammalian SWI/SNF function will be measured. The second set of experiments will use a chemically inducible dimerization system in tissue culture cells to add various distinct regions of proteins known to promote phase separation to a mutant CBX2 protein that no longer generates condensates. These experiments will determine whether addition of an condensate forming region of an unrelated protein can rescue PRC1 biological function. These regions come from proteins with no similarity in either amino acid sequence or function with PRC1 other than the ability to form condensates. This will test the hypothesis that forming condensates per se is important for the maintenance of repression. The last two sets of experiments will investigate differences between paralogs of PRC1 components during differentiation. Three CBX paralogs, CBX2, CBX4 and CBX8, have the same organization and have similar in vitro functions. Single, double, and triple knockouts of these genes will be performed in ES cells and the impact of those deletion on differentiation along a neuronal lineage pathway will be characterized. This will uncover the extent to which these proteins are redundant or have differing capabilities during differentiation. The ability of various PRC1 paralogs to function will also be characterized using an organoid system that can differentiate into multiple distinct lineages. We will determine which PRC1 components are expressed in which lineages during differentiation. We will then use conditional knockout strategies to determine what role these components play during differentiation. These studies build on our thirty years of experience analyzing PRC1 function by evaluating which mechanistic functions are necessary for appropriate developmental progression and hence are used in the key biological role played by PRC1.