Combinatorial epigenetic readout of methylated DNA and histone methylation marks by ICBP90/UHRF1

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The many functions that all cells of our body carry out require that their genetic material is maintained, read and translated in a highly organized manner. The molecular target of genome regulation is chromatin, in which DNA is wrapped around histone proteins. A large variety of chemical modifications of DNA and histones are at the core of essential so called epigenetic processes. The biochemical principles of translation of discrete chromatin modifications by local recruitment of specific binding proteins are currently being worked out. While these factors constitute essential links between chromatin modification patterns and chromatin function, little is known about their regulation. UHRF1 (also referred to as ICBP90 or NP95 in mouse) is a multidomain protein that crucially links DNA methylation to histone methylation and in particular the repressive mark histone H3 lysine 9 trimethylation (H3K9me3). The factor is involved in maintenance of DNA methylation patterns during replication and its deletion in mice is embryonic lethal. UHRF1/NP95 contains different domains, which have been implicated in binding methylated DNA, unmodified H3 and H3K9me3, respectively. We have obtained evidence that UHRF1/NP95 is controlled in its heterochromatin association by a small cellular molecule, namely phosphatidylinositol 5-phosphate (PI5P). While phosphatidylinositol phosphates (PIP) are generally well known for their signaling function at the cell membrane and in the cytoplasm, a separate pool of these lipids exists in the cell nucleus with largely unknown biochemistry and function. Based on our preliminary work, we hypothesize that PI5P levels modulated in response to defined cellular processes such as the cell cycle and toxic stresses regulate the chromatin association of UHRF1/NP95 by allosterically inducing distinct conformations of the protein. These distinct conformations differ in the accessibility of the histone modification and DNA methylation binding domains of UHRF1/NP95. To investigate the validity of this idea we want to (i) establish the molecular details of PI5P regulating UHRF1 chromatin association using a combination of biochemical, biophysical and structural approaches, and (ii) define the cellular role of PI5P in regulating UHRF1/NP95 chromatin association by analyzing individual cells as well as cell pools and by looking at single gene loci as well as at the whole genome.If successful, this work will provide novel insights into regulation of an important epigenetic factor as well as the function of PI5P in the cell nucleus. Beyond that the study might have considerable impact onto our general understanding of chromatin regulation and the biology of nuclear PIP. Also, we might define new avenues of functional manipulation of chromatin modification binding proteins by small molecules/drugs thereby providing novel approaches of epigenetic therapy in curing diseases (e.g. cancer, diabetes).