Chao Lu, PhD

The regulation and biological function of many histone and DNA marks had been well-defined individually. In contrast, much less is understood about how chromatin modifications can “communicate” with each other. Enzymatic activities of chromatin modifiers are known to be sensitive to the local chromatin environment, such that various biochemical and functional interactions exist among chromatin marks. This “crosstalk” between chromatin modifications critically contributes to the partitioning of the epigenome in a stable and sometimes heritable manner. Importantly, disease-associated alterations in one chromatin modification/regulator can have ripple effects on other modifications, creating synthetic vulnerability that is potentially therapeutically exploitable. Thus, our lab (https://chaolulab.com/) seeks to dissect the complex chromatin regulatory network using cutting-edge (epi)genome profiling and editing technologies. We have three main research directions:

(1) Functional interplays between DNA and histone methylation.

Our investigation is inspired by the human exome sequencing studies of childhood overgrowth and intellectual disability (OGID) syndromes. OGID syndromes refer to a group of monogenic growth disorders defined as having increased pre- and post-natal skeletal growth parameters, intellectual disability, facial dysmorphism, and advanced bone age. Exome sequencing studies have identified enzymes involved in chromatin regulation as a major class of pathogenic factors implicated in OGID syndromes. For instance, mutations in histone/DNA methyltransferases NSD1, EZH2, and DNMT3A have been associated with Sotos syndrome, Weaver syndrome, and Tatton-Brown syndrome, respectively.

DNMT3A catalyzes de novo DNA methylation. NSD1 catalyzes the di-methylation of histone H3 lysine 36 (H3K36me2), whereas EZH2 is part of the polycomb repressive complex 2 (PRC2), facilitating tri-methylation of histone H3 lysine 27 (H3K27me3). Since germline mutations in these chromatin enzymes result in largely overlapping accelerated growth phenotypes in humans, we are interested in exploring the functional interactions between NSD1, EZH2, DNMT3A, and their corresponding histone/DNA modifications.

(2) Systems genetics approaches to dissect chromatin regulatory network.

We are interested in harnessing the power of CRISPR-Cas9 genetic screens to uncover novel chromatin crosstalk. Our first effort focused on co-dependency mapping using DepMap database to discover gene-gene functional relationships. To this end, we identified 145 co-dependency “modules” and further defined the molecular context underlying the essentiality of these modules. These analyses assign new chromatin complex composition and function, and predict new functional interactions, including an unexpected co-dependency between two transcriptionally counteracting chromatin complexes - polycomb repressive complex 2 (PRC2) and MLL-MEN1 complex. We will continue to develop the regulatory interactome of chromatin modifications in a high-throughput manner using novel genome-editing technologies.

(3) Chromatin-metabolism crosstalk.

Many chromatin-modifying reactions require not only the proteinaceous enzymes but also small-molecule substrates/co-factors that are intermediates of central carbon metabolism. It has become increasingly evident that cellular metabolic fluctuations affect levels of chromatin modification via altered supply of substrates/co-factors and other mechanisms. We are interested in leveraging our genetic screen platforms to functionally dissect the interplay between metabolic pathways and chromatin modifications in a multiplexed manner.