RESEARCH OVERVIEW
We investigate how chromatin organization controls genome functions, with a major focus on two areas:
(i) exploring the molecular mechanisms underlying the lifelong reorganization of the epigenetic modification landscape in mammalian organisms, and
(ii) developing mass spectrometry-based approaches for in-depth quantitative analysis of chromatin proteins and histone post-translational modifications at subnuclear and single-cell resolution.
Advancing Chromatin Research with Cutting-Edge Proteomics
In eukaryotic cells, genomes combine with histone proteins and other factors to form chromatin - a dynamic structure that regulates DNA-templated processes. Chromatin carries a variety of covalent modifications that control genome activities by directing nuclear proteins to specific loci. These modifications primarily cluster on histones, forming complex patterns known as the 'histone code' (Fig. 1a). Unlike the static genetic code, histone modifications are dynamic, allowing genome organization and transcription to adapt to cellular needs. This adaptability is crucial for many processes, including development, while disruptions in modification pathways are linked to diseases and age-related functional decline. Although the regulatory roles of many individual modifications are well characterized, how dynamic changes in the combinatorial histone modification patterns shape genome function remains unclear.
Figure 1: A schematic illustrating the intricate nature of epigenetic regulation and the importance of examining chromatin organization through multiple lenses.
a - A word cloud depicting various combinatorial modifications found on the histone H3 tails in vivo.
b - Nuclei isolated from mammalian cells at various ages, representing starting material for downstream analyses that aim to reveal how subnuclear genome organization changes across the lifespan.
c - Co-existing histone modifications work together to modulate the binding and enzymatic activities of nuclear proteins that orchestrate downstream genomic functions.
Mass spectrometry-based proteomic approaches, integrated with next-generation sequencing, enable detailed profiling of histone modification patterns (d), genome-wide distribution (e), and the chromatin-associated proteome (f) of specific nuclear domains of interest.
Our research, along with findings from others, reveals that modifications frequently function collaboratively, with each capable of modulating the placement, removal, and regulatory effect of others (Fig. 1c). Furthermore, the binding of many critical factors - such as transcriptional activators, repressors, and chromatin remodelers - is often controlled by multiple histone modifications (see our work to learn more). To understand how dynamic changes in chromatin organization influence genome function, we must therefore thoroughly investigate both histone modification patterns and the nuclear proteins that work together to shape specific regulatory outcomes. This poses a significant technical challenge, as most current techniques, like chromatin immunoprecipitation followed by sequencing (ChIP-seq), are limited to a narrow range of target modifications and proteins, restricting their ability to capture the full complexity of chromatin regulatory circuits. To overcome these limitations, we are developing advanced mass spectrometry-based proteomics methods for comprehensive, quantitative profiling of chromatin-associated proteins and histone modifications within specific nuclear regions. Combined with next-generation sequencing, these approaches offer a deep molecular view of distinct chromatin domains (Fig. 1d-f), enabling us to examine their dynamic remodeling across processes like aging, cellular differentiation, and reprogramming. Drawing on our expertise in proteomics and recent advances in mass spectrometry, we aim to establish integrative multi-omics pipelines that will provide critical insights into chromatin regulation in health and disease.
Decoding Lifelong Epigenetic Trajectories to Combat Aging
Epigenetic information, encoded in complex modification patterns on DNA and histone proteins, enables eukaryotic cells to differentially utilize the same genome, allowing them to perform specialized functions required for the formation of complex multicellular life forms. Mammalian organisms are composed of hundreds of distinct cell types, most of which acquire their unique epigenetic makeup during early development. Various molecular pathways then ensure that the cell-type-specific epigenomes are maintained over time to preserve cell identity and functions.
Paradoxically, we and others have shown that the epigenetic landscapes of mammalian cells are not static but progressively change in a non-random manner throughout life (Fig. 2; see our work for more on histone modification changes, and studies by others on DNA methylation changes). Although the full extent of age-related epigenetic reorganization remains to be elucidated, many aberrations observed in aged cells, such as heterochromatin loss, have been directly linked to genomic dysfunctions and are considered as key drivers of age-associated physiological decline and disorders.
Figure 2: A schematic inspired by Waddington's epigenetic landscape, illustrating the concept that the cellular epigenome undergoes progressive, non-random changes throughout life, which ultimately contribute to genome misregulation.
Strikingly, emerging data suggest that at least some age-related epigenetic aberrations can be reversed, offering the potential to restore key physiological functions. However, despite this great promise, our understanding of the intricate relationship between epigenetics and aging remains in its infancy. While most research has centered on age-associated changes in DNA methylation, much less is known about how other epigenetic factors - such as distinct histone modifications and non-canonical histone variants - dynamically change throughout the lifespan. It also remains unclear what factors drive the reorganization of the epigenetic modification landscape and how this reorganization impacts chromatin and genome functions. Addressing these questions is essential for building a foundation to understand the mechanisms underlying physiological decline and the emergence of age-related pathologies, as well as for exploring new avenues to develop targeted interventions aimed at extending a healthy lifespan.
Our scientific mission is to provide a systematic comprehensive characterization of how chromatin modification and protein landscapes change over the course of life. By integrating unbiased quantitative proteomics with genomics approaches we aim to capture the full scope and spatiotemporal dynamics of age-related epigenetic alterations across different tissues and cell types, using mice as a model organism. By combining this data with functional biochemical assays, gene editing tools, and various cellular models, we aspire to dissect the molecular mechanisms underlying genome dysfunction in aged cells and uncover key pathways that drive age-associated epigenetic decline.