1. (ATP-dependent) Chromatin Remodelers
A central question in the field of chromatin remodeling is how remodelers navigate and manipulate the extensive histone–DNA contacts within nucleosomes to generate diverse chromatin states. Multiple mechanistic models have been proposed, and high-resolution biophysical and structural studies have significantly advanced our understanding to date.
Chromatin remodelers are generally categorized into four major families, among which the SWI/SNF and ISWI types exhibit the most prominent biochemical activities. SWI/SNF-type remodelers facilitate histone eviction, engage in diverse modes of transcriptional regulation, often interact with the pre-initiation complex, and can function within nucleosome-depleted regions. In contrast, ISWI-type remodelers primarily regulate nucleosome spacing across gene bodies and are closely linked to nucleosome assembly. Biochemically, these two classes generate markedly distinct outcomes, likely dictated by the manner in which they translocate or apply force to the nucleosomal substrate.
Additionally, chromatin remodelers of the CHD-type and INO80/SWR-type exist. CHD-type remodelers (chromodomain helicase DNA-binding proteins) are structurally diverse and functionally versatile, with some members (e.g., CHD1) linked to transcriptional elongation, and others (e.g., CHD4) associated with transcriptional repression and chromatin silencing as part of the NuRD complex. Their chromodomains often enable histone modification–dependent targeting, integrating epigenetic signals with remodeling activity. The INO80/SWR-type is distinct in that it couples ATP-dependent chromatin remodeling with histone variant exchange. The SWR1 complex deposits H2A.Z into nucleosomes near gene promoters and regulatory elements, modulating transcriptional competence and genome stability. The INO80 complex, conversely, is involved in nucleosome repositioning, DNA repair, and replication stress responses, often in a spreading or resetting mode of action.
Although these remodeler families share a conserved ATPase motor domain, their divergent domain architectures and associated subunits endow them with unique remodeling mechanisms and biological outcomes. Notably, their biochemical effects—ranging from nucleosome sliding, eviction, to histone variant exchange—are determined in large part by how each complex engages and mobilizes the nucleosomal substrate, often in a directional and context-dependent manner.
During transcription, RNA polymerase II (RNAPII) must traverse DNA that is tightly wrapped around nucleosomes. In vitro studies have demonstrated that even a single nucleosome constitutes a substantial barrier to RNAPII progression, often causing transcriptional arrest or pausing. This occurs via a mechanism known as backtracking, wherein the 3′ end of the nascent RNA extrudes through RNAPII’s secondary channel.
In sharp contrast, in vivo chromatin immunoprecipitation (ChIP) analyses consistently show that RNAPII is capable of elongating at remarkably high velocities across nucleosome-rich genomic regions. This apparent discrepancy raises a fundamental question: how does RNAPII overcome the nucleosomal barrier in vivo?
Our laboratory investigates the molecular mechanisms by which diverse chromatin remodelers in both yeast and mammalian systems overcome the nucleosomal barrier during transcription. We are particularly focused on elucidating the interplay between transcription and mRNA processing during the early elongation and termination phases of RNA polymerase II (RNAPII). To address these fundamental questions in transcriptional regulation, we employ a combination of next-generation sequencing (NGS)–based approaches, along with complementary biochemical and genetic methodologies.
2. Mechanisms of RNA polymerase II Pausing during Transcription
In eukaryotic cells, RNAPII synthesizes mRNA at variable rates, playing a central role in the regulation of gene expression. Efficient mRNA production is tightly linked to co-transcriptional RNA processing events, which are, in turn, modulated by the dynamics of RNAPII elongation. For instance, RNAPII undergoes promoter-proximal pausing before entering productive elongation, and similarly encounters pausing or stalling near transcription termination sites. These transient pauses facilitate the coordinated recruitment of RNA processing machineries such as capping enzymes, splicing factors, and 3′-end processing complexes. Chromatin architecture is thought to play a critical role in modulating these pausing events, with chromatin-associated factors influencing RNAPII dynamics during early elongation.
Our laboratory investigates the molecular basis of RNAPII pausing at the +1 nucleosome and at transcription termination sites in both yeast and mammalian systems. Specifically, we aim to elucidate the mechanistic interplay between RNAPII pausing, chromatin structure, and co-transcriptional RNA processing.
3. The Principles of 3D genome Architecture in Eukaryotic Cells
Since the invention of the microscope, scientists have been fascinated by the highly compact and condensed nature of chromosomes—far beyond what one might intuitively expect. One of the most fundamental questions in chromosome biology is how human chromosomes undergo more than a 10,000-fold compaction during the transition from interphase to mitosis every 24 hours, and how this process has been stably maintained from embryogenesis to adulthood across generations.
Two key principles have emerged to explain the organization of chromosomes in three-dimensional space. First, cohesin-mediated loop extrusion drives long-range chromatin interactions, forming structural domains. Second, the directional binding of CTCF defines domain boundaries, such as those observed in topologically associating domains (TADs) and chromatin loops in mammals. However, a critical question remains: how are contact domains formed in eukaryotic organisms that lack CTCF—such as yeast or C. elegans—but still contain cohesin? This raises the possibility that either additional, yet unidentified, principles exist or that cohesin alone is sufficient to drive domain formation through alternative mechanisms.
Our laboratory focuses on elucidating the molecular basis of contact domain formation in yeast, particularly in systems where CTCF is absent. We investigate how stable domains are generated and maintained, and aim to identify diverse molecular mechanisms underlying this process. Just as protein tertiary structure is guided by its primary sequence through hierarchical folding, we hypothesize that the linear chromatin context influences its higher-order architecture. Accordingly, we study how chromatin-associated proteins that shape the linear genome may also contribute to its three-dimensional folding. Furthermore, we explore the evolutionary conservation of these mechanisms from yeast to mammals and examine how they may have been adapted or modified in mammalian systems.
4. Regulatory mechanism of DNA supercoiling in transcription
DNA supercoiling is a fundamental property of closed DNA structures, such as circular DNA, and has long been recognized as a key topological feature of the genome. Supercoiling can be modulated by various molecular machineries, including RNA and DNA polymerases, topoisomerases, cohesin, and chromatin remodelers, as well as by DNA-binding proteins.
Recent advances—such as the development of chemical tools like Crick chemistry and techniques capable of distinguishing positive and negative supercoils—have significantly expanded our understanding of supercoiling domains, including their formation, regulation, and structural properties. These insights support the notion that the propagation of DNA supercoiling can influence chromatin architecture both locally and genome-wide.
While it is widely acknowledged that the effects of supercoiling in eukaryotes must be interpreted within the chromatin context, our mechanistic understanding of this process remains limited.
Our laboratory aims to elucidate the role of DNA supercoiling as an epigenetic layer of information by leveraging genetically tractable model organisms and applying various next-generation sequencing (NGS) techniques. Through this approach, we seek to uncover the molecular mechanisms by which DNA supercoiling contributes to the regulation of transcription and chromatin structure.