Eukaryotic genomes are organized into the 3D genome structure that is known to participate in various nuclear events including transcriptional regulation, DNA replication, and repair. Also, the disorganization of the genome structure is connected to human diseases, including various cancers and developmental syndromes. Therefore, understanding of the 3D genome organization is clearly important for the basic and medical research fields, but genome-organizing mechanisms and functions of the genome structures in distinct nuclear events are largely unclear.

Protein complexes consisting of the structural maintenance of chromosomes (SMC) proteins are essential for the faithful segregation of chromosomes.  Two of the best-studied SMC complexes are condensin and cohesin, which are required for mitotic chromosome assembly and for holding sister chromatids together, respectively.  Besides the textbook paradigms, recent studies indicate that these SMC complexes are involved in genomic contacts including enhancer-promoter interactions and domain formation.  However, how condensin and cohesin establish the 3D genome structure and how they contribute to nuclear events remains largely unclear.  Therefore, our ongoing research projects are to determine how they mediate the 3D genome organization.  We have applied genomic, genetic, cell biological, and biochemical approaches to human cells and the fission yeast model system.

Cellular Senescence in Humans

Cellular senescence was defined by Dr. Leonard Hayflick, as human fibroblasts cannot proliferate infinitely but reach “the Hayflick limit” and senesce. These days, cellular senescence is known as a state of very stable cell-cycle arrest caused by exhausting the capacity of DNA replication or by various cellular stresses such as DNA damage and oncogene expression. Our ongoing research focuses on the two types of senescence that are oncogene-induced senescence (OIS), which is induced by oncogene expression, and replicative senescence (RS), which is induced by telomere shortening.

Cellular senescence is an important tumor suppression mechanism that limits the propagation of cells subjected to insults such as oncogene activation. Senescent processes are known to drastically alter expression of many genes, especially genes encoding the Senescence-Associated Secretory Phenotype (SASP) factors. The SASP factors include interleukins, chemokines, growth factors, and matrix metalloproteinases. In addition, p53 target genes are up-regulated in senescent cells. SASP, p53 target and other genes up-regulated and involved in senescent processes are collectively referred to as senescence genes.

Senescent processes also entail significant alterations of the global 3D genome structure, such as the formation of Senescence-Associated Heterochromatic Foci (SAHF) and the distension of centromeric satellites. Therefore, it appears that the 3D genome reorganization occurs upon senescence, but how the specific genome structure is established in senescent cells and contributes to the gene regulation that is characteristic of the senescent state remains unclear.

Our recent study shows how the key genome-organizing machinery, condensin, participates in the establishment and maintenance of the senescent state (Yokoyama et al. Cell Cycle 2015; Iwasaki et al. Nature Communications 2019).  In addition, condensin maintains the 3D genome structure in senescent cells.  Moreover, condensin is required for full activation of senescence genes including p53 targets and SASP genes.  Our ongoing projects are to elucidate how condensin concomitantly regulates senescence genes and the 3D genome structure in senescent cells.  Ultimately, we aim to understand how the disruption of condensin-mediated 3D genome organization contributes to oncogenic processes.

Projects Related to Cellular Senescence

• Elucidate how condensin regulates p53 targets and SASP genes in human senescent cells.
• Elucidate how condensin regulates the 3D genome structure in human senescent cells.
• Determine how condensin contributes to both Oncogene-Induced Senescence (OIS) and Replicative Senescence (RS).

3D Genome Mechanisms in the Fission Yeast Model Organism

Condensin and cohesin are the important molecular machines that establish the 3D genome architecture.  Using a chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) genomic approach, we show that cohesin and condensin often localize at the same loci, but they tend to mediate local and long-range gene contacts, respectively, and generate small and larger chromatin domains (Kim et al. Nature Genet 2016).

We also performed genome-wide chromosome conformation capture (in situ Hi-C) and found that condensin-organized chromatin domains are promoted during mitosis and serve as chromosomal compaction units (Tanizawa et al. Nature Structural & Molecular Biology 2017).  Please note that how condensin mediates mitotic chromosomal assembly is a long-standing question in the chromosome biology field.  We will determine the condensin- and cohesin-mediated genome-organizing mechanisms, details of which were discussed in my recent review (Noma, Annual Review of Genetics 2017).

We recently found that condensin directly or indirectly interacts with a general transcription factor, TATA-box binding protein (TBP), and transcription factors (Iwasaki et al. Mol Cell 2015; Kim et al. Nature Genet 2016), but how those transcription-associated factors mediate condensin-directed genome organizations remains unclear.  We will elucidate how these transcription-associated factors and condensin cooperate to establish the 3D genome structure.  Our new concept is that condensin is the molecular link that bridges 3D genome organization and transcriptional regulation.  More importantly, our data have demonstrated that the fission yeast mechanisms are conserved in human cells.

Projects Related to 3D Genome Mechanisms

• Elucidate how condensin mediates 3D genome organization via its interactions with TBP and transcription factors in fission yeast cells.
• Elucidate how the condensin-mediated 3D genome organization participates in transcriptional regulation.
• Elucidate how the 3D genome mechanisms characterized using the fission yeast system function in human cells.