MERIT Award Recipient: Terumi Kohwi-Shigematsu, Ph.D.
Studies on Gene Regulation by Chromatin Organization
Many biological mechanisms contribute to the onset, growth, and spread of cancer, but what they have in common is that they involve control of specific changes in how genes are expressed. In recent years the way that DNA is organized in the cell’s nucleus has emerged as an important contributor in regulating gene expression. In humans and other mammals, strands of DNA with some three billion base pairs per strand are tightly packaged inside the cell nucleus in the form of chromatin (a complex of DNA, proteins called histones, and other proteins). Failure to control chromatin organization can lead to the inappropriate expression of large numbers of genes. Regulation of chromatin folding is therefore a fundamentally important process with wide implications in biology, from normal stem-cell function to many diseases including cancer. Our laboratory is addressing how chromatin folding regulates the expression or repression of specific sets of genes at the right time in each different cell type.
We originally identified a class of unusual DNA sequences, whose nucleotide bases had a very high tendency to “pop open,” readily becoming unpaired. These sequences are characterized by a special DNA sequence context and we refer to them as base-unpairing regions (BURs). BURs occur throughout the genome but more frequently where genes are most plentiful. We then found a protein that binds to BURs (in their double-stranded form) by recognizing their distinctive structure, and named the protein SATB1. By studying the interaction between SATB1 and its target BURs, we discovered a new mechanism of gene regulation.
SATB1 forms a cage-like network inside the nucleus to which it tethers BURs near specific gene locations, targeting large cohorts of genes. In this way chromatin is folded into loops, and SATB1 recruits protein complexes involved in chromatin remodeling and transcription factors required for gene expression to the target gene locations. BURs thus emerge as critical landmarks in the genome, providing focal points for chromatin remodeling and modifying where the machinery for gene transcription is assembled. Our research on SATB1 and BURs thus introduced a new concept in gene regulation, that of the genome organizer.
With a series of experiments using new methods to detect chromatin-looping events and the proteins that regulate them, we showed that SATB1 has important roles in normal cellular functions, but it also has an essential role in cancer. When expressed in breast cancer cells, SATB1 widely reprograms chromatin structure to alter the expression of approximately a thousand genes, inducing changes that favor expression of aggressive cancer-promoting genes and discourage expression of tumor suppressor genes. In fact, we found that when otherwise non-metastatic breast cancer cells are experimentally manipulated to express SATB1, invasive metastatic tumors are induced in mice. Conversely, removing SATB1 from metastatic cells abolishes both metastasis and tumor growth, a complete reversal of the aggressive cell type. These observations suggest a new paradigm in cancer biology: instead of metastasis resulting only from an accumulation of multiple mutations, a single protein such as SATB1 can direct and coordinate the expression/non-expression of a large number of genes to promote metastasis. A better understanding of how chromatin architecture is controlled by SATB1 and other factors could improve cancer diagnosis and treatment.
In addition to our work on SATB1 and cancer, experiments are underway in our lab to identify other novel genome-organizer proteins in mouse embryonic stem cells. This research aims to identify specific chromatin architectures, formed by interactions between genome organizers and BURs, needed for stem cell self-renewal and differentiation.
These examples illustrate how my colleagues and I are beginning to unravel the complex processes involved in establishing functional chromatin architectures. We’re learning how these mechanisms can reprogram the processes and structures that control gene expression and the organization of the genome during cancer progression, as well as the self-renewal and versatility of somatic stem cells. What we learn from these studies will benefit cancer patients and victims of other diseases that result from mis-regulation of the genome.