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Gavin Schnitzler, Ph.D. Assistant Professor, Tufts Department of Biochemistry
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Links:ResearchLab MembersRecent Publications |
Research Summary:The Schnitzler laboratory is interested in fundamental mechanisms of transcriptional regulation in the context of chromatin. Human DNA is coated with histone proteins to form nucleosomes and chromatin, which blocks transcription factor access. The human SWI/SNF complex is an ATP-dependent enzyme that is recruited to promoters by over two dozen transcription factors, including steroid receptors, p53, c-myc and Rb, to activate (or sometimes repress) transcription. It is required for mammalian development and the differentiation of many cell types, and is a tumor suppressor complex that limits aberrant cell division. We are working to understand how hSWI/SNF regulates transcription, by measuring how it alters nucleosome positions and chromatin structure on the promoters of its target genes. Chromatin is a sufficiently complex molecule that a wide range of approaches is needed to understand functional changes in its structure and characteristics. Our ongoing research uses a combination of chromatin biochemistry, single molecule imaging, cell culture and bioinformatic approaches to examine the specific functions of hSWI/SNF as a tumor suppressor and transcriptional coregulator, and to explore the general mechanisms by which DNA sequence and chromatin remodeling machines work together to regulate transcription. |
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The assembly of DNA and histones into nucleosomes inhibits the binding of most transcription factors and the movement of RNA polymerase II. Moreover, recent studies have shown that most nucleosomes adopt specific positions on genomic DNA, and that functional transcription factor binding sites are localized in spacer regions between nucleosomes. Nucleosome positions are established, in part, by DNA elements called nucleosome positioning sequences (NPSes). These positions, however, can be altered by members of an evolutionarily-conserved family of ATP-dependent chromatin remodeling complexes, which play diverse roles in transcriptional activation and repression, DNA repair and recombination. The overall goal of our research is to discover how the combination of genetic DNA elements and chromatin remodeling complexes work together to regulate DNA accessibility and control transcription.
One focus of our research is the human SWI/SNF remodeling complex (hSWI/SNF). SWI/SNF complexes are transcriptional coregulators that have been conserved from yeast to man. Mammalian SWI/SNF complexes are essential for development and for the differentiation of muscle, fat, brain and blood cells. Human SWI/SNF is also a tumor suppressor found mutated in several human cancers. hSWI/SNF is important for transcriptional coactivation by over two dozen human transcriptional activators (including almost all steroid receptors, p53, SP1 and MyoD), as well as corepression though the retinoblastoma protein and other transcriptional repressors. These factors recruit hSWI/SNF to promoters containing their binding sites, where hSWI/SNF is thought to somehow alter promoter chromatin structure to regulate transcription. Despite its critical regulatory importance, very little is known about the mechanism by which hSWI/SNF coactivates or corepresses transcription.
To begin to fill this gap in our knowledge, we have examined the specific biochemical effects hSWI/SNF has on nucleosomes and chromatin. We find that hSWI/SNF has two major effects on chromatin. First, it moves nucleosomes along DNA, from NPSes to hSWI/SNF favored sequences. This sequence-directed repositioning could activate transcription, for instance, by moving a repressive nucleosomes away from transcriptional activator binding sites. These observations indicate that the sequence preference of hSWI/SNF and other remodeling complexes may be integral to their functions. They also suggest that promoter sequences may be evolutionarily selected for both default and remodeled nucleosome positions, thereby establishing genetically encoded chromatin switches which can epigenetically flipped by recruitment of a specific remodeler. Second, we find that hSWI/SNF converts about a third of all nucleosomes to structurally-altered dinucleosomes, termed “altosomes”. Our data indicate that the altered wrapping of DNA around the histone octamers in altosomes changes the accessibility of the DNA to transcription factors. In addition, altosomes are metastable structures that revert to normal nucleosomes over several hours, and this reversion could potentially act as a timer that automatically attenuates transcription an hour or so after hSWI/SNF leaves a promoter.
The novel insights from these biochemical studies have laid the groundwork for new studies that employ a combination of biochemistry, cell culture, single molecule imaging, microarray and bioinformatics approaches to explore the essential mechanisms by which the combined effects of DNA sequence and remodeling complexes control human transcription. These studies aim to unveil both general mechanisms of gene regulation in chromatin, and also to explore specific functions of chromatin remodeling complexes in human development and disease. For instance, we are examining how sequence-directed nucleosome repositioning and altosome formation by hSWI/SNF control transcription at nuclear hormone receptor-regulated genes and at critical cell cycle control genes.
For more details, please see the publications below.
