Jacob G Kirkland, Ph.D. - US grants

Within the nucleus, DNA is packaged into chromatin states that vary in accessibility. Importantly, accessibility allows DNA binding proteins such as transcription factors, and repair and replication proteins to contact the DNA fiber. Chromatin Regulators set up, maintain, and reverse chromatin states thereby controlling gene expression, chromatin structure, and genome fidelity. Understanding the mechanisms by which chromatin states are modulated is medically significant because approximately 50% of tumors have alterations in chromatin regulators. The family of chromatin regulators that is the focus of this proposal, the mammalian SWI/SNF family (also known as BAF complexes), is mutated in 20% of all tumors. In mammals there are 3 distinct major forms: cBAF, pBAF, and gBAF. All three share common subunits but also contain unique subunits. Of the three major BAF subtypes, the cBAF complex has the best understood role in chromatin regulation. However, much less is known about the mechanisms and function of the pBAF complex, including how common cancer mutations or subunit deletions affect the complex. A multitude of cancer genomics studies shows that alterations in cBAF and pBAF are frequent, but largely occur in cancers of different tissue origins suggesting divergent roles. Polycomb proteins act to oppose transcription, through histone modifications, recruitment of other proteins, and local chromatin organization changes. While the cBAF complex has many different roles in the cell, recent studies of cBAF mechanism have shown that one of the primary roles is to oppose polycomb proteins, thereby creating a more accessible locus. In most cases accessibility alone is not sufficient for transcriptional activation. However, I found that cBAF recruitment using a Cas9 based chemical induced proximity approach (FIRE-Cas9) is sufficient for transcriptional activation of a bivalent locus providing a suitable model locus of chromatin and transcription changes after inducible SWI/SNF recruitment. While it is known that cBAF and/or gBAF complexes opposes polycomb when recruited what is not known is how recruitment of pBAF affects polycomb, the chromatin state in general or the transcriptional state. My long-term goal is to define the mechanistic differences between the mSWI/SNF pBAF and cBAF/gBAF complexes in regard to polycomb localization, histone modifications, chromatin accessibility, transcription, and genome stability. I will achieve this goal through the following two specific aims: (1) Characterize genomic alterations after acute loss of the pBAF complex and (2) Compare the kinetics and mechanisms of cBAF vs. pBAF mediated chromatin changes. I expect this study will lead to a better understanding of alterations in chromatin structure that lead to an oncogenic state.