LABORATORY INTEREST: DEVELOPMENTAL ROLES OF CHROMATIN REMODELING
Understanding the Words of Chromatin Remodeling We are exploring the role of chromatin regulation in verebrate development using genetic, proteomic and genomic approaches in mice. Our studies suggest that an important mechanism for production of specific chroamtin landscapes during development arises from the combinatorial assembly of chromatin remodeling complexes. We discovered that chromatin remodeling complexes are combinatorially assembled by proteomic analysis of endogenous SWI-SWF like ATP dependent remodeling complexes. These complexes have 12 subunits that are encoded by gene families and use the alternative ATPases Brg and Brm (BAF complexes). We envision that the subunit genes empart specificity to the complexes in the way that letters are combined into words. To date the most informative chromatin remodeling "words" are found in pluriptotent cells, neural stem cells and committed neurons.
ATP-dependent chromatin remodeling in the development of the nervous system. Pluripotent cells express a specific assembly of subunits (esBAF) and as cells enter the neural lineage a second assembly is found in neural stem cells (npBAF) which contain BAF45a/53a (green below in the sub ventricular (SVZ) stem cell niche). Finally at mitotic exit two subunits are removed from this complex and replaced by two homologous subunits (BAF53b and BAF45b, red below) to generate the nBAF complex in post mitotic neurons. The Figure below shows the subunits of the SWI/SNF-like BAF complexes as cells move from pluripotent to multipotent to committed neurons. Note the mutually exclusive expression of the different subunits. Each of these assemblies appear to be essential for the specific state of development. Andrew Yoo and Brett Staahl in our lab have found that the npBAF to nBAF switch is mediated by miR124 and 9* (Nature 2009). We hope to understand how these switches are regulated during development.
Genome-wide Studies of ATP-Dependent Chromatin Remodeling in Stem Cells: Lena Ho in our laboratory conducted genome-wide CHIP-seq studies of the occupancy by this complex. Combined with conditional null alleles and transcript array studies, her work indicates that these complexes bind with Oct4, Sox2 and Nanog and are essential elements of the core pluripotency circuitry. In contrast to expectations the complexes repress most direct target genes by mechanisms that are unclear. The esBAF complexes also bind over the entire ES cell genome with Smad1 and STAT3 that are essential for BMP and LIF signaling. Having gained a genome-wide view of the roles of these complexes and their functions we hope to understand their essential roles in establishing a pluripotent chromatin landscape. Our present view of the role of esBAF in the core pluripotency circuitry and LIF/BMP signaling is summarized below:
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