Sanika Ambre:
Title: Zea: a model to study bacterial RBPs
Abstract:
RNA-binding proteins (RBPs) regulate their RNA targets’ metabolism, including their stability, translation, and modification. The binding of an RBP to RNA is often mediated by an RNAbinding domain. While many eukaryotic RNA-binding domains have been studied, bacterial RBPs do not seem to have canonical structural RNA-binding domains. To study how bacterial RBPs bind RNA, we will use a recently discovered bacterial RBP called Zea as a model. Zea is
secreted by Listeria monocytogenes to extracellularly stabilize prophage RNA of the bacteria. Interestingly, immunofluorescence data shows that Zea also localizes to the nucleus of the bacterial host.
The three-dimensional structure of Zea suggests that it is a homo-hexamer, wherein each monomer has two beta sheets. In this conformation, each Zea monomer swaps a beta hairpin loop into the next monomer. Although the structure of Zea has been determined, its mechanism of RNA binding and its underlying biologically relevant stoichiometry are unknown. Moreover, we do not know the significance of the domain swap in oligomer stability or in RNA binding. Hence, we aim to use biophysical and biochemical techniques like cross-linking mass spectrometry, X-ray crystallography, and mutagenesis followed by binding assays to elucidate the RNA-binding mechanism of Zea. This study will not only shed light on how the first discovered secreted bacterial RBP binds RNA and help us define an RNA binding domain in bacteria, but it will also expand our understanding of the significance of oligomerization in bacterial RBP function.
Berman Lab
Emmy Brown:
Title: Investigating the role of the mSWI/SNF (BAF) nucleosome remodeling complex in regulating neural differentiation
Abstract:
Stem cells are characterized by their capacity to either self-renew or acquire a specialized cell fate. Differentiation of stem cells into specialized cell-types requires re-organization of the genome to establish accessibility at the necessary protein-coding and regulatory loci for appropriate function of the new cell. This process is governed by an orchestra of regulatory components including nucleosome remodeling complexes, transcription factors (TFs), and histone post-translational modification deposition. However, the role of the non-protein-coding transcriptome in regulating cell fate decisions is not well understood. The mSWI/SNF (BAF) complex is the only nucleosome remodeling complex that is essential at every major stage of development. Within distinct cell types, BAF complexes are combinatorially assembled from a variety of potential protein subunit options to give rise to unique cell-type specific BAF complex compositions, which are essential for both maintenance of self-renewal in embryonic stem (ES) cells and proper cell fate commitment in neurogenesis and cardiomyocyte differentiation. Interestingly, members of the BAF complex are mutated in approximately 20% of all cancers and are also highly mutated across a range of neurological disorders with widely heterogenous disease phenotypes.
The BAF complex assembly present in ES cells, esBAF, regulates nucleosome positioning to facilitate chromatin accessibility at critical pluripotency TF binding sites, functions as a global repressor of non-coding transcription, and is essential for maintenance of pluripotency. My project is a mechanisticinvestigation into how the BAF complex regulates differentiation along the neuroectoderm lineage. I am utilizing novel synthetic biology approaches to understand how the non-coding transcriptome, chromatin accessibility, TF localization, and histone modification deposition are impacted genome-wide when the ATPase activity that confers catalytic functionality to the BAF complex is abolished, either via chemical degradation or pharmacological inhibition. This work will uncover novel regulatory functions of cell-type specific BAF complex assemblies and provide insight into the role of the BAF complex in both developmental and disease contexts, ultimately informing potential therapies.
Hainer Lab
Friday, September 1st, 2023
12:00PM
Langley A219B