Short RNAs, as regulators of cellular function, can impact the maintenance of genomic integrity and stability, on cell growth, differentiation and developmental processes, and on the antiviral RNA-silencing response. RNA silencing refers to small interfering RNA (siRNA)-mediated post-transcriptional gene regulation, resulting in the silencing of viral genes and transgenes. Such interactions involve highly specific, adaptive, mobile, and systemic processes that operate in essence as an RNA-based immune response.
The packaging of DNA within chromosomes, the orderly replication and distribution of chromosomes, the maintenance of genomic integrity, and the regulated expression of genes depend upon nucleosomal histone proteins. Our long-term goals are directed toward gaining structural and mechanistic insights into the functional relevance of histone covalent modification(s). Currently, we are structurally investigating the binding of effectors targeted to specific covalent marks in a context-dependent fashion.
The role of RNA in information transfer and catalysis highlights its dual functionalities. Our laboratory has a long-standing interest in RNA folding, recognition, and catalysis. We are especially interested in both natural and in vitro selected RNA aptamer-based systems, because they serve as exceptional scaffolds for ligand recognition and catalysis, exhibiting tunable specificities and enantiomeric selectivities. Much of our effort is also focused on mRNA because of its functional importance at the cellular level and because a diverse set of ligand and protein interactions control its transcription, splicing, export, localization, translation, and degradation functions.
A number of cancer-related neurodegenerative diseases are associated with RNA-binding proteins. These include FMRP protein in fragile X mental retardation (FXMR) syndrome and Nova and Hu proteins in paraneoplastic opsoclonus-myoclonus ataxia (POMA) syndrome. These also include the La and Ro60 autoantigens, identified in patients with the autoimmune diseases systemic lupus erythematosus and Sjörgen’s syndrome. More recently, we are investigating protein-RNA complexes involved in alternate splicing, with the initial emphasis on muscleblind MBNL protein that have impact on muscular dystrophy.
Genomic integrity depends critically on the fidelity and efficiency of DNA replication. Processive polymerases can stall at DNA damage sites and translesion synthesis is then dominated by bypass polymerases, involving error-free (mutation-avoiding) or error-prone (mutation-generating) pathways. Our long-term goals are directed toward understanding the molecular interactions that define the mutagenic spectrum of activities associated with replication of damage sites by bypass polymerases. The initial efforts are focused on oxidative damage lesions and their processing by the bypass polymerase Dpo4.
Lipid transfer proteins are important in membrane vesicle biogenesis and trafficking, signal transduction and immunological presentation processes. The conserved and ubiquitous mammalian glycolipid transfer proteins (GLTPs) serve as potential regulators of cell processes mediated by glycosphingolipids (GSLs), ranging from differentiation and proliferation to invasive adhesion, neurodegeneration, and apoptosis. We have initiated a structural biology program toward defining a framework for understanding how GLTPs acquire and release GSLs during lipid intermembrane transfer and presentation processes.
It has been widely accepted that DNA can adopt other biologically relevant structures beside the Watson-Crick double helix. Our laboratory has focused its efforts on the structure and recognition of multi-stranded DNA architectures adopted by guanine-rich sequences. Such purine-rich sequences are frequently located within gene regulatory regions and recombination hot spot sites, and as tandem repeats in telomeric, centromeric, and triplet repeat disease sequences. Our emphasis is on discovering the range of topologies adopted by G-quadrulex scaffolds.
Aminoglycoside antibiotics are polycationic saccharides that exhibit therapeutic potential against bacterial infections. Functionally they interfere with translation and induce bacterial cell death through site-specific targeting of ribosomal 16S RNA, as well as inhibit viral regulatory protein-RNA interactions. Our research has focused on aminoglycoside antibiotic-RNA aptamer complexes in an effort to deduce common structural principles associated with molecular recognition and encapsidation of the bound aminoglycoside antibiotic by the tertiary fold of the RNA pocket.