The definition of a protein encoding gene as a continuous and defined unit of double-stranded DNA that gives rise to a single polypeptide chain, was radically revised by the discovery of what initially was referred to as 'split genes' (see website for historical background). We currently understand that most human protein encoding genes are certainly not continuous units; rather, the protein encoding regions (the exons) are 'split' or interrupted by regions not protein encoding (the introns). The intron(s) must be excised and the exons spliced together to generate the messenger RNA for its subsequent translation into a polypeptide. Importantly, the exons of a gene can be brought together or spliced in various arrangements. The implications of this process, termed alternative splicing, are profoundly significant to the development of higher eukaryotes, offering both enormous protein diversity and regulatory control to a cell.

The process of pre-mRNA splicing is catalyzed by a large and dynamic macromolecular complex termed the 'spliceosome.' Integral to the spliceosome are small nuclear ribonucleoprotein particles or snRNPs (U1, U2, U4, U5, and U6). The initial stage in pre-mRNA splicing is the recognition of the junction between the 5' exon and intron (the 5' splice site) by the U1 snRNP. This stage initiates the assembly of the remaining snRNPs and the subsequent catalytic reactions that result in the splicing of two exons and removal of the intron. The U1 snRNP-5' splice site recognition event is a focus for the binding of factors that act to regulate 5' splice site selection (alternative splicing).

I previously worked to determine the crystal structure of the human U1 snRNP, an eleven subunit complex, to understand the role of its various subunits, their participation in stabilizing the particle and in recognition of the 5' exon-intron junction (see structure). This work revealed the first detailed structure of an snRNP and provided considerable insight into snRNP architectural principles as well as the mechanism of 5'-splice site recognition by U1 snRNP. At Brandeis University, my colleagues and I are interested in further understanding how the initial stages in pre-mRNA splicing occur and are regulated in the human cell.

We employ a diverse range of methods in our studies, in particular structural approaches (crystallography and electron microscopy) and biochemistry. View images of the laboratory, equipment and environment.

Selected Recent Publications

Hernandez H, Makarova OV, Makarov E, Morgner N, Muto Y, Pomeranz Krummel DA, & Robinson CV. Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP. PLoS One, 4: e7202 (2009).

Oubridge C, Pomeranz Krummel DA, Leung A, Li J, & Nagai K. Interpreting a low resolution map of human U1 snRNP using anomalous scatterers. Structure, 17, 930-938 (2009).

Pomeranz Krummel, DA, Oubridge C, Leung A, Li J, & Nagai, K. Crystal structure of human spliceosomal U1 snRNP at 5.5 Å resolution. Nature 458, 475-480 (2009). (Comment in: Structural biology: Spliceosome subunit revealed. Nature 458, 418-419 (2009); Protein structures: Structures of desire. Nature 459, 24-27 (2009); see also Brandeis University Press Release, http://www.brandeis.edu/now/2009/march/splicepressrelease.html).

 

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Last update: November 18, 2009.