dapkDaniel Pomeranz Krummel, Ph.D.
Assistant Professor, Biochemistry
Regulation of Gene Expression

Ph.D., Yale University

Contact Information
Lab website

Daniel Pomeranz Krummel is moving to Emory University in June 2016

My colleagues and I are interested in eukaryotic RNA processing mechanisms. Specifically, we are investigating: (1) the very large and dynamic macromolecular assemblage (the spliceosome) that catalyzes the splicing of eukaryotic precursor-mRNA transcripts; and (2) the significant and dynamic structural changes that occur in the eukaryotic cell induced by its exposure to stress. In our studies we employ a diverse range of Description: Image_U1snRNPmethods, including structural approaches (crystallography and electron microscopy), biochemistry, and studies in cell culture. See images of the laboratory, equipment and environment.

1. Splicing of precursor-mRNA transcripts

Precursor-mRNA splicing is catalyzed by an extraordinarily large and highly dynamic macromolecular assemblage termed the 'spliceosome.' Integral to the spliceosome are five small nuclear ribonucleoprotein particles or U snRNPs (U1, U2, U4, U5, and U6) that assemble onto a precursor-mRNA transcript to catalyze its splicing, illustrated on your right (van der Feltz et al., Biochemistry 2012). The initial stage in precursor-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 assembly of the remaining U snRNPs and the subsequent catalytic reactions that result in the splicing of two exons and removal of the intron. I previously determined the crystal structure of the human U1 snRNP (see structure on your right), an 11-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 (Pomeranz Krummel et al., Nature 2009). This work revealed the first detailed structure of a U snRNP and provided considerable insight into U snRNP architectural principles as well as the mechanism of 5' splice-site recognition by U1 snRNP. We are continuing studies along this line of investigation to provide insight into how U snRNPs cooperate to catalyze precursor-mRNA splicing.

2. Molecular basis for stress granule assembly

Description: Pwpt_Image_Ddx3A eukaryotic cell possesses nuclear and cytoplasmic non-membranous subcellular organelles critical to processing and synthesis of RNA. The functions of these organelles include: neuronal mRNA transport (transport granules); RNA turnover and mRNA silencing by microRNAs (processing bodies); and assembly of telomerase and U snRNPs as well as other RNA-protein complexes (Cajal bodies). One of the most fascinating of these aggregates is the stress granule. A eukaryotic cell undergoes substantial biochemical and structural changes induced by stress, including formation in the cytoplasm of dynamic 100-200 nm diameter stress granules that appear to contribute to translational inhibition by sequestering mRNAs. We are investigating how this sub-cellular aggregate is formed, disassembled, and what is integral to its activity - including an RNA helicase called DDX3X shown above at left (Pugh et al., Nature 2012).

Selected 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).

Pomeranz Krummel DA, Nagai K, & Oubridge C. Structure of spliceosomal ribonucleoproteins. F1000 Biology Reports, 2: 39 (2010).

van der Feltz C, Anthony K, Brilot A, & Pomeranz Krummel DA. Architecture of the spliceosome. Biochemistry, 51: 3321-3333 (2012).

Pugh TJ, Weeraratne D, Archer TC, Pomeranz Krummel DA, et al. Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature, 488: 106-110 (2012). (see Press Release and Brandeis blog)

Anthony, K.C., and Pomeranz Krummel, D.A. (2013) Spliceosome, In eLS, John Wiley & Sons, Ltd.

Anthony, K.C., You, C., Piehler, J, and  Pomeranz Krummel, D.A. (2014) High-affinity gold nanoparticle pin to label and localize histidine-tagged proteins in macromolecular assemblies. Structure. Apr 8; 22:628-35.

Pomeranz Krummel, D.A. & MacMillan, A.M. (2014) It takes two to tangle: Prp24 and spliceosome assembly. Nature Structural and Molecular Biology, 21: 503-504.


Last update: June 9, 2014

 

 
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