Research interests

The study of the role and impact of genetic variation in the sequence elements that control mRNA processing, with a specific focus on polyadenylation

Our recent studies have helped to illuminate the functional significance of systematic alternative polyadenylation at different stages of development, in different cell types, and in primary tumor samples. Carrying this work forward, we will now extend these studies to explore the relationship of genetic variability and control of alternative polyadenylation. We will build upon our existing database of polyA sites (PACdb,http://harlequin.jax.org/pacdb/), including new, large-scale analyses derived from microarray and high-throughput mRNA sequencing efforts. Through this research program, we expect to generate and disseminate a genome-wide view of polyadenylation in mouse, the preeminent model mammalian system. Integration with genetic variation, reinforced with experimental validation of selected predictions, will provide new insights into the control, extent and consequences of alternative polyadenylation

The role and downstream consequences of disrupted regulation of mRNA processing in tumorigenesis

We recently developed and applied a probe-level microarray analysis to data obtained from mouse models of pre-B-cell lymphoma, resulting in the identification of genome-wide, systematic, and characteristic changes in mRNA processing. This work contributed to a growing understanding of the role of alternative processing (specifically alternative polyadenylation) as a part of tumorigenesis. This work has the potential to provide new models for, and understanding of, the disruption in regulation that accompanies tumor initiation and progression. As we move forward, we plan to broaden the studies to additional types of tumors, while also switching from microarray to mRNA-seq or other high-throughput sequencing-based methodologies.

The continued development and validation of computational approaches to regulatory motif identification and characterization

We have an interest in developing improved methods for identification and characterization of the regulatory sequences that guide mRNA processing and gene regulation. The majority of the approaches available in popular tools pay little or no attention to positioning of the motifs, despite the clear role that positioning plays in many critical processes, such as splicing and polyadenylation. Our recent work includes a novel motif characterization based on non-negative matrix factorization. Our methodology has the unique feature of simultaneously determining both sequence content and positioning. We envision a number of improvements and investigations of alternative approaches as the work progresses.

Publications

• Singh P, Alley TL, Wright SM, Kamdar S, Schott W, Wilpan RY, Mills KD, Graber JH. 2009. Global changes in processing of mRNA 3’ untranslated regions characterize clinically distinct cancer subtypes. Cancer Research. (in press)
• Salisbury J, Hutchison KW, Wigglesworth K, Eppig JJ, Graber JH. 2009. Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation. PLoS One. 4(10):e7479
• Hutchins LN, Murphy SM, Singh P, Graber JH. 2008. Position-dependent motif characterization using non-negative matrix factorization. Bioinformatics. 24(23):2684-90.
• Paigen K, Szatkiewicz JP, Sawyer K, Leahy N, Parvanov ED, Ng SH, Graber JH, Broman KW, Petkov PM. 2008. The recombinational anatomy of a mouse chromosome. PLoS Genet. 4(7):e1000119.
• DeVries WN, Evsikov AV, Brogan LJ, Anderson CP, Graber JH, Knowles BB, Solter D. 2008. Reprogramming and Differentiation in Mammals: Motifs and Mechanisms. Cold Spring Harbor Symp Quant Biol. 73:33-8.
• Graber JH, Salisbury J, Hutchins LN, Blumenthal T. 2007. C. elegans sequences that control trans-splicing and operon pre-mRNA processing. RNA. 13(9):1409-26
• Liu D, Brockman JM, Dass B, Hutchins LN, Singh P, McCarrey JR, MacDonald CC, Graber JH. 2007. Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis. Nucleic Acids Res. 35(1):234-46.
• Liu D, Graber JH. 2006. Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation. BMC Bioinformatics 7:77.
• Salisbury J, Hutchison KW, Graber JH. 2006. A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif. BMC Genomics 7:55.
• Evsikov AV, Graber JH, Brockman JM, Hampl A, Holbrook AE, Singh P, Eppig JJ, Solter D, Knowles BB. 2006. Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo. Genes Dev. 20(19):2713-27.
• Graber JH, Churchill GA, Dipetrillo KJ, King BL, Petkov PM, Paigen K. 2006. Patterns and mechanisms of genome organization in the mouse. J Exp Zoolog. 305A(9):683-8.
• Petkov PM, Graber JH, Churchill GA, Dipetrillo K, King BL, Paigen K. 2005. Evidence of a large-scale functional organization of mammalian chromosomes. PLoS Genet 1:e33.
• Brockman JM, Singh P, Liu D, Quinlan S, Salisbury J, Graber JH. 2005. PACdb: PolyA cleavage site and 3'-UTR database. Bioinformatics 21:3691-3693.
• Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, Knowles BB. 2004. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell 7:597-606.
• Graber JH. 2003. Variations of 3’-processing cis-elements in yeast correlate with transcript stability. Trends Genet 19:473-6.