BIOINFORMATICS OF 3 PRIME-UTR-BASED POST-TRANSCRIPTIONAL REGULATORY ELEMENTS

点击翻译按钮获取中文摘要

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our work is focused on the development and use of computational tools to further our understanding of gene regulation, with an emphasis on the identification and characterization of the regulatory sequences that control post-transcriptional gene regulation. Post-transcriptional regulatory sequences are typically embedded within the sequence of the precursor mRNA, therefore our analysis is largely based on studies of expressed sequences, including, but not limited to, expressed sequence tags (ESTs) and indexing schemes, such as SAGE or MPSS. We are particularly interested in the delineation of evolutionarily conserved sequences that can be tested for functionality in the model systems utilized by our experimental collaborators. The principal efforts in my group are going into the continued improvement and collection of data for our integrated set of sequence analysis databases: pacdb, seqgen, and estdb. These databases combine to represent and make useable our genome-based analysis of expressed sequences, for the identification of functional features, specifically focusing on identification of mRNA 3-processing sites (Brockman et al, 2005). We have subsequently used our databases in further studies, including a broad comparative study of metazoan mRNA 3-processing signals (Salisbury et al, 2006), an investigation of systematic effects in the sampling of transcripts during cDNA/EST library creation (Liu and Graber, 2006), an investigation of systematic changes in 3-processing during mammalian spermatogenesis, and several collaborative studies (Peaston et al, 2004, Petkov et al, 2005, Graber et al, 2006, and Evsikov et al 2006).