A Bioinformatics Tool for Analyzing G-quadruplexes in the mRNA Untranslated Regions Zachary Zappala

But why?To map theoretical existence of Quadruplex forming G-Rich Sequences in cytoplasmic mRNAs

Utility BeltAccess to NCBI Entrez GenePHP/MySQL/C++/JavaScriptLaptop (Dell Latitude D505 1.6 ghz 512 DDR)Internet serverPerseveranceStarbucks Frappucinos

Bioinformatics?A hybrid of information sciences and biologySimilar, but not the same as computational biologyEnlists the help of databases and tools to analyze large masses of data to find patterns that are not easily discernable by the human eyeTools like NCBI BLAST are especially well know

Biology? In computer science?Well, its not that complicatedThe biology involved in this project is transcription/translationGenetics!Quick overview:DNA (double helix; 2 nucleotide strands)RNA (single nucleotide strands)DNA is transcripted into RNA, which travels to ribosomes, which translate the RNA data into amino acids, the building blocks of proteins

Eukaryotic mRNA!transcription5 UTRGene expression regulation factors?

G-quadrawhats?Thats right: G-quadruplexesA type of secondary structure that forms in single stranded nucleotide sequences (aka..mRNA)

GG~GG~GG~GG

Plates (tetrads) form between 4 guanine molecules that line up

Why is this important?Since all this work is theoretical, its important to know that there could be an applicationQGRS in pre-mRNA has already been shown to play an important role in pre-mRNA splicing (Kikin, DAntonio, Bagga 2006)So, what about cytoplasmic mRNA?Gene expression control (since not all mRNA become proteins)Internal Ribosomal Entry Sites (IRES)Allows entry of ribosomes to start translation not at the beginning of the 5 UTR

But how to predict?Prior research has given several clues to what constitutes a strong QGRSFor instance, it is known that only one loop can have a length of zeroAlso, the more tetrad plates that are forming, the more likely it is that the QGRS will exist

QGRS Motif:GxNy1GxNy2GxNy3Gx

G-score is assigned using a straightforward function

Divining the QGRS in an mRNA sequenceWhen a gene is requested by the user, data is parsed from NCBI and given as parameters for a C++ programExecutes and saves data from the sequence, which is then picked up again by the PHP program to be displayed to the user

Program Flow!Behind the scenesInterfacePHP SessionVariable

Screenshots!

more screenshots!

and more screenshots!

But thats not all!In order to not overload you with pretty pictures, lets just say that you can also view direct data tables and a sequence view that block out the QGRS locationsProgram executes in a small time frame, and due to the nature of mRNA there are not many abnormal situationsPoor internet connects do tend to slow displaybut thats your ISP

Successes & FailuresResearch on the NRAS oncogene has shown, using crystallography, that a QGRS exists @ the -222 CDS bp position (within the 5 UTR)When QGRS Mapper 2 analyzed the same gene, it predicted a QGRS at the same positionIncomplete NCBI entries have prevented full verification of the reported dataUnfortunately, not enough data is available for research to be done on IRES sitesAll IRES sites must be determined empirically as no strict pattern has been shown to exist yet

Think of tomorrowCurrently analyzing various oncogenes, especially the NRAS to find out if the Mapper successfully maps the conservative QGRSGRS UTRdb is currently being built as well, making it possible for large calculations to be applied to mapped dataThe design of this database is

Entity Relationship Diagrams!ORACLE Certified!Shows the relationships between different tables in the databaseIs currently being populated, and is not yet public

Want to try mapping yourself?Go to http://bioinformatics.ramapu.edu/QGRS2/index.phpWhile the Mapper program is publicly available, the database is still not ready for public access

Related References

Watashi wa mRNA no QGRS o benkyousimasu.mRNA no QGRS wa tousha to chokuyaku no kimete desu ka?NCBI Entrez Gene to laptop to coffee mochimasu.Bioinformatics wa baioroji to konpyu-ta- desu.mRNA wa san chitai mochimasu.QGRS wa ni-kai no kibo desu.mRNA no QGRS wa tousha no kimete desu.

QGRS wa soutei mochimasu.Programmu wa ii desu.