INTELLECTUAL MERIT. MicroRNAs (miRNAs) are noncoding RNAs widely believed to function primarily in repressing the translation of protein coding messenger RNAs (mRNAs) through complementary basepairing. While novel miRNA discovery has led to the identification of over 24,000 of these ~20 nucleotide RNAs over the last decade, progress in deciphering what genes individual miRNAs are regulating has proven exceptionally challenging largely due to miRNAs requiring very little sequence complementarity to the mRNAs they coordinate. In contrast to short interfering RNAs (siRNAs) which depend upon almost perfect complementarity to direct message degradation, miRNA target recognition and consequent repression can be mediated through as few as 7 base pairs. This CAREER project will characterize several novel caveats to accurate miRNA targeting including: 1) a subset of miRNAs whose targets cannot be identified by examining genomic sequence as they regulate edited RNAs in the transcriptome, 2) a subset of miRNAs whose targets cannot be identified by screening mRNA sequences as these miRNAs were originally formed from, and therefore likely regulate, other noncoding RNAs, and 3) a subset of miRNAs initially formed from transposable elements, which leads them to target mRNAs containing related transposable element sequences. This research will fill in major gaps in our knowledge of miRNA function and significantly clarify and potentially transform miRNA target prediction through improving the parameters widely utilized by thousands of miRNA research scientists currently using internet-based target prediction programs to generate hypotheses and design experimental strategies.
BROADER IMPACTS. The proposed CAREER research activities are intimately intertwined with an extensive educational framework incorporating high school, undergraduate and graduate students. In the classroom, education and research will be integrated through a novel computational genomics course, recently developed by PI Borchert, which will directly utilize undergraduates to execute the computational analyses outlined here. Utilizing a project-based learning strategy, this course equips students with a novel informatics tool set and teaches them how to work independently and in small groups to complete a class-wide research analysis. Significantly, in its first two semesters, this pilot course has generated 35 student authorships on peer-reviewed articles. Additional impacts accompanying the adoption of this course include the development of departmental infrastructure for research and education through the enhancement of computer lab facilities, presentations at professional meetings on incorporating research into the undergraduate classroom, and disseminating class informatics training exercises and guidelines for instructors on how to implement similar project based learning strategies on the course website. In the laboratory, education and research will be integrated through mentoring high school, undergraduate and graduate students in hypothesis-driven research projects at the interface of biology and computer science. While undergraduate and graduate researchers will be primarily charged with executing the experimentation outlined here, the Borchert laboratory will also offer summer internships to promising local high school students for the duration of this award. While there are several outstanding high schools in the Mobile area, there are also several struggling, predominately African-American inner city schools that will be directly targeted for the recruitment of interested, talented summer interns. Importantly, at least one position will be reserved for a local minority student each summer helping to expose these students to role models in the biological sciences. These efforts are intended to increase successful completion of BS degrees, increase pursuit of graduate education, and increase freshman enrollment in biology by members of underrepresented groups.
