CAREER: Elucidating MicroRNA Function: What Are They Targeting?

智力优势。MicroRNA（miRNAs）是一类非编码RNA，被广泛认为主要通过互补碱基配对抑制蛋白质编码信使RNA（mRNA）的翻译。虽然在过去十年中，新的miRNA的发现已经导致了这20种核苷酸RNA中超过24，000种的鉴定，但在破译单个miRNA调节的基因方面的进展已经证明是非常具有挑战性的，这主要是由于miRNA需要与它们协调的mRNA非常少的序列互补性。与依赖于与直接信息降解几乎完全互补的短干扰RNA（siRNA）相反，miRNA靶识别和随后的抑制可以通过少至7个碱基对介导。这个CAREER项目将描述几个新的警告，以准确的miRNA靶向，包括：1）其靶标不能通过检查基因组序列来鉴定的miRNA的子集，因为它们调节转录组中的编辑RNA，2）其靶标不能通过筛选mRNA序列来鉴定的miRNA的子集，因为这些miRNA最初由其他非编码RNA形成，因此可能调节其他非编码RNA，和3）最初由转座因子形成的miRNA的子集，其引导它们靶向含有相关转座因子序列的mRNA。这项研究将填补我们对miRNA功能的认识中的主要空白，并通过改进目前数千名miRNA研究科学家广泛使用的参数来明确和潜在地改变miRNA靶点预测，这些科学家目前使用基于互联网的靶点预测程序来生成假设和设计实验策略。更广泛的影响。拟议的职业研究活动与广泛的教育框架密切相关，包括高中，本科和研究生。在课堂上，教育和研究将通过一个新的计算基因组学课程，最近由PI Borchert开发，这将直接利用本科生执行这里概述的计算分析集成。利用基于项目的学习策略，本课程为学生配备了一套新颖的信息学工具，并教他们如何独立工作，并在小组中完成整个班级的研究分析。值得注意的是，在头两个学期，这一试点课程在同行评审的文章中产生了35名学生作者。伴随着通过本课程的其他影响包括通过计算机实验室设施的增强，在专业会议上将研究纳入本科课堂的演示文稿部门的基础设施的研究和教育的发展，并传播类信息学培训练习和指导教师如何实施类似的基于项目的学习策略在课程网站上。在实验室，教育和研究将通过指导高中，本科和研究生在生物学和计算机科学的接口假设驱动的研究项目相结合。虽然本科生和研究生研究人员将主要负责执行这里概述的实验，但Borchert实验室还将在此奖项期间为有前途的当地高中生提供暑期实习机会。虽然在移动的地区有几所优秀的高中，但也有几所苦苦挣扎的、以非洲裔美国人为主的内城学校，将直接成为招募有兴趣、有才华的暑期实习生的目标。重要的是，每年夏天至少有一个位置将保留给当地少数民族学生，帮助这些学生接触生物科学的榜样。这些努力的目的是增加成功完成学士学位，增加研究生教育的追求，并增加新生入学人数的生物学代表性不足的群体的成员。

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.