CAREER: Elucidating MicroRNA Function: What Are They Targeting?

智力上的优点。MicroRNAs(MiRNAs)是广泛认为的非编码RNA，主要功能是通过互补碱基对抑制蛋白质编码信使RNAs(MRNAs)的翻译。虽然在过去的十年中，新的miRNA发现已经导致了超过24,000个这样的~20个核苷酸RNA的鉴定，但在破译单个miRNAs调控什么基因方面的进展被证明是异常具有挑战性的，主要是因为miRNAs需要与它们所协调的mRNAs几乎不需要序列互补。与依赖几乎完全互补来直接信息降解的短干扰RNA(SiRNAs)相比，miRNA靶标识别和随之而来的抑制可以通过少至7个碱基对来介导。这个职业项目将描述准确的miRNA靶向的几个新的警告，包括：1)其靶标不能通过在调节转录组中编辑的RNA时检查基因组序列来识别的miRNAs的子集，2)其靶标不能通过筛选mRNA序列来识别的miRNAs的子集，因为这些miRNAs最初是由其他非编码RNA形成的，因此可能调节，以及3)最初由转座元件形成的miRNAs的子集，这导致它们靶向包含相关转座元件序列的mRNAs。这项研究将填补我们对miRNA功能知识的主要空白，并通过改进数千名miRNA研究科学家目前使用基于互联网的目标预测程序来生成假设和设计实验策略的广泛使用的参数，显着阐明并有可能改变miRNA目标预测。更广泛的影响。拟议的职业研究活动与包括高中、本科生和研究生在内的广泛教育框架密切相关。在课堂上，教育和研究将通过一门由Pi Borchert最近开发的新的计算基因组学课程来整合，该课程将直接利用本科生来执行这里概述的计算分析。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，并教会他们如何独立工作并以小组形式完成全班的研究分析。值得注意的是，在最初的两个学期，这门试点课程已经产生了35名学生在同行评议文章上的署名。采用本课程的其他影响包括通过加强计算机实验室设施，为研究和教育发展部门基础设施，在专业会议上介绍将研究纳入本科生课堂，以及在课程网站上向教师传播课堂信息学培训练习和指导方针，指导如何实施类似的基于项目的学习策略。在实验室，教育和研究将通过指导高中生、本科生和研究生在生物学和计算机科学的界面上进行假设驱动的研究项目来整合。虽然本科生和研究生研究人员将主要负责执行这里列出的实验，但博尔切特实验室也将在该奖项期间为有前途的当地高中生提供暑期实习机会。虽然莫比尔地区有几所优秀的高中，但也有几所苦苦挣扎的、以非裔美国人为主的市中心学校，将直接面向招聘感兴趣的有才华的暑期实习生。重要的是，每年夏天将为当地少数民族学生保留至少一个职位，帮助这些学生接触生物科学领域的榜样。这些努力的目的是为了提高学士学位的成功完成，增加研究生教育的追求，并增加代表性不足群体成员在生物学方面的新生入学人数。

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.