Syed Ather
Year: 2014
Faculty Advisor: Zhangjun Fei

RNA-Seq analysis of lncRNAs and cis-natural antisense transcript (cis-NAT) in developing tomatoes

Project Summary

Since the sequencing of the human genome, it has been revealed that the vast majority of DNA does not code for proteins. However, upon transcription, some of these regions are not fruitless, but produce long noncoding RNAs (lncRNAs), which recently have been reported to play important roles in a number of biological processes in eukaryotes. When a certain RNA sequence is transcribed from DNA, it may be inhibited from translation by another transcribed RNA sequence in proximity. If this inhibiting RNA, known as antisense RNA, occurs on the opposite DNA strand, it is referred to as a cis-Natural Antisense Transcript (cis-NAT). RNA-seq, a revolutionary tool for transcriptome analysis has been used to systematically discover and characterize lncRNAs and cis-NATs in plants and animals. In my study, strand-specific RNA-seq data from tomato fruits at two critical developmental stages (mature green and breaker) were used to identify lncRNAs and cis-NATs and to investigate their differential expression during tomato development. Through identification and expression analysis of cis-NATs and linc RNAs in tomato we can obtain deeper insight in the regulatory mechanism of fruit ripening, which can help improve fruit quality to fight problems of malnutrition.

My Experience

The Boyce Thompson Institute internship provided a challenging, meaningful experience of every kind in scientific study. I was given a balanced mix of completing projects on schedule with the flexibility of learning what interested me. This freedom, allowed me to be innovative and learn a lot in the process. I pursued my goals in both software engineering and biological research from the abstract theories to practical use; learning how to work in a group, with my mentor and professor was the only way it was possible. Working with my mentor to correct my mistakes and to seek guidance helped me understand how to manage projects, to solve problems effectively. Though I arrived with a strong computational background but little interest in plant studies, the BTI internship taught me to appreciate nature and see the importance of plant science.