Undergraduate students lead the development of an RNA regulatory binding analysis system

Research results announced in the international journal, Nucleic Acids Research.

Expected to aid the development of new RNA medicines for many diseases and illnesses.

▲ From left, Sihyung Park, Eun Sol Cho, Seung Hyun Ahn, and Professor Sung Wook Chi.

Under the guidance of Professor Sung Wook Chi, Sihyung Park (’14) and Eun Sol Cho (’13) of Korea University’s College of Life Sciences and Biotechnology, Division of Life Sciences, along with Life Science major graduate student, Seung Hyun Ahn, developed CLIPick, an analytical system that can detect regulators of RNA binding. As co-first authors, they published their findings in the internationally renowned journal "Nucleic Acids Research" (top 4.8% in the field, Impact factor 11.561).

- Title : “CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals”

- Co-first author : Sihyung Park (Division of Life Science, Korea University College of Life Sciences and Biotechnology), Seung Hyun Ahn (Korea University Department of Life Sciences), Eun Sol Cho (Korea University College of Life Sciences and Biotechnology)

- Corresponding author : Sung Wook Chi (Korea University College of Life Sciences and Biotechnology, associate professor)

- Publication date : October 17 online, November 30 (Volume 46, Issue 21) offline expected.

CLIPick more specifically and sensitively identifies transcript level binding between a gene's RNA and regulatory elements in diseases such as cancer and heart disease. As undergraduate research students, Sihyung Park headed the development and implementation of the analytical technology and Eun Sol Cho applied it to discover a new target sequence characteristic of microRNA, a gene regulatory element. To confirm the superiority of the method, Seung Hyun Ahn compared it with existing analysis technologies and data.

In many diseases, RNA regulators are known to bind to various transcriptional RNAs to control the expression of target genes and, according to those changes, alter related biological functions, thereby leading to the disease. In order to understand such regulation, CLIP, a technique for analyzing RNA binding sites using a next-generation sequence analyzer, has been developed and is currently widely used. However, this method suffers the drawback that, in the process of converting the nucleotide sequence information to the RNA binding site, errors are generated related to the varied expression levels of transcriptional RNA.

The team developed a simulation method based on RNA expression information through which they were able to complete a CLPick analysis technique that returns only the binding site information and at a higher resolution. This method allows researchers to sensitively detect the binding of RNAs that had previously been undetectable due to their low expression and to effectively remove nonspecifically generated noise due to high expression. This method allows researchers to perform a more specific RNA binding analysis than any other method.

Therefore, the team expects CLIPick to be able to more accurately analyze the RNA regulatory binding mechanism and its particular characteristics in various diseases and illnesses. This will allow the development of new RNA medicines through the more accurate detection of RNA control abnormalities, and better selection of therapeutic drug targets.

This study was conducted with the support of the Ministry of Health and Welfare’s ‘World-Class Biomedical Scientist Project’. As undergraduate researchers, Sihyung Park and Eun Sol Cho led the research in Professor Chi’s lab over two years after starting to produce the results as 3rd year college students.