Upgrading Transcriptome Map
Professor Nam Jin-wu (Department of Life Science)
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Incredible amount of transcriptomes encoded by eukaryotic genomes has been produced as RNA-sequencing reads are published in piles. The transcriptome is the sum of all RNA information contained in a body’s cells, which is an indispensable data when creating the transcriptome map of the body. The current map, however, is not its apotheosis since it was constructed based on RNA-seq reads that lack their orientations and certain boundary information. In his paper “High-confidence coding and noncoding transcriptome,” Professor Nam Jin-wu of Department of Life Science has presented the transcriptome map with RNA-seq reads with high accuracy and efficiency.
RNA and the map
In the past 10 years, with the technology of next generation sequencing (NGO), data of individual’s genome and transcriptome has been developing at a rapid pace. Genetic information of both healthy and diseased individuals aggregates to approximately 10 peta bytes from all over the world, from which Nam focused specifically on analyzing the transcriptome, disregarding the genome for the moment. A critical difference between the two is that genome has orientation while transcriptome lacks it. This indicates that it would be extremely difficult and inconvenient to arrange the little pieces of information to form the whole genetic map of transcriptome.
“What it means by ‘lack of orientation’ is, simply picture this situation: putting batteries in a remote control which has no plus or minus indicators. You would have to find the right direction by just trying. It is also like jigsaw puzzles where you have to search thoroughly the scattered pieces and find and put the right ones together until you get the whole picture,” explained Nam. Constructing a genetic map with orderless pieces of information could be an arduous task, since the massive bio-big data offers a tremendous amount of genetic information and they lack orientation.
What Nam has created through his research is an algorithm that predetermines the orientation and boundaries of transcripts and genetic information. This will not only lessen the work of constructing the transcriptome map by assembling RNA-seq reads that lack orientation but also increase the accuracy and quality of the resulting maps. The outcome of his research, in a word, orients the directionless RNA-seq reads and locate them where they belong. Now with the more accurate and systematic transcriptome map, the amount and structure of RNA in a cell in the body could be figured.
Nam first started this research three years ago, spending the first two years constructing the algorithm and spending the last year producing data using NGS. He is currently researching on the noncoding RNA (RNA that does not produce protein), which is highly related with various types of cancer and other rare diseases. The ultimate goal of Nam’s studies is to solve the mystery of unexplored RNA. 98% of RNA in human body belongs to the noncoding category, so how exactly do they affect the way a human being is and how do they account for different anomalies?
Jeon Chae-yun email@example.com
Photos by Choi Min-ju
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