糖心视频

(糖心视频) -- Data from high-throughput next generation sequencers (NGS) and genome tiling arrays have greatly enhanced scientists鈥� ability to recreate RNA molecular structures, which is vital to disease and biotechnology research. However, high levels of noise and bias in some processes lead to uneven gene-expression values for segments belonging to the same molecule. Reconstructing the complete, or 鈥榝ull-length鈥�, information of molecules as they occur in cells is therefore difficult.

To improve accuracy by reducing noise and bias, Tetsuro Toyoda, Shuji Kawaguchi, and Kei Iida at the RIKEN Bioinformatics And Systems Engineering division (BASE) in Yokohama, together with scientists from the RIKEN Plant Science Center, have developed a statistical algorithm for reconstructing full-length information of RNA molecules using output from tiling arrays and NGS. They implemented this algorithm in a computer program called 鈥楢Rabidopsis Tiling-Array-based Detection of Exons鈥� (ARTADE). 

The genome encoded in an organism鈥檚 DNA holds the blueprint for building and maintaining cells. For this building and maintenance to work, the DNA blueprint is copied, or 鈥榯ranscribed鈥�, by molecules of RNA 鈥榯ranscripts鈥�. RNA molecules use this code to create proteins or act themselves as functional molecules and regulate cell activities. Transcriptome is the name given to all the transcripts present at any one time in a cell. Transcriptomes hold vital information about living organisms, including how different protein genes are switched on and off in response to different environmental stresses.

Toyoda and his team further developed ARTADE, ARTADE2, so they could rebuild a virtual representation of the transcriptomes comprising RNA molecules. 鈥淯nderstanding transcriptomes is essential for research on molecular mechanisms of diseases and development of biotechnology with plant species,鈥� Toyoda explains. 鈥淏oth genome tiling arrays and NGS have output problems with uneven expression values from fragmentation and noise and bias from machinery. This makes it difficult to form a perfect reconstruction.鈥�

ARTADE2 uses a new 鈥榩ositional correlation analysis鈥� developed by Kawaguchi and Iida so that it can analyze any species and be used for NGS output (Fig. 1). This process identifies areas where the transcriptional activities among multiple cellular conditions鈥攕uch as differences in tissues, developmental stage, or environment鈥攁re highly correlated. Positional correlation removes output problems, providing a better representation of the original molecules.

The team has now begun developing a database using information from the rebuilt transcriptomes. This new technology and database will lead to deeper understanding of molecular structures and their alteration according to environmental stresses and disease, furthering understanding of the relationship between genome sequences and cell activities.