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Vol 24, No. 07, July 2020   |   Issue PDF view/purchase
“Dark Matter” DNA and Rice Production
Researchers from the Okinawa Institute of Science and Technology Graduate University (OIST) shed light on the reproductive role of non-coding DNA in rice.

Published in Nature Communications the study findings revealed that a specific non-coding genomic region is essential for the proper development of the male and female reproductive organs in rice.

In complex organisms like plants and animals, a large portion of the genome – typically between 90 to 98 percent – does not code for any proteins. This group of non-coding DNA many biologists have dubbed as the “dark matter” of the genome. However, recent studies have suggested that many of these non-coding regions may play key roles in development and reproduction.

Dr. Reina Komiya, senior author of the research paper and associate researcher from the OIST Science and Technology Group, is particularly interested in reproduction-specific microRNA. Specifically, a major class of small non-coding RNAs called microRNA2118.

Deletion of the region of DNA that gives rise to microRNA2118 in mutant rice strains allowed the scientists to discover that the mutant strains were sterile and displayed abnormalities in structure of the stamen and pistil.

"This means that the role of microRNA2118 in the proper development of the stamens and pistils is essential for plant fertility," said Dr. Komiya.

Upon further analysis of how microRNA2118 controls the development of the anther, the scientists were able to identify other molecules that are affected by microRNA2118. The team found that microRNA2118 triggered the cleavage of long non-coding RNA, producing many tiny RNA molecules known as secondary small RNAs.

"Interestingly, these small RNAs were rich in uracil, one of the four nucleotide bases found in RNA, which is very unusual compared to other small RNAs," said Dr. Komiya. "We hope to find out the exact function of these small RNAs - and whether this difference in nucleotide composition is important - in further research."

It was also discovered that two Argonaute proteins specifically produced in the stamen were dependent on the presence of microRNA2118. These proteins have been shown by previous studies to team up with small RNAs to carry out many regulatory functions, such as silencing genes and cleaving RNA.

The team then proposed the interaction between Argonaute proteins with microRNA2118 in triggering production of the secondary small RNAs. The proteins may also interact with the secondary small RNAs to silence specific regions of the genome. The team hopes to elucidate exactly how the Argonaute proteins and secondary small RNAs affect development of the plant reproductive system in further research.

"Reproduction is an important phenomenon of passing genetic information to the next generation and is essential for maintaining a stable yield supply. However, development of the reproductive system is complicated, and many aspects remain unknown," concluded Dr. Komiya. "This study shows that non-coding RNAs, derived from regions of the genome that were thought to be non-functional, are vital for plant reproduction. Exploring non-coding RNAs further is an exciting and important area of research."


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