'Dark matter' DNA is vital for rice reproduction
Regions of DNA that give rise to non-coding RNA are required for proper development of plant reproductive organs.

Date:
June 19, 2020
Source:
Okinawa Institute of Science and Technology (OIST) Graduate
University
Summary:
Researchers have shed light on the reproductive role of 'dark
matter' DNA - non-coding DNA sequences that previously seemed to
have no function.

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



FULL STORY ========================================================================== Researchers from the Okinawa Institute of Science and Technology
Graduate University (OIST) have shed light on the reproductive role of
'dark matter' DNA -- non-coding DNA sequences that previously seemed to
have no function.


========================================================================== Their findings, published today in Nature Communications, have revealed
that a specific non-coding genomic region is essential for the proper development of the male and female reproductive organs in rice.

"Rice is one of the major global crops and is the staple food in many countries, including Japan," said Dr. Reina Komiya, senior author of
the research paper and associate researcher from the OIST Science and Technology Group. "Further research into how these genomic regions affect
plant reproduction could potentially lead to increased productivity
and more stable yields of rice." Many previous developmental studies
have focused on genes -- the sections of DNA that provide instructions
for making proteins. But in complex creatures like plants and animals,
a large fraction of the genome -- typically between 90-98% -- doesn't
actually code for proteins.

The vast expanse of this 'junk DNA' has long puzzled biologists, with many dubbing it the 'dark matter' of the genome. But recent research suggests
that many of these non-coding genomic regions may have a function after
all, giving rise to non-coding RNA.

Scientists have now identified numerous types of non-coding RNA, ranging
from small molecules only 20-30 nucleotide bases in length to long
molecules of over 200 nucleotides. Although studies show that non-coding
RNA plays a vital role in the regulation of gene expression -- the process where a gene's instructions are used to make RNA or protein -- the precise function of each specific non- coding RNA remains poorly understood.



==========================================================================
Dr. Komiya is particularly interested in reproduction-specific
RNAs. "These are non-coding RNAs that are produced as the reproductive
system forms. I wanted to uncover what role they play in the development
of stamens and pistils, the male and female reproductive organs in
plants." Making mutants In the study, Dr. Komiya's group focused on
a reproduction-specific microRNA - - a major class of small non-coding
RNAs -- called microRNA2118.

The scientists created mutant rice strains by deleting a region of
the genome that contains multiple copies of the specific DNA sequence
that gives rise to microRNA2118. They found that the mutant strains
were sterile and showed abnormalities in the structure of the stamens
and pistils.

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



========================================================================== Revealing RNA and probing proteins In order to delve deeper into how microRNA2118 controlled development of the anther, the scientists then identified which other molecules were affected by microRNA2118.

They found that microRNA2118 triggered the cleavage of long non-coding
RNA, producing many tiny RNA molecules, called 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." The scientists also discovered
that two Argonaute proteins that were only produced in the stamen
were dependent on the presence of microRNA2118. Previous research has
shown that Argonaute proteins team up with small RNAs to carry out many regulatory functions, such as silencing genes and cleaving RNA.

Dr. Komiya's group therefore proposes that the Argonaute proteins may
interact with microRNA2118 to trigger 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."

========================================================================== Story Source: Materials provided by Okinawa_Institute_of_Science_and_Technology_(OIST)
Graduate_University. Original written by Dani Ellenby. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Saori Araki, Ngoc Tu Le, Koji Koizumi, Alejandro Villar-Briones,
Ken-Ichi
Nonomura, Masaki Endo, Haruhiko Inoue, Hidetoshi Saze, Reina Komiya.

miR2118-dependent U-rich phasiRNA production in rice anther
wall development. Nature Communications, 2020; 11 (1) DOI:
10.1038/s41467-020- 16637-3 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/06/200619090525.htm

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