Life science
Medical care, Drug discovery

Study of intracellular architecture by noncoding RNAs
Graduate School of Frontier Biosciences
Professor Tetsuro Hirose
Researchmap https://researchmap.jp/tets_hirose

Life science

Abstract
Among numerous long noncoding RNAs (lncRNAs) produced by
the human genome, some act as the scaffold of intracellular structures. Soft matter physics theory and experimental verification haverevealed that micellarization by RNA-protein complex is the key toconstruction of a massive lncRNA-based structure. On the otherhand, functional analyses of the lncRNA-based structures revealedthat it regulates thermal stress responsive gene expression by
sponge function via methylated lncRNAs.

(nSBs) formed on the heat-inducible lncRNA acts as a “molecularsponge” to regulate temperature-dependent gene expression
through sequestration of regulatory proteins via methylated lncRNAs. In addition to the function of the protein phosphorylation
reaction as a "crucible" that we previously reported, nSBs broadly
control temperature-dependent gene expression by two independent mechanisms of action, "sponge" and "crucible". Our research
clearly showed the biological significance of the lncRNA-induced
phase separation in the cells.

▍ Background & Results
Numerous lncRNAs were discovered in the post-genome era.
We have identified lncRNAs that induce phase separation to form
intracellular structures. In this study, we show that the lncRNA-induced phase separation by RNA occurs through micellarization,
which is different from the typical liquid-liquid phase separation byproteins broadly studied. It can be a pioneering result as the basisof phase separation research. On the other hand, we addressed
the mechanism of action of the phase separated structures in cells.
Our results show importance of intracellular phase separation inwhich the temperature-dependent gene expression is controlled by
the sponge mechanism of the structure via RNA methylation. Our
results can be the basic knowledge for understanding the molecular mechanism and biological function of intracellular phase separation.

▍ Significance of the research and Future perspective
Decoding the human genome in the early 21st century revealed
that only 2% of the human genome encodes protein information.
Subsequently, numerous lncRNAs were discovered to be synthesized from the noncoding regions of the genome, and its function
as a "genomic dark matter " attracted a great deal of attention. We
have discovered for the first time in the world a lncRNA that acts
as the scaffold of the intracellular structure. On the other hand, theintracellular phase separation has been studied and become an
active research field in cell biology. The phase separation is considered to be a general mechanism of cell space compartmentalization as a mechanism for transiently forming an isolated space ina crowded intracellular environment. Intracellular phase separation
is induced by biopolymers such as intrinsically disordered proteins
and RNAs. It was clarified that the above-mentioned structure formation by the lncRNA was achieved by phase separation, and alsothat the lncRNA induces the phase separation. In this study, themechanism of lncRNA-dependent structural formation was clarified
by soft matter physics theory and its verification experiments, andrevealed that the paraspeckle nuclear body is formed by micellarization of the RNA-protein complex. Our study paved the way forthe theoretical design of RNA-based phase separated structures.
On the other hand, we also analyzed the role of the phase-separated structure in the cell. We found that the nuclear stress bodies

Figure 1.Paraspeckle nuclear body is formed through micellization of NEAT1 lncRNA-protein complex (block copolymer)

Figure 2. Nuclear stress body is formed upon thermal stress exposure and regulates gene expression during stress recovery through crucible function of protein
phosphorylation and sponge function mediated by RNA methylation both ofwhich occur in the phase separated environment.

P a t e n t
Yamazaki, Tomohiro; Yamamoto, Tetsuya; Yoshino, Hyura et al. Paraspeckles are constructed as block copolymer micelles. The EMBO Journal 2021;
40(12): e107270. doi: 10.15252/embj.2020107270
Ninomiya, Kensuke; Iwakiri, Junichi; Aly, Mahmoud K et al. m6A modification of HSATIII lncRNAs regulates temperature-dependent splicing. The EMBO
Journal 2021; 40(15): e107976. doi: 10.15252/embj.2021107976
https://resou.osaka-u.ac.jp/ja/research/2021/20210422_1
URL
https://resou.osaka-u.ac.jp/ja/research/2021/20210629_1
K e y w o r d noncoding RNA, gene expression, intracellular structure, phase separation, stress response
Tr e a t i s e