Biomolecular Networks Laboratories
RNA Biofunction Laboratory
Non-coding RNA (ncRNA), Phase separation, Membraneless organelle, Stress response, Disease
We study the architectural function of non-coding RNAs to build intracellular structures.
Transcriptome analysis has revealed that large portions of eukaryotic genomes produce numerous non-coding RNAs (ncRNAs), which expectedly play important regulatory roles in various biological processes. Our goal is to elucidate the functions of these ncRNAs and reveal the underlying new genetic code, thereby redefining the basic concept of genome function. We recently found that ncRNAs play architectural roles in membraneless organelles. Now we are studying the mode of action and cellular function of these ncRNAs using basic molecular and cellular experimental techniques combined with biophysical and bioinformatic tools.
Architectural ncRNA can construct membraneless organelles through phase separation. The ncRNAs harbor distinct functional domains to function as chromatin hubs and reaction crucibles for specific biochemical reactions, particularly in the nucleus.
Images: Paraspeckle as an ncRNA-dependent membraneless organelle detected by a confocal microscope (left), a super-resolution microscope (middle) and an electron microscope (right).
|Tetsuro Hirose (Professor)||hirose[at]fbs.osaka-u.ac.jp|
|Tomohiro Yamazaki (Associate Professor)||tyamazaki[at]fbs.osaka-u.ac.jp|
|Kensuke Ninomiya (Associate Professor)||k-ninomiya[at]fbs.osaka-u.ac.jp|
|Ichiro Taniguchi (Assistant Professor)||taniguchi.ichiro.fbs[at]osaka-u.ac.jp|
|Kanako Kita (Assistant Professor, Graduate School of Medicine)|
|Naoko Fujiwara (Researcher)|
|Miwako Okamura (Technical Assistant)|
|Rieko Takahashi (Technical Assistant)|
|Junko Fujita (Secretary)|
|Hiroko Yasui (Secretary)|
You could probably reach more information of individual researchers by Research Map and researcher's search of Osaka-U.
- ※Change [at] to @
- What is your hot research topic?
- Decoding the ncRNA code
- Mechanism of phase separation or transition induced by ncRNA
- Mechanism of ncRNA bodies-chromatin intereactions
- Function of genomic repetitive elements
- Acquisition mechanism of species-specific traits
- What is your breakthrough or research progress in the last 5 years?
- Our group discovered a novel ncRNA function that works as a structural scaffold of membraneless organelles. The ncRNA can sequestrate multiple proteins with intrinsically disordered domains, thereby inducing liquid-liquid phase separation that is a driving force to construct the massive membraneless organelles. Multiple ncRNAs with the similar function were additionally identified as products of the human genome. Based on these results, we proposed to term these ncRNAs “architectural ncRNAs” as a new functional subcategory in ncRNAs.
- What kind of background do your lab members have？
- Our group members with various backgrounds join the laboratory after graduation of Faculty of Science, Engineering, Agriculture or Medicine.
- Do you collaborate with other institutions and universities?
- Our group has been collaborating with a number of laboratories in Japan (Hokkaido Univ., Univ. of Tokyo, AIST and RIKEN) as well as in foreign countries (CNRS in FR, MPI in DEU, Fraincis Crick Inst in UK, Univ. of Rochester in USA, Univ. of Western Australia in AUS and KAUST in SA)
- What kind of careers do your Lab's alumni go on to?
- Many of the former laboratory members successfully got the academic positions (e.g. Kumamoto Univ., Ritsumeikan Univ., NCGH and Univ. of Arizona) and the researcher position in bio-venture company.
- How do you develop your research?
- Understanding ncRNA functions and decoding the ncRNA code will reconstruct the basic concept on the mode of the genome functions and also facilitate the research by new perspective to understand the mechanism of various physiological events and diseases.
- Recent Representative Publications
- Hirose et al. (2022) Nat Rev Mol Cell Biol.
Ninomiya et al. (2021) EMBO J. 40, e107976
Yamazaki et al. (2021) EMBO J. 40, e107270
Ninomiya et al. (2020) EMBO J. 39, e102729
Yamazaki et al. (2018) Mol. Cell 70, 1038-1053
Chujo et al. (2017) EMBO J. 30, 1447-1462
Mannen et al. (2016) J. Cell Biol. 214, 45-59
Kawaguchi et al. (2015) PNAS 112, 4304-4309
Publications (Research Articles, Reviews, Books)
SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns
Nat Commun. 12(1):4910 2021
Control of condensates dictates nucleolar architecture
Science. 373(6554):486-487 2021
m6A modification of HSATIII lncRNAs regulates temperature-dependent splicing
EMBO J. 40(15) e107976 2021 （PMID：34184765 DOI：10.15252/embj.2021107976）
ArcRNAs and the formation of nuclear bodies
Mamm genome. 2021 （ DOI：10.1007/s00335-021-09881-5）
Paraspeckles are constructed as block copolymer micelles
EMBO J. 40(12) e107270 2021 （PMID：33885174 DOI：10.15252/embj.2020107270）
Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model
Nat Commun. 12(1):236-236 2021 （PMID：33431896 DOI：10.1038/s41467-020-20487-4）
CRISPR-Mediated Mutagenesis of Long Noncoding RNAs
Methods Mol Biol. 2254:283-303 2021 （PMID：33326083 DOI：10.1007/978-1-0716-1158-6_18）
Inhibition of the long non-coding RNA NEAT1 protects cardiomyocytes from hypoxia in vitro via decreased pri-miRNA processing
Cell Death Dis. 11(8):677 2020 （PMID：32826883 DOI：10.1038/s41419-020-02854-7）
Functional annotation of human long noncoding RNAs via molecular phenotyping
Genome Res. 30(7):1060-1072 2020 （PMID：32718982 DOI：10.1101/gr.254219.119）
NONO Is a Negative Regulator of SOX2 Promoter
Cancer Genomics Proteomics. 17(4):359-367 2020 （PMID：32576581 DOI：10.21873/cgp.20195）
Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice
Transl Psychiatry 10(1):171-171 2020 （PMID：32467583 DOI：10.1038/s41398-020-0854-2）
Phase separation driven by production of architectural RNA transcripts
Soft Matter. 16(19):4692-4698 2020 （PMID：32396591 DOI：10.1039/c9sm02458a）
Detailed analyses of the crucial functions of Zn transporter proteins in alkaline phosphatase activation
Journal of Biological Chamistry 295(17):5669-5684 2020 （PMID：32179649 DOI：10.1074/jbc.RA120.012610）
Our ideal candidate (as a graduate student)
We are looking for a highly motivated person to work on our research topics as our lab member. Our lab welcomes the person who loves taking care of creatures, hand working and handcraft too. Any kind of background (such as your expertise or major) is available.
RNA Biofunction Laboratory, Graduate School of Frontier Biosciences, Osaka University,
1-3 Yamadaoka, Suita, Osaka 565-0871 Japan.
E-mail: hirose[at]fbs.osaka-u.ac.jp (Prof. Tetsuro Hirose)
- ※Change [at] to @