Hokkaido University: Institute for Genetic Medicine

Laboratories

RNA Biofunction

Research on biological function of noncoding RNA and related diseases

  • Professor Tetsuro HIROSE,PhD
  • Assistant Professor Dai IWAKIRI,PhD
  • Assistant Professor Tomohiro YAMAZAKI, PhD
  • Research Assistant Professor Taro MANNEN, PhD

In the beginning of 21st century, it was discovered that a large number of long noncoding RNAs (ncRNAs) were produced from mammalian genomes. Our research is aimed to unveil molecular mechanism of actions of long noncoding RNAs and their physiological functions. We also challenge to establish basic tools which link our basic research to new medical and pharmatheutical technologies that target to ncRNAs. Our group also studied on the molecular mechanism of oncogenesis induced by EB virus infection.

Analysis of novel functions of architectural ncRNA

Among long ncRNAs produced from mammalian genomes, we discovered the architectural ncRNAs that function as skeleton of intracellular structure. We have been studying on the mechanism of actions of these architectural ncRNAs, their physiological roles as well as their related diseases. In this research period, we carried out an extensive analysis of function of the proteins that are colocalized with architectural NEAT1 ncRNA in the subnuclear structure called paraspeckles. It was revealed that the paraspeckle construction proceeds in conjunction with the biogenesis of NEAT1 long ncRNA (Naganuma et al. EMBO J 2012). To understand cellular functions of the ncRNA-dependent nuclear structure, we identified the conditions in which NEAT1 expression was markedly induced. The functional analyses under this condition revealed that the paraspeckle acts as a molecular sponge that sequestrates various regulatory proteins and regulates gene expression (Hirose et al., Mol Biol Cell 2014) (Figure 1). As a collaborative research, we detected the formation of aberrant paraspeckles in the spinal motor neuron from the neurodegenerative disease patients (Nishimoto et al., Mol Brain 2013).


Figure 1. The paraspeckle sponge model. The induced NEAT1 expression triggers to construct paraspeckle structure. The paraspeckle sequestrates nuclear regulatory proteins and regulates expression of the respective target genes.

Development of new methodologies for identifying novel genomically encoded functions of ncRNAs

New methodologies for searching functional architectural ncRNAs were developed. First, the nuclear bodies were enriched by density gradient centrifugation and the RNAs contained in the enriched fractions were extensively analyzed using the next generation sequencer. This analysis identified primate-specific ncRNA-like transcripts that are specifically localized in the unidentified nuclear foci. Second, we established the method of co-localization screening to identify the proteins that are co-localized with specific ncRNAs using the full length (FLJ) cDNA resource (Figure 2). This analysis identified multiple RNA-binding proteins that are localized in the paraspeckles which are formed on NEAT1 ncRNAs (Naganuma et al., EMBO J 2012). It was also identified that multiple proteins related to the specific neurodegenerative disease are contained in paraspeckles. Furthermore, using the full length cDNA resource, we established another method to identify new RNA granules.

Figure 2. Co-localization screening method to identify novel nuclear body-localized proteins using human FLJ cDNA resource.

Molecular mechanism of EBV-mediated oncogenesis

We analyzed the effect of EBV infection on epithelial cells by using EBV-converted epithelial cells and revealed that the extracellular signal- regulated kinase (ERK) is constitutively activated by EBV-latent membrane 2A (LMP2A). Further study demonstrated that LMP2A-mediated ERK activation induces resistance to anoikis, a type of apoptosis induced by cell detachment, by down-regulating the pro-anoikis mediator Bim. These findings suggest that LMP2A-meidated ERK activation contributes to the generation of EBV-associated epithelial malignancies.