Mammalian RNA Granules

Aravinth kumar Jayabalan,Takbum Ohn 대한의생명과학회 2014 Biomedical Science Letters Vol.20 No.1

RNA granules such as Stress Granules (SG) and P-Bodies (PB) are aggregates of translationally stalled messenger ribonucleoprotein (mRNP) complexes induced by a wide range of stresses. Over the past decade, extensive studies described key components of RNA granules, their molecular interactions and signaling pathways require for their assembly and disassembly. However, researches defining their exact roles under stress conditions have not been performed so far, although several studies suggested their roles in neurodegenerative diseases recently. In this review, we provide an introduction about their basic properties, key components, and the dynamic nature for their assembly.

MicroRNAs as Novel Biomarkers for the Diagnosis of Alzheimer`s Disease and Modern Advancements in the Treatment

Tamil Iniyan Gunasekaran,Takbum Ohn 대한의생명과학회 2015 Biomedical Science Letters Vol.21 No.1

Alzheimer"s disease is a common form of dementia occurring among the elderly population and can be identified by symptoms such as cognition impairments, memory loss and neuronal dysfunction. Alzheimer"s disease was found to be caused by the deposition of β-amyloid plaques and neurofibrillary tangles. In addition, mutation in the APP (Amyloid precursor protein), Presenilin 1 (PSEN1) and Presenilin 2 (PSEN2) genes were also found to contribute to Alzheimer"s disease. Since the potential conformational diagnosis of Alzheimer"s disease requires histopathological tests on brain through autopsy, potential early diagnosis still remains challenging. In recent years, several researches have proposed the use of biomarkers for early diagnosis. In cerebrospinal fluid (CSF), β-amyloid(1-42), phosphorylated-tau and total tau were suggested to be effective biomarkers for Alzheimer"s disease diagnosis. However, a single biomarker might not be sufficient for potential diagnosis of Alzheimer"s disease. Thus, the use of RNA interference (RNAi) through microRNAs (miRNAs) has been proposed by several researchers for simultaneous analysis of several biomarkers using microarray technology. These miRNA based biomarkers can be analysed from both blood and CSF, but miRNAs from blood are advantageous over CSF as they are non-invasive and simple for collection. Moreover, the RNAi based therapeutics by siRNA (short interference RNA) or shRNA (short hairpin RNA) have also been proposed to be effective in the treatment of Alzheimer"s disease. This review describes the promising application of RNAi technology in therapeutics and as a biomarker for both Alzheimer"s disease diagnosis and treatment.

Oxidative stress-induced aberrant G9a activation disturbs RE-1-containing neuron-specific genes expression, leading to degeneration in human SH-SY5Y neuroblastoma cells

Ho-Tae Kim,Takbum Ohn,Sin-Gu Jeong,Anji Song,Chul Ho Jang,Gwang-Won Cho 대한약리학회 2021 The Korean Journal of Physiology & Pharmacology Vol.25 No.1

Oxidative stress-induced neurodegeneration is one of several etiologies underlying neurodegenerative disease. In the present study, we investigated the functional role of histone methyltransferase G9a in oxidative stress-induced degeneration in human SH-SY5Y neuroblastoma cells. Cell viability significantly decreased on H₂O₂ treatment; however, treatment with the G9a inhibitor BIX01294 partially attenuated this effect. The expression of neuron-specific genes also decreased in H₂O₂-treated cells; however, it recovered on G9a inhibition. H₂O₂-treated cells showed high levels of H3K9me2 (histone H3 demethylated at the lysine 9 residue), which is produced by G9a activation; BIX01294 treatment reduced aberrant activation of G9a. H3K9me2 occupancy of the RE-1 site in neuron-specific genes was significantly increased in H₂O₂-treated cells, whereas it was decreased in BIX01294-treated cells. The differentiation of H₂O₂-treated cells also recovered on G9a inhibition by BIX01294. Consistent results were observed when used another G9a inhibitor UCN0321. These results demonstrate that oxidative stress induces aberrant activation of G9a, which disturbs the expression of neuron-specific genes and progressively mediates neuronal cell death. Moreover, a G9a inhibitor can lessen aberrant G9a activity and prevent neuronal damage. G9a inhibition may therefore contribute to the prevention of oxidative stress-induced neurodegeneration.

Depletion of PDCD4 Accelerates Stress Granule Assembly Through Sensitization of Stress Response Pathways

Kim, Jeeho,Chang, In Youb,Lee, Wooje,Ohn, Takbum The Basic Science Institute Chosun University 2019 조선자연과학논문집 Vol.12 No.4

Programmed cell death 4 (PDCD4) is a novel tumor suppressor that function in the nucleus and the cytoplasm and appears to be involved in the regulation of transcription and translation. Stress granules (SGs) are cytoplasmic foci at which untranslated mRNAs accumulate when cells exposed to environmental stresses. Since PDCD4 has implicated in translation repression through direct interaction with eukaryotic translation initiation factor 4A (eIF4A), we here investigated if PDCD4 has a functional role in the process of SG assembly under oxidative stresses. Using immunofluorescence microscopy, we found that PDCD4 is localized to SGs under oxidative stresses. Next, we tested if knockdown of PDCD4 has an effect on the assembly of SG using PDCD4-specific siRNA. Interestingly, SG assembly was accelerated and this effect was caused by sensitization of phosphorylation of eIF2α and dephosphorylation of eIF4E binding protein (4E-BP). These results suggest that PDCD4 has an effect on SG dynamics and possibly involved in cap-dependent translation repression under stress conditions.

SRSF3-regulated miR-132/212 controls cell migration and invasion by targeting YAP1

Kim, Hye Ree,Hwang, Su Jin,Shin, Chang Hoon,Choi, Kyung Hee,Ohn, Takbum,Kim, Hyeon Ho Elsevier 2017 Experimental cell research Vol.358 No.2

<P><B>Abstract</B></P> <P>Although SRSF3 (Serine/arginine-rich splicing factor 3) plays a significant role in various biological processes, many of its functions still remain unclear. More particularly, little is known about SRSF3's involvement in the regulation of miRNA. In this report, we found that invasive and migratory abilities were inhibited in SRSF3-silenced U2OS and HeLa cells. We also found that a knockdown of SRSF3 results in a decreased expression level of REST (RE1-silencing transcription factor). The silencing of REST increased the expression of primary miR-132/212 as well as their mature forms. In particular, miR-132-3p and miR-212-3p possess an identical seed sequences and a common target gene. Overexpression of miR-132-3p and miR-212-3p suppressed the expression of YAP1 (Yes-associated protein 1) by directly binding to the 3՚UTR of its mRNA. <I>CCND1</I> (Cyclin D1), which acts downstream of YAP1, was downregulated in both miR-132-3p and miR-212-3p-overexpressed cells, in correlation with diminished YAP1 levels. Taken together, our results reveal that SRSF3 controls the expression of the miR-132/212 cluster through regulating REST expression, and that the REST-elicited alteration of miRNA expression is implicated in enabling the migratory and invasive abilities of cancer cells.</P> <P><B>Highlights</B></P> <P> <UL> <LI> REST is involved in the SRSF3-mediated migration and invasion. </LI> <LI> SRSF3 regulates the expression of miR-132/212 through REST. </LI> <LI> miR-132/212 suppresses YAP1 expression by directly binding to the 3′UTR of its mRNA. </LI> <LI> miR-132/212 inhibits migratory and invasive abilities via downregulation of YAP1/CyclinD1. </LI> <LI> miR-132/212 is responsible for the oncogenic function of SRSF3. </LI> </UL> </P>

Identifying the cellular location of brain cytoplasmic 200 RNA using an RNA-recognizing antibody

( Heegwon Shin ),( Jungmin Lee ),( Youngmi Kim ),( Seonghui Jang ),( Takbum Ohn ),( Younghoon Lee ) 생화학분자생물학회(구 한국생화학분자생물학회) 2017 BMB Reports Vol.50 No.6

Brain cytoplasmic 200 RNA (BC200 RNA) is a neuron-specific non-coding RNA, implicated in the inhibition of local synaptodendritic protein synthesis, and is highly expressed in some cancer cells. Although BC200 RNA has been shown to inhibit translation in vitro, the cellular location of this inhibition is unknown. In this study, we used a BC200 RNA-recognizing antibody to identify the cellular locations of BC200 RNA in HeLa cervical carcinoma cells. We observed punctate signals in both the cytoplasm and nucleus, and further discovered that BC200 RNA co-localized with the p-body decapping enzyme, DCP1A, and the heterogeneous nuclear ribonucleoprotein E2 (hnRNP E2). The latter is a known BC200 RNA-binding partner protein and a constituent of p-bodies. This suggests that BC200 RNA is localized to p-bodies via hnRNP E2. [BMB Reports 2017; 50(6): 318-322]

Resveratrol relieves hydrogen peroxide-induced premature senescence associated with SIRT1 in human mesenchymal stem cells

Choi, Mi Ran,Han, Dal Mu Ri,Kim, Sun Hwa,Ohn, Takbum,Jung, Kyoung Hwa,Chai, Young Gyu THE KOREAN SOCIETY OF TOXICOGENOMICS AND TOXICOPRP 2014 MOLECULAR AND CELLULAR TOXICOLOGY Vol.10 No.1

Cellular senescence of mesenchymal stem cells (MSCs) is often induced during in vitro expansion, by multiple experimental stimuli including oxidative stress. In this study, we investigated expression of senescence-associated proteins including SIRT1after inducing premature senescence of MSCs with hydrogen peroxide ($H_2O_2$). We also analyzed the effect of resveratrol (RSV) on premature senescence. We found that $H_2O_2$ triggered the recruitment of RCK (p54) to P-bodies in MSCs. Premature senescence of MSCs in response to $H_2O_2$ induced a decrease in SIRT1expression and activity (indirectly identified by measuring H3-K9ac). Cellular expression of p21 and phosphorylation of ERK1/2 and p38 kinases were increased in response to $H_2O_2$, whereas phosphorylation of pRb was decreased. In contrast, RSV pretreatment resulted in a decrease in the premature senescence of MSCs. In addition, RSV pretreatment before exposing cells to $H_2O_2$ not only alleviated changes in the levels of proteins that were sensitive to the $H_2O_2$ treatment (SIRT1, p21,ERK1/2 and p38) but also inhibited the decrease of SIRT1 induced by nicotinamide (NAM). Our results suggest that MSCs may exhibit an increased tolerance for $H_2O_2$-induced oxidative stress via the senescence-associated proteins that are regulated by RSV.

Splicing inhibition of U2AF⁶⁵ leads to alternative exon skipping

Cho, Sunghee,Moon, Heegyum,Loh, Tiing Jen,Jang, Ha Na,Liu, Yongchao,Zhou, Jianhua,Ohn, Takbum,Zheng, Xuexiu,Shen, Haihong National Academy of Sciences 2015 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.112 No.32

<P><B>Significance</B></P><P>Transcription is a biological procedure in which DNA is transcribed to an RNA molecule. However, only fragments of this RNA are needed for protein synthesis. These fragments are exons that are interrupted by introns. Introns are removed by so-called RNA splicing process. Some exons could be alternatively included or excluded from the final RNA molecule. In this study, we have found that U2 snRNP auxiliary factor 65 kDa (U2AF<SUP>65</SUP>), a general splicing regulator, can significantly promote the exclusion of alternative exons. Strikingly, U2AF<SUP>65</SUP> suppresses flanking intron splicing of alternative exons, and even constitutive intron splicing. We deduce that the stimulatory effects of U2AF<SUP>65</SUP> on alternative exon exclusion are induced by the splicing inhibitory effects of U2AF<SUP>65</SUP>.</P><P>U2 snRNP auxiliary factor 65 kDa (U2AF<SUP>65</SUP>) is a general splicing factor that contacts polypyrimidine (Py) tract and promotes prespliceosome assembly. In this report, we show that U2AF<SUP>65</SUP> stimulates alternative exon skipping in spinal muscular atrophy (SMA)-related survival motor neuron (<I>SMN</I>) pre-mRNA. A stronger 5′ splice-site mutation of alternative exon abolishes the stimulatory effects of U2AF<SUP>65</SUP>. U2AF<SUP>65</SUP> overexpression promotes its own binding only on the weaker, not the stronger, Py tract. We further demonstrate that U2AF<SUP>65</SUP> inhibits splicing of flanking introns of alternative exon in both three-exon and two-exon contexts. Similar U2AF<SUP>65</SUP> effects were observed in Fas (Apo-1/CD95) pre-mRNA. Strikingly, we demonstrate that U2AF<SUP>65</SUP> even inhibits general splicing of adenovirus major late (Ad ML) or β-globin pre-mRNA. Thus, we conclude that U2AF<SUP>65</SUP> possesses a splicing Inhibitory function that leads to alternative exon skipping.</P>

Identification of Neuregulin-2 as a novel stress granule component

( Jin Ah Kim ),( Aravinth Kumar Jayabalan ),( Vinoth Kumar Kothandan ),( Ramesh Mariappan ),( Younghoon Kee ),( Takbum Ohn ) 생화학분자생물학회(구 한국생화학분자생물학회) 2016 BMB Reports Vol.49 No.8

Stress Granules (SGs) are microscopically visible, phase dense aggregates of translationally stalled messenger ribonucleoprotein (mRNP) complexes formed in response to distinct stress conditions. It is generally considered that SG formation is induced to protect cells from conditions of stress. The precise constituents of SGs and the mechanism through which SGs are dynamically regulated in response to stress are not completely understood. Hence, it is important to identify proteins which regulate SG assembly and disassembly. In the present study, we report Neuregulin-2 (NRG2) as a novel component of SGs; furthermore, depletion of NRG2 potently inhibits SG formation. We also demonstrate that NRG2 specifically localizes to SGs under various stress conditions. Knockdown of NRG2 has no effect on stress-induced polysome disassembly, suggesting that the component does not influence early step of SG formation. It was also observed that reduced expression of NRG2 led to marginal increase in cell survival under arsenite-induced stress. [BMB Reports 2016; 49(8): 449-454]

Proteomic Analysis of the Copper Ion-Induced Stress Response in a Human Embryonic Carcinoma Cell Line

Han, Dal Mu Ri,Choi, Mi Ran,Jung, Kyoung Hwa,Lee, Hyung Tae,Park, Ji Hyun,Ohn, Takbum,Chai, Young Gyu SAGE Publications 2012 International journal of toxicology Vol.31 No.4

<P> Excessive exposure to copper, a redox-active metal, generates free radicals, which can cause cellular damage. In this study, we aim to identify the proteins that are up- or downregulated by copper exposure in human embryonic carcinoma (NCCIT) cells and to understand the mechanisms that play a role in the copper-induced stress response. After exposure to copper ions, the cells showed upregulated levels of 78 kDa glucose-regulated protein, fibrillin 1, CWC22 spliceosome-associated protein (KIAA1604), heat shock protein (HSP) 60, and HSP70, while the tumor necrosis factor receptor-associated factor 6, vimentin, 14-3-3 protein zeta, and RAC-beta (AKT2) serine/threonine protein kinase were downregulated. The GeneGo Process Networks of the proteins upregulated by copper ions were analyzed, and the 3 highest-scoring networks from the proteins upregulated by copper ions are presented here. In particular, the increased level of HSP70 in response to copper ions occurred in a dose-dependent manner, indicating that HSP70 could be a potential biomarker for copper toxicity in mammalian cells. </P>