NEAT1 Long Noncoding RNA and Paraspeckle Bodies Modulate HIV-1 Posttranscriptional Expression

Zhang, Quanhai; Chen, Chia‐Yen; Yedavalli, Venkat R. K.; Jeang, Kuan‐Teh

doi:10.1128/mbio.00596-12

Cited by 319 publications

(337 citation statements)

References 82 publications

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“…siRNAs against NEAT1 long noncoding RNA (lncRNA) were those described previously and were obtained from Sigma-Aldrich (13). The RBM14 antiserum (ab70636) and PACS1 antiserum (ab56072) were obtained from Abcam.…”

Section: Methodsmentioning

confidence: 99%

“…1]) is a nuclear protein, and it has been shown to function in transcription activation and pre-mRNA splicing (26). RBM14 localizes in nuclear paraspeckles, nuclear structures implicated in regulating transport of HIV-1 unspliced transcripts (12,13). PACS1 (complex H [ Fig.…”

Section: Identification Of Xpo1-associated Proteinsmentioning

confidence: 99%

“…The formation of paraspeckles is dependent on the presence of a long noncoding RNA (lncRNA) termed NEAT1 (11). Depletion of NEAT1 enhances HIV-1 replication by a mechanism that involves an increase in Rev-XPO1-dependent nuclear export of INS-containing viral RNAs, further suggesting that paraspeckles retain INS RNAs in the nucleus (13). Additional studies have extended Rev's role beyond viral RNA export into facilitating efficient encapsidation of viral genomic RNA into virions that assemble at the plasma membrane, as well as in promoting translation of viral mRNAs through poorly understood mechanisms (14)(15)(16).…”

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confidence: 99%

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Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Budhiraja

Liu

Couturier

et al. 2015

J Virol

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By recruiting the host protein XPO1 (CRM1), the HIV-1 Rev protein mediates the nuclear export of incompletely spliced viral transcripts. We mined data from the recently described human nuclear complexome to identify a host protein, RBM14, which associates with XPO1 and Rev and is involved in Rev function. Using a Rev-dependent p24 reporter plasmid, we found that RBM14 depletion decreased Rev activity and Rev-mediated enhancement of the cytoplasmic levels of unspliced viral transcripts. RBM14 depletion also reduced p24 expression during viral infection, indicating that RBM14 is limiting for Rev function. RBM14 has previously been shown to localize to nuclear paraspeckles, a structure implicated in retaining unspliced HIV-1 transcripts for either Rev-mediated nuclear export or degradation. We found that depletion of NEAT1 RNA, a long noncoding RNA required for paraspeckle integrity, abolished the ability of overexpressed RBM14 to enhance Rev function, indicating the dependence of RBM14 function on paraspeckle integrity. Our study extends the known host cell interactome of Rev and XPO1 and further substantiates a critical role for paraspeckles in the mechanism of action of Rev. Our study also validates the nuclear complexome as a database from which viral cofactors can be mined. IMPORTANCEThis study mined a database of nuclear protein complexes to identify a cellular protein named RBM14 that is associated with XPO1 (CRM1), a nuclear protein that binds to the HIV-1 Rev protein and mediates nuclear export of incompletely spliced viral RNAs. Functional assays demonstrated that RBM14, a protein found in paraspeckle structures in the nucleus, is involved in HIV-1 Rev function. This study validates the nuclear complexome database as a reference that can be mined to identify viral cofactors. Since the HIV-1 genome encodes only 15 proteins, the virus must exploit the function of host cofactors at every step in its replication cycle (1). A meta-analysis of genome-wide small interfering RNA (siRNA) screens suggests that more than 2,410 proteins, or 9.5% of human genes, may be involved in HIV-1 replication (2). While data from siRNA screens provide insight into virus-host interactions and provide an opportunity to identify "druggable" targets to inhibit virus replication, these screens have limitations. Comparison of different genome-wide siRNA screens reveal minimal overlap in the host genes involved in HIV-1 replication, and these screens may frequently yield false-positive results due to siRNA off-target effects (3).In the present study, we utilized a novel strategy to identify host factors involved in HIV-1 replication. The human nuclear "complexome" was recently described in a high-throughput immunoprecipitation/mass spectrometry (IP/MS) study (4). This complexome describes endogenous protein complexes defined by identification of proteins that coimmunoprecipitated in more than 3,000 immunoprecipitations of HeLa cell nuclear extracts. We mined the nuclear complexome to identify cellular proteins found in complexe...

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Section: Methodsmentioning

confidence: 99%

Section: Identification Of Xpo1-associated Proteinsmentioning

confidence: 99%

mentioning

confidence: 99%

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Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Budhiraja

Liu

Couturier

et al. 2015

J Virol

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“…It is known that the transcription of NEAT1 RNAs and the formation of paraspekles are induced upon virus infection or poly(I:C) treatment (Saha et al 2006;Zhang et al 2013a;Imamura et al 2014). We therefore investigated whether CARM1-regulated nuclear retention is affected by poly(I:C) treatment.…”

Section: Carm1 Is Involved In the Poly(i:c)-stimulated Enhancement Ofmentioning

confidence: 99%

Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus

Xiang

et al. 2015

Genes Dev.

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In many cells, mRNAs containing inverted repeated Alu elements (IRAlus) in their 3′ untranslated regions (UTRs) are inefficiently exported to the cytoplasm. Such nuclear retention correlates with paraspeckle-associated protein complexes containing p54 nrb . However, nuclear retention of mRNAs containing IRAlus is variable, and how regulation of retention and export is achieved is poorly understood. Here we show one mechanism of such regulation via the arginine methyltransferase CARM1 (coactivator-associated arginine methyltransferase 1). We demonstrate that disruption of CARM1 enhances the nuclear retention of mRNAs containing IRAlus. CARM1 regulates this nuclear retention pathway at two levels: CARM1 methylates the coiled-coil domain of p54 nrb , resulting in reduced binding of p54 nrb to mRNAs containing IRAlus, and also acts as a transcription regulator to suppress NEAT1 transcription, leading to reduced paraspeckle formation. These actions of CARM1 work together synergistically to regulate the export of transcripts containing IRAlus from paraspeckles under certain cellular stresses, such as poly(I:C) treatment. This work demonstrates how a post-translational modification of an RNA-binding protein affects protein-RNA interaction and also uncovers a mechanism of transcriptional regulation of the long noncoding RNA NEAT1.

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“…Interestingly, NEAT1/paraspeckles appear to have innate immunity functions in viral infection (40)(41)(42) through infection-mediated induction of NEAT1 and the resulting paraspeckle formation (40). As is commonly the case for successful viruses, at least HIV is known to have adapted to utilize this pathway to regulate its own infection cascade (42).…”

Section: Lytic Transcription At the Ebv Latency Origin Of Replicationmentioning

confidence: 99%

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP , Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

Cao

Moss

O’Grady

et al. 2015

J Virol

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We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long noncoding RNAs (vlncRNAs) that are expressed during reactivation. Here we show that the EBV latency origin of replication (oriP) is transcribed bi-directionally during reactivation and that both leftward (oriPtLs) and rightward (oriPtRs) transcripts are largely localized in the nucleus. While the oriPtLs are most likely noncoding, at least some of the oriPtRs contain the BCRF1/vIL10 open reading frame. Nonetheless, oriPtR transcripts with long 5= untranslated regions may partially serve noncoding functions. Both oriPtL and oriPtR transcripts are expressed with late kinetics, and their expression is inhibited by phosphonoacetic acid. RNA sequencing (RNA-seq) analysis showed that oriPtLs and oriPtRs exhibited extensive "hyperediting" at their Family of Repeat (FR) regions. RNA secondary structure prediction revealed that the FR region of both oriPtLs and oriPtRs may form large evolutionarily conserved and thermodynamically stable hairpins. The doublestranded RNA-binding protein and RNA-editing enzyme ADAR was found to bind to oriPtLs, likely facilitating editing of the FR hairpin. Further, the multifunctional paraspeckle protein, NONO, was found to bind to oriPt transcripts, suggesting that oriPts interact with the paraspeckle-based innate antiviral immune pathway. Knockdown and ectopic expression of oriPtLs showed that it contributes to global viral lytic gene expression and viral DNA replication. Together, these results show that these new vlncRNAs interact with cellular innate immune pathways and that they help facilitate progression of the viral lytic cascade. IMPORTANCERecent studies have revealed that the complexity of lytic herpesviral transcriptomes is significantly greater than previously appreciated with hundreds of viral long noncoding RNAs (vlncRNAs) being recently discovered. Work on cellular lncRNAs over the past several years has just begun to give us an initial appreciation for the array of functions they play in complex formation and regulatory processes in the cell. The newly identified herpesvirus lncRNAs are similarly likely to play a variety of different functions, although these functions are likely tailored to specific needs of the viral infection cycles. Here we describe novel transcripts derived from the EBV latency origin of replication. We show that they are hyperedited, that they interact with a relatively newly appreciated antiviral pathway, and that they play a role in facilitating viral lytic gene expression. These investigations are a starting point to unraveling the complex arena of vlncRNA function in herpesvirus lytic replication. The Epstein-Barr virus (EBV) is an oncogenic human herpesvirus that infects 95% of the world's population (1). Although infection is typically asymptomatic, the virus will persist in the host for the duration of its life. In most immunocompetent individuals, the virus poses little serious health risk and its presence is unremarkable. Nevertheless, in...

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NEAT1 Long Noncoding RNA and Paraspeckle Bodies Modulate HIV-1 Posttranscriptional Expression

Cited by 319 publications

References 82 publications

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP , Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

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