Relationship of Long Noncoding RNA and Viruses
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View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Genomics 107 (2016) 150–154 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Review Relationship of long noncoding RNA and viruses Yao-zhong Ding, Zhong-wang Zhang, Ya-li Liu, Chong-xu Shi, Jie Zhang ⁎, Yong-guang Zhang ⁎ a State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China article info abstract Article history: Long noncoding (lnc)RNAs comprise a diverse group of transcripts including large intervening noncoding Received 26 November 2015 (linc)RNAs, natural antisense transcripts (NATs) and intronic lncRNAs. The functions and mechanisms of more Received in revised form 5 January 2016 than 200 lncRNAs have been studied in vitro and the results suggest that lncRNAs may be molecular markers Accepted 26 January 2016 of prognosis in cancer patients. Some lncRNAs can promote virus replication and allow escape from cytosolic sur- Available online 28 January 2016 veillance to suppress antiviral immunity. For example, lncRNA can cause persistent infection by Theiler's virus, and microRNA (miR)-27a/b is important for efficient murine cytomegalovirus (MCMV) replication. The available Keywords: Long noncoding RNA evidence suggests that lncRNAs may be potential targets of novel antiviral drugs. Epstein–Barr virus © 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license Theiler's virus (http://creativecommons.org/licenses/by-nc-nd/4.0/). Adenovirus Cytomegalovirus Contents 1. Introduction.............................................................. 150 2. LncRNAexpression........................................................... 151 3. LncRNAfunctions............................................................ 151 4. RelationshipofLncRNAswithviruses................................................... 151 5. The lncRNA and Epstein–Barrvirus(EBV)................................................. 151 6. LncRNAandTheiler'svirus........................................................ 152 7. LncRNAandadenovirus......................................................... 152 8. LncRNAandcytomegaloviruses...................................................... 152 9. Discussion............................................................... 152 Competinginterests............................................................. 152 Authorcontributions............................................................. 153 Acknowledgments.............................................................. 153 References.................................................................. 153 1. Introduction of the eukaryotic genome that is transcribed thus produces a broad array of RNA molecules of differing size, abundance, and protein- Cells transcribe a broad spectrum of RNA molecules, ranging from coding ability [1]. The functions of only a small number of non- long protein-coding mRNAs to short noncoding transcripts that fre- protein-coding transcripts have been experimentally described, but quently overlap or are interleaved on either strand. A large proportion disease-associated mutations have rarely been identified in other than protein-coding genes. Wang et al. [2] proposed, following the annota- tion of cDNA sequences, that much of the mouse genome's repertoire ⁎ Corresponding authors at: State Key Laboratory of Veterinary Etiological Biology, of non-protein-coding might be inconsequential transcriptional noise. National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research The non-coding RNA (ncRNA) transcribed by eukaryotic cells can be Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China. E-mail addresses: [email protected] (J. Zhang), [email protected] divided into two groups, regulatory and housekeeping RNAs depending (Y. Zhang). on their expression pattern and function. Housekeeping RNAs include http://dx.doi.org/10.1016/j.ygeno.2016.01.007 0888-7543/© 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Y. Ding et al. / Genomics 107 (2016) 150–154 151 tRNA and rRNA. Regulatory RNAs are characterized by sequence length Cytoplasmic LncRNAs include competing endogenous RNA (ceRNA), either as small regulatory RNA (b100 nucleotides) or as long noncoding that bind microRNA response elements (MREs), forming an extensive (lnc)RNA (N100 nucleotides). regulatory “crosstalk” network across the transcriptome. Competition LncRNAs do not encode any proteins, have a polyA tail, promoter se- between ceRNAs and mRNAs for binding to MREs expands the function- quence, are spliced, and are specifically expressed in different tissues al genetic information and plays an important role in pathological con- and developmental processes. The functional concept was first reported ditions. Briefly, lncRNAs competitively combine with endogenous by Japanese scientists in 2002 [3]. Three types of lncRNA have been rec- miRNA to release the target mRNA accelerate its translation [28,29]. ognized. These include at least 5000 large intervening ncRNAs LncRNAs also transactivate Staufen1 (STAU1)-mediated mRNA decay (lincRNAs) present in intergenic regions of the genome, natural anti- by duplexing with 3′-UTRs via Alu elements. Previous studies defined sense transcripts (NATs) and intronic lncRNAs [4].Recentpublications the STAU1 binding site (SBS) within ADP ribosylation factor 1 (ARF1) estimate that the three lncRNAs include approximately 20,000 tran- mRNA [30]. Other researchers have failed to find the structures within scripts [5]. A report by Rinn et al. in 2007 [6] describing the function the 3′-UTRs of other SMD targets [31], but found that SBSs can form of HOTAIR (HOX transcript antisense RNA), a 2.2 KB lncRNA stimulated by imperfect base-pairing between an Alu element within the 3′-UTR additional research on the physiological and pathological functions of of an SMD target and another Alu element within a cytoplasmic, lncRNAs. The functions and mechanisms of lncRNA, which have been polyadenylated lncRNA. LncRNAs can downregulate a subset of SMD the subject of recent reviews [7,8], are still in the initial stage. targets, and different lncRNAs can downregulate the same SMD target. To date, evidence from in vitro studies of over 200 lncRNAs [4] sug- The finding that STAU1 binding to mRNAs can be transactivated by gests that lncRNA may have clinical importance as molecular markers to lncRNAs reveals an unexpected strategy used by cells to recruit proteins predict the prognosis of cancer patients [4,9,10]. Several lncRNA mole- to mRNAs and mediate their decay [31]. Another recent study described cules have been associated with prognosis in liver cancer resection, a 3.7-kilobase lncRNA TINCR that bound STAU1 protein to stabilize a tar- liver transplantation [11–13], and after surgical treatment of tumors get mRNA required for tissue differentiation [32]. A third cytoplasmic [14,15]. Questions remain concerning the special relationship of lncRNA can bind with a coding gene exon overlapping antisense RNA lncRNAs and viruses. We review here what is currently known of ex- BACE1-AS to increase the stability of β-secretase-1 (BACE1) and pro- pression and regulation of lncRNAs that interact with viruses to foster mote Alzheimer's disease. Recent evidence indicates that a conserved continuing research on both lncRNAs and viruses. noncoding antisense transcript for BACE1, is a key enzyme in Alzheimer's disease pathophysiology. The BACE1-antisense transcript (BACE1-AS) regulates BACE1 mRNA and thus BACE1 protein expression 2. LncRNA expression in vitro and in vivo. BACE1 mRNA expression may thus be controlled by a regulatory ncRNA that drives the Alzheimer's disease-associated path- Recent studies of lncRNA transcription and function have compared ophysiology [20]. it to micro (mi)RNA; most lncRNAs, such as lincRNA, can be divided into independent transcription units by RNA polymerase. Some studies [16, 4. Relationship of LncRNAs with viruses 17] have confirmed that the transcription of lncRNAs is similar to coding genes, including the acetylation of histones and DNA methylation. Tran- The function, type, quantity and the mechanism of lncRNAs have not scription assays have shown that some lncRNAs can promote the ex- yet been defined. Current research indicates that those viruses can mod- pression of neighboring genes [18]. Following DNA damage, p53 can ulate host and/or viral gene expression via lncRNAs that maintain the induce transcription of lncRNA-p21, which then represses the expres- virus latency or replication [33]. Some lncRNAs assist virus replication, sion of genes transcriptionally regulated by p53 [19].Thesefindings escape from cytosolic surveillance, and decrease antiviral immunity. Re- suggest that lncRNAs can participate in the regulation of gene expres- vealing the relationship between the lncRNAs and viruses would pro- sion and function in eukaryotic cells. vide a new perspective of viral disease and may reveal ncRNAs as a Other ways of producing lncRNAs are derived from shear though potential targets for