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Chen LL, Carmichael GG. Long noncoding RNAs in mammalian cells: what, where, and why? WILEY INTERDISCIPLINARY REVIEWS. RNA 2010; 1:2-21. [PMID: 21956903 DOI: 10.1002/wrna.5] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Not all long, polyadenylated cellular RNAs encode polypeptides. In recent years, it has become apparent that a number of organisms express abundant amounts of transcripts that lack open reading frames or that are retained in the nucleus. Rather than accumulating silently in the cell, we now know that many of these long noncoding RNAs (lncRNAs) play important roles in nuclear architecture or in the regulation of gene expression. Here, we discuss some recent progress in our understanding of the functions of a number of important lncRNAs in mammalian cells.
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Chen LL, Carmichael GG. Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol 2010; 22:357-64. [PMID: 20356723 DOI: 10.1016/j.ceb.2010.03.003] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/15/2010] [Accepted: 03/03/2010] [Indexed: 01/22/2023]
Abstract
Long non-coding RNAs (lncRNAs) are mRNA-like, non-protein-coding RNAs that are pervasively transcribed throughout eukaryotic genomes. Rather than silently accumulating in the nucleus, many of these are now known or suspected to play important roles in nuclear architecture or in the regulation of gene expression. In this review, we highlight some recent progress in how lncRNAs regulate these important nuclear processes at the molecular level.
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Chen LL, Carmichael GG. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell 2009; 35:467-78. [PMID: 19716791 DOI: 10.1016/j.molcel.2009.06.027] [Citation(s) in RCA: 503] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 03/12/2009] [Accepted: 06/08/2009] [Indexed: 01/12/2023]
Abstract
In many cells, mRNAs containing inverted repeats (Alu repeats in humans) in their 3' untranslated regions (3'UTRs) are inefficiently exported to the cytoplasm. Nuclear retention correlates with adenosine-to-inosine editing and is in paraspeckle-associated complexes containing the proteins p54(nrb), PSF, and PSP1 alpha. We report that robust editing activity in human embryonic stem cells (hESCs) does not lead to nuclear retention. p54(nrb), PSF, and PSP1 alpha are all expressed in hESCs, but paraspeckles are absent and only appear upon differentiation. Paraspeckle assembly and function depend on expression of a long nuclear-retained noncoding RNA, NEAT1. This RNA is not detectable in hESCs but is induced upon differentiation. Knockdown of NEAT1 in HeLa cells results both in loss of paraspeckles and in enhanced nucleocytoplasmic export of mRNAs containing inverted Alu repeats. Taken together, these results assign a biological function to a large noncoding nuclear RNA in the regulation of mRNA export.
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Huang Y, Carmichael GG. RNA processing in the polyoma virus life cycle. Front Biosci (Landmark Ed) 2009; 14:4968-77. [PMID: 19482599 DOI: 10.2741/3581] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Not only is gene regulation in polyoma interesting, but it has also proven to be highly informative and illustrative of a number of novel concepts in gene regulation. Of special interest and importance are the mechanisms by which this virus switches from the expression of early gene products to late gene products after the onset of viral DNA replication. This switch is mediated at least in part by changes in transcription elongation and polyadenylation in the late region, and by the formation and editing of dsRNA in the nucleus. In this review we will summarize the regulation of RNA synthesis and processing during polyoma infection, and will point out in particular those aspects that have been most novel.
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Gu R, Zhang Z, DeCerbo JN, Carmichael GG. Gene regulation by sense-antisense overlap of polyadenylation signals. RNA (NEW YORK, N.Y.) 2009; 15:1154-63. [PMID: 19390116 PMCID: PMC2685520 DOI: 10.1261/rna.1608909] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 03/26/2009] [Indexed: 05/19/2023]
Abstract
We show here that expression of genes from convergent transcription units can be regulated by the formation of double-stranded RNA (dsRNA) in the region of overlapping polyadenylation signals. The model system employed is the mouse polyomavirus. The early and late genes of polyomavirus are transcribed from opposite strands of the circular viral genome. At early times after infection, the early genes are expressed predominantly. Late gene expression increases dramatically upon the onset of DNA replication, when a major defect in polyadenylation of the late primary transcripts generates multigenomic RNAs that are precursors to the mature late mRNAs. Embedded in these late pre-mRNAs are sequences complementary to the early RNAs that act to down-regulate early gene expression via A-to-I editing of dsRNAs. In this system, the defective polyadenylation, and consequently the production of multigenomic late RNAs, depends on the context, and perhaps also, on the A-to-I editing of the poly(A) signal that overlaps the 3'-end of early transcripts.
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Chen LL, Carmichael GG. Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats. Cell Cycle 2008; 7:3294-301. [PMID: 18948735 DOI: 10.4161/cc.7.21.6927] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Alu elements are conserved approximately 300 nucleotide long repeat sequences that belong to the SINE family of retrotransposons found abundantly in primate genomes. Although the vast majority of Alu elements appear to be genetically inert, it has been tempting to consider the great majority of them as "junk DNA." However, a growing line of evidence suggests that transcribed Alu RNAs are in fact functionally involved in a number of diverse biological processes. Pairs of inverted Alu repeats in RNA can form duplex structures that lead to A-to-I editing by the ADAR enzymes. In this review we discuss the possible biological effects of Alu editing, with particular focus on the regulation of gene expression by inverted Alu repeats in the 3'-UTR regions of mRNAs.
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Zhou J, Wang Q, Chen LL, Carmichael GG. On the mechanism of induction of heterochromatin by the RNA-binding protein vigilin. RNA (NEW YORK, N.Y.) 2008; 14:1773-1781. [PMID: 18648073 PMCID: PMC2525967 DOI: 10.1261/rna.1036308] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Accepted: 05/22/2008] [Indexed: 05/26/2023]
Abstract
Vigilin is an RNA-binding protein localized to both the cytoplasm and the nucleus and has been previously implicated in heterochromatin formation and chromosome segregation. We demonstrate here that the C-terminal domain of human vigilin binds to the histone methyltransferase SUV39H1 in vivo. This association is independent of RNA and maps to a site on vigilin that is not involved in its interaction with several other known protein partners. Cells that express high levels of the C-terminal fragment display chromosome segregation defects, and ChIP analyses show changes in the status of pericentric beta-satellite and rDNA chromatin from heterochromatic to more euchromatic form. Finally, a cell line with inducible expression of the vigilin C-terminal fragment displays inducible alterations in beta-satellite chromatin. These and other results lead us to present a new model for vigilin-mediated, RNA-induced gene silencing.
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Gu R, Zhang Z, Carmichael GG. How a small DNA virus uses dsRNA but not RNAi to regulate its life cycle. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:293-9. [PMID: 17381309 DOI: 10.1101/sqb.2006.71.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mouse polyomavirus contains a circular DNA genome, with early and late genes transcribed from opposite strands. At early times after infection, genes encoded from the early transcription unit are predominantly expressed. After the onset of viral DNA replication, expression of genes encoded from the late transcription unit increases dramatically. At late times, late primary transcripts are inefficiently polyadenylated, leading to the generation of multigenomic RNAs that are precursors to mature mRNAs. These transcripts contain sequences complementary to the early RNAs and downregulate early-strand gene expression by inducing RNA editing. Our recent work leads to a model where the production of the multigenomic late RNAs is also controlled by the editing of poly(A) signals, directed by overlapping primary transcripts.
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MESH Headings
- Animals
- Base Sequence
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Viral
- Genome, Viral
- Mice
- Models, Biological
- Polyomavirus/genetics
- Polyomavirus/growth & development
- Polyomavirus/physiology
- RNA Interference
- RNA Splicing
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Virus Replication/genetics
- Virus Replication/physiology
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Abstract
Recent work reveals that adenosine-to-inosine editing occurs in a number of cellular microRNAs (miRNAs). Such editing is shown to diminish the expression of one miRNA and alter the target specificity of another. This changes our current views significantly by not only increasing the repertoire of miRNAs and their potential targets, but also providing mechanisms for how to regulate them and direct them to alternative targets.
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Sun M, Hurst LD, Carmichael GG, Chen J. Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res 2006; 16:922-33. [PMID: 16769979 PMCID: PMC1484459 DOI: 10.1101/gr.5210006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Given that humans have about the same number of genes as mice and not so many more than worm, what makes us more complex? Antisense transcripts are implicated in many aspects of gene regulation. Is there a functional connection between antisense transcription and organismic complexity, that is, is antisense regulation especially prevalent in humans? We used the same robust protocol to identify antisense transcripts in humans and five other metazoan genomes (mouse, rat, chicken, fruit fly, and nematode), and found that the estimated proportions of genes involved in antisense transcription are highly sensitive to the number of transcripts included in the analysis. By controlling for transcript abundance, we find that the probability that any given transcript is putatively involved in sense-antisense regulation is no higher in humans than in other vertebrates but appears unusually high in flies and especially low in nematodes. Similarly, there is no evidence that the proportion of sense-antisense transcripts is especially higher in humans than other vertebrates in a given subset of transcript sequences such as mRNAs, coding sequences, conserved, or nonconserved transcripts. Although antisense transcription might be enriched in mammalian brains compared with nonbrain tissues, it is no more enriched in human brain than in mouse brain. Overall, therefore, while we see striking variation between multicellular animals in the abundance of antisense transcripts, there is no evidence for a link between antisense transcription and organismic complexity. More particularly, we see no evidence that humans are in any way unusual among the vertebrates in this regard. Instead, our results suggest that antisense transcription might be prevalent in almost all metazoan genomes, nematodes being an unexplained exception.
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Sun M, Hurst LD, Carmichael GG, Chen J. Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Res 2005; 33:5533-43. [PMID: 16204454 PMCID: PMC1243798 DOI: 10.1093/nar/gki852] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although both the 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs may play a crucial role in posttranscriptional gene regulation, we observe that cis-encoded natural antisense RNAs have a striking preferential complementarity to the 3'-UTRs of their target genes in mammalian (human and mouse) genomes. A null neutral model, evoking differences in the rate of 3'-UTR and 5'-UTR extension, could potentially explain high rates of 3'-to-3' overlap compared with 5'-to-5' overlap. However, employing a simulation model we show that this null model probably cannot explain the finding that 3'-to-3' overlapping pairs have a much higher probability (>5 times) of conservation in both mouse and human genomes with the same overlapping pattern than do 5'-to-5' overlaps. Furthermore, it certainly cannot explain the finding that overlapping pairs seen in both genomes have a significantly higher probability of having co-expression and inverse expression (i.e. characteristic of sense-antisense regulation) than do overlapping pairs seen in only one of the two species. We infer that the function of many 3'-to-3' overlaps is indeed antisense regulation. These findings underscore the preference for, and conservation of, 3'-UTR-targeted antisense regulation, and the importance of 3'-UTRs in gene regulation.
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Abstract
Double-stranded RNA (dsRNA) is often formed in the nuclei of mammalian cells, but in this compartment it does not induce the effects characteristic of cytoplasmic dsRNA. Rather, recent work has suggested that nuclear dsRNA is a target for the ADAR class of enzymes, which deaminate adenosines to inosines. Further, there are a number of distinct fates of such edited RNA, including nuclear retention and perhaps also gene silencing.
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Chen J, Sun M, Hurst LD, Carmichael GG, Rowley JD. Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Trends Genet 2005; 21:326-9. [PMID: 15922830 DOI: 10.1016/j.tig.2005.04.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 02/18/2005] [Accepted: 04/07/2005] [Indexed: 11/22/2022]
Abstract
Is sense-antisense (SA) pairing of transcripts a common mode of gene regulation in the human genome? Although >20% of human genes might form SA pairs, the extent to which they are involved in antisense regulation is unknown. Simultaneous expression of paired sense and antisense genes is an essential step and an important indicator of antisense regulation. In this article, we demonstrate that human SA pairs tend to be co-expressed and/or inversely expressed more frequently than expected by chance. Moreover, co-expressed and inversely expressed SA pairs exhibit a striking pattern of evolutionary conservation. These findings suggest that antisense regulation is a common and important mechanism of gene regulation in the human genome.
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Wang Q, Zhang Z, Blackwell K, Carmichael GG. Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin. Curr Biol 2005; 15:384-91. [PMID: 15723802 DOI: 10.1016/j.cub.2005.01.046] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Revised: 11/27/2004] [Accepted: 11/30/2004] [Indexed: 01/09/2023]
Abstract
The fate of double-stranded RNA (dsRNA) in the cell depends on both its length and location . The expression of dsRNA in the nucleus leads to several distinct consequences. First, the promiscuous deamination of adenosines to inosines by dsRNA-specific adenosine deaminase (ADAR) can lead to the nuclear retention of edited transcripts . Second, dsRNAs might induce heterochromatic gene silencing through an RNAi-related mechanism . Is RNA editing also connected to heterochromatin? We report that members of the conserved Vigilin class of proteins have a high affinity for inosine-containing RNAs. In agreement with other work , we find that these proteins localize to heterochromatin and that mutation or depletion of the Drosophila Vigilin, DDP1, leads to altered nuclear morphology and defects in heterochromatin and chromosome segregation. Furthermore, nuclear Vigilin is found in complexes containing not only the editing enzyme ADAR1 but also RNA helicase A and Ku86/70. In the presence of RNA, the Vigilin complex recruits the DNA-PKcs enzyme, which appears to phosphorylate a discrete set of targets, some or all of which are known to participate in chromatin silencing. These results are consistent with a mechanistic link between components of the DNA-repair machinery and RNA-mediated gene silencing.
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Chen J, Sun M, Hurst LD, Carmichael GG, Rowley JD. Human antisense genes have unusually short introns: evidence for selection for rapid transcription. Trends Genet 2005; 21:203-7. [PMID: 15797613 DOI: 10.1016/j.tig.2005.02.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We suggest that small introns are favored in genes requiring a minimal response time ('nimble' genes), and that antisense genes might be prime candidates for such nimble genes. In this article, we show that antisense genes have significantly shorter introns than all other gene categories, which supports our proposal that the short introns of antisense genes might be functionally important and integrally related to their potential role in efficient gene regulation.
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Abstract
Recent bioinformatic analyses suggest that almost all human transcripts are edited by adenosine deaminases; most of this editing is in Alu elements. Recent bioinformatic analyses suggest that almost all human transcripts are edited by adenosine deaminases (ADARs), converting adenosines to inosines. Most of this editing is in Alu element transcripts, which are unique to primates. This editing might have no function or might be involved in functions such as the regulation of splicing, chromatin or nuclear localization of transcripts.
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Wang Q, Carmichael GG. Effects of length and location on the cellular response to double-stranded RNA. Microbiol Mol Biol Rev 2004; 68:432-52, table of contents. [PMID: 15353564 PMCID: PMC515255 DOI: 10.1128/mmbr.68.3.432-452.2004] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since double-stranded RNA (dsRNA) has not until recently generally been thought to be deliberately expressed in cells, it has commonly been assumed that the major source of cellular dsRNA is viral infections. In this view, the cellular responses to dsRNA would be natural and perhaps ancient antiviral responses. While the cell may certainly react to some dsRNAs as an antiviral response, this does not represent the only response or even, perhaps, the major one. A number of recent observations have pointed to the possibility that dsRNA molecules are not seen only as evidence of viral infection or recognized for degradation because they cannot be translated. In some instances they may also play important roles in normal cell growth and function. The purpose of this review is to outline our current understanding of the fate of dsRNA in cells, with a focus on the apparent fact that their fates and functions appear to depend critically not only on where in the cell dsRNA molecules are found, but also on how long they are and perhaps on how abundant they are.
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Zhang Z, Carmichael GG. Methods for the analysis of adenosine-to-inosine editing in RNA. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2004; 257:75-84. [PMID: 14769997 DOI: 10.1385/1-59259-750-5:075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
In this work we describe methods for the analysis of RNAs that have been edited by the double-strand RNA-specific adenosine deaminase, ADAR. These RNAs contain inosine residues that can be detected and quantified by a variety of approaches, including base hydrolysis and thin-layer chromatography, reverse transcription polymerase chain reaction, primer extension, and inosine-specific base cleavage. The most common method for the analysis of editing will be described here. This method involves complete hydrolysis of edited RNAs to nucleoside monophosphates, followed by separation of the products using thin-layer chromatography.
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MESH Headings
- Animals
- Antiviral Agents/immunology
- Antiviral Agents/metabolism
- Antiviral Agents/pharmacology
- Gene Silencing/drug effects
- Genome, Viral
- HIV-1/drug effects
- HIV-1/genetics
- HIV-1/growth & development
- HIV-1/immunology
- Humans
- Mice
- Poliovirus/drug effects
- Poliovirus/genetics
- Poliovirus/growth & development
- Poliovirus/immunology
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- RNA, Double-Stranded/pharmacology
- RNA, Small Interfering
- RNA, Untranslated/genetics
- RNA, Untranslated/immunology
- RNA, Untranslated/metabolism
- RNA, Untranslated/pharmacology
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Virus Replication/drug effects
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Zhang Z, Carmichael GG. The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell 2001; 106:465-75. [PMID: 11525732 DOI: 10.1016/s0092-8674(01)00466-4] [Citation(s) in RCA: 377] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
How do cells discriminate between selectively edited mRNAs that encode new protein isoforms, and dsRNA-induced, promiscuously edited RNAs that encode nonfunctional, mutant proteins? We have developed a Xenopus oocyte model system which shows that a variety of hyperedited, inosine-containing RNAs are specifically retained in the nucleus. To uncover the mechanism of inosine-induced retention, HeLa cell nuclear extracts were used to isolate a multiprotein complex that binds specifically and cooperatively to inosine-containing RNAs. This complex contains the inosine-specific RNA binding protein p54(nrb), the splicing factor PSF, and the inner nuclear matrix structural protein matrin 3. We provide evidence that one function of the complex identified here is to anchor hyperedited RNAs to the nuclear matrix, while allowing selectively edited mRNAs to be exported.
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Huang Y, Wimler KM, Carmichael GG. Intronless mRNA transport elements may affect multiple steps of pre-mRNA processing. EMBO J 1999; 18:1642-52. [PMID: 10075934 PMCID: PMC1171251 DOI: 10.1093/emboj/18.6.1642] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have reported recently that a small element within the mouse histone H2a-coding region permits efficient cytoplasmic accumulation of intronless beta-globin cDNA transcripts. This sequence lowers the levels of spliced products from intron-containing constructs and can functionally replace Rev and the Rev-responsive element (RRE) in the nuclear export of unspliced HIV-1-related mRNAs. In work reported here, we further investigate the molecular mechanisms by which this element might work. We demonstrate here through both in vivo and in vitro assays that, in addition to promoting mRNA nuclear export, this element acts as a polyadenylation enhancer and as a potent inhibitor of splicing. Surprisingly, two other described intronless mRNA transport elements (from the herpes simplex virus thymidine kinase gene and hepatitis B virus) appear to function in a similar manner. These findings prompt us to suggest that a general feature of intronless mRNA transport elements might be a collection of phenotypes, including the inhibition of splicing and the enhancement of both polyadenylation and mRNA export.
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