201
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A Function for the hnRNP A1/A2 Proteins in Transcription Elongation. PLoS One 2015; 10:e0126654. [PMID: 26011126 PMCID: PMC4444011 DOI: 10.1371/journal.pone.0126654] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 03/13/2015] [Indexed: 12/16/2022] Open
Abstract
The hnRNP A1 and A2 proteins regulate processes such as alternative pre-mRNA splicing and mRNA stability. Here, we report that a reduction in the levels of hnRNP A1 and A2 by RNA interference or their cytoplasmic retention by osmotic stress drastically increases the transcription of a reporter gene. Based on previous work, we propose that this effect may be linked to a decrease in the activity of the transcription elongation factor P-TEFb. Consistent with this hypothesis, the transcription of the reporter gene was stimulated when the catalytic component of P-TEFb, CDK9, was inhibited with DRB. While low levels of A1/A2 stimulated the association of RNA polymerase II with the reporter gene, they also increased the association of CDK9 with the repressor 7SK RNA, and compromised the recovery of promoter-distal transcription on the Kitlg gene after the release of pausing. Transcriptome analysis revealed that more than 50% of the genes whose expression was affected by the siRNA-mediated depletion of A1/A2 were also affected by DRB. RNA polymerase II-chromatin immunoprecipitation assays on DRB-treated and A1/A2-depleted cells identified a common set of repressed genes displaying increased occupancy of polymerases at promoter-proximal locations, consistent with pausing. Overall, our results suggest that lowering the levels of hnRNP A1/A2 elicits defective transcription elongation on a fraction of P-TEFb-dependent genes, hence favoring the transcription of P-TEFb-independent genes.
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202
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Abstract
Efficient transcription of the HIV-1 genome is regulated by Tat, which recruits P-TEFb from the 7SK small nuclear ribonucleoprotein (snRNP) and other nucleoplasmic complexes to phosphorylate RNA polymerase II and other factors associated with the transcription complex. Although Tat activity is dependent on its binding to the viral TAR sequence, little is known about the cellular factors that might also assemble onto this region of the viral transcript. Here, we report that the splicing factor SRSF1 (SF2/ASF) and Tat recognize overlapping sequences within TAR and the 7SK RNA. SRSF1 expression can inhibit Tat transactivation by directly competing for its binding to TAR. Additionally, we provide evidence that SRSF1 can increase the basal level of viral transcription in the absence of Tat. We propose that SRSF1 activates transcription in the early stages of viral infection by recruiting P-TEFb to TAR from the 7SK snRNP. Whereas in the later stages, Tat substitutes for SRSF1 by promoting release of the stalled polymerase and more efficient transcriptional elongation.
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Affiliation(s)
- Sean Paz
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA
| | | | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA
- To whom correspondence should be addressed. Tel: +1 5612970627;
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203
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Eshar S, Altenhofen L, Rabner A, Ross P, Fastman Y, Mandel-Gutfreund Y, Karni R, Llinás M, Dzikowski R. PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs. Mol Microbiol 2015; 96:1283-97. [PMID: 25807998 DOI: 10.1111/mmi.13007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2015] [Indexed: 11/28/2022]
Abstract
Plasmodium species have evolved complex biology to adapt to different hosts and changing environments throughout their life cycle. Remarkably, these adaptations are achieved by a relatively small genome. One way by which the parasite expands its proteome is through alternative splicing (AS). We recently identified PfSR1 as a bona fide Ser/Arg-rich (SR) protein that shuttles between the nucleus and cytoplasm and regulates AS in Plasmodium falciparum. Here we show that PfSR1 is localized adjacent to the Nuclear Pore Complex (NPC) clusters in the nucleus of early stage parasites. To identify the endogenous RNA targets of PfSR1, we adapted an inducible overexpression system for tagged PfSR1 and performed RNA immunoprecipitation followed by microarray analysis (RIP-chip) to recover and identify the endogenous RNA targets that bind PfSR1. Bioinformatic analysis of these RNAs revealed common sequence motifs potentially recognized by PfSR1. RNA-EMSAs show that PfSR1 preferentially binds RNA molecules containing these motifs. Interestingly, we find that PfSR1 not only regulates AS but also the steady-state levels of mRNAs containing these motifs in vivo.
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Affiliation(s)
- Shiri Eshar
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Lindsey Altenhofen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.,Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Alona Rabner
- Department of Biology, Israel Institute of Technology-Technion, Haifa, Israel
| | - Phil Ross
- Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Yair Fastman
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | | | - Rotem Karni
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Manuel Llinás
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.,Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Ron Dzikowski
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
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204
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SRSF1 RNA Recognition Motifs Are Strong Inhibitors of HIV-1 Replication. J Virol 2015; 89:6275-86. [PMID: 25855733 DOI: 10.1128/jvi.00693-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/27/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Replication of the integrated HIV-1 genome is tightly regulated by a series of cellular factors. In previous work we showed that transactivation of the HIV-1 promoter is regulated by the cellular splicing factor SRSF1. Here we report that SRSF1 can downregulate the replication of B, C, and D subtype viruses by >200-fold in a cell culture system. We show that viral transcription and splicing are inhibited by SRSF1 expression. Furthermore, SRSF1 deletion mutants containing the protein RNA-binding domains but not the arginine serine-rich activator domain can downregulate viral replication by >2,000-fold with minimal impact on cell viability and apoptosis. These data suggest a therapeutic potential for SRSF1 and its RNA-binding domains. IMPORTANCE Most drugs utilized to treat the HIV-1 infection are based on compounds that directly target proteins encoded by the virus. However, given the high viral mutation rate, the appearance of novel drug-resistant viral strains is common. Thus, there is a need for novel therapeutics with diverse mechanisms of action. In this study, we show that the cellular protein SRSF1 is a strong inhibitor of viral replication. Furthermore, expression of the SRSF1 RNA-binding domains alone can inhibit viral replication by >2,000-fold in multiple viral strains without impacting cell viability. Given the strong antiviral properties of this protein, the RNA-binding domains, and the minimal effects observed on cell metabolism, further studies are warranted to assess the therapeutic potential of peptides derived from these sequences.
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205
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Shi J, Pabon K, Scotto KW. Methylxanthines Increase Expression of the Splicing Factor SRSF2 by Regulating Multiple Post-transcriptional Mechanisms. J Biol Chem 2015; 290:14986-5003. [PMID: 25818199 DOI: 10.1074/jbc.m114.624254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Indexed: 01/20/2023] Open
Abstract
We have previously reported that the methylxanthine caffeine increases expression of the splicing factor SRSF2, the levels of which are normally controlled by a negative autoregulatory loop. In the present study we have investigated the mechanisms by which methylxanthines induce this aberrant overexpression. RT-PCR analyses suggested little impact of caffeine on SRSF2 total mRNA levels. Instead, caffeine induced changes in the levels of SRSF2 3' UTR splice variants. Although some of these variants were substrates for nonsense-medicated decay (NMD), and could potentially have been stabilized by caffeine-mediated inhibition of NMD, down-regulation of NMD by a genetic approach was not sufficient to reproduce the phenotype. Furthermore, cell-based assays demonstrated that some of the caffeine-induced variants were intrinsically more efficiently translated than others; the addition of caffeine increased the translational efficiency of most SRSF2 transcripts. MicroRNA array analyses revealed a significant caffeine-mediated decrease in the expression of two SRSF2-targeting miRs, both of which were shown to repress translation of specific SRSF2 splice variants. These data support a complex model whereby caffeine down-regulates SRSF2-targeting microRNAs, leading to an increase in SRSF2 translation, which in turn induces SRSF2 splicing. SRSF2 splice variants are then stabilized by caffeine-mediated NMD inhibition, breaking the normal negative feedback loop and allowing the aberrant increase in SRSF2 protein levels. These findings highlight the complexity of SRSF2 gene regulation, and suggest ways in which SRSF2 expression may be dysregulated in disease.
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Affiliation(s)
- Jia Shi
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
| | - Kirk Pabon
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
| | - Kathleen W Scotto
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
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206
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Merkin JJ, Chen P, Alexis MS, Hautaniemi SK, Burge CB. Origins and impacts of new mammalian exons. Cell Rep 2015; 10:1992-2005. [PMID: 25801031 DOI: 10.1016/j.celrep.2015.02.058] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/09/2015] [Accepted: 02/23/2015] [Indexed: 02/08/2023] Open
Abstract
Mammalian genes are composed of exons, but the evolutionary origins and functions of new internal exons are poorly understood. Here, we analyzed patterns of exon gain using deep cDNA sequencing data from five mammals and one bird, identifying thousands of species- and lineage-specific exons. Most new exons derived from unique rather than repetitive intronic sequence. Unlike exons conserved across mammals, species-specific internal exons were mostly located in 5' UTRs and alternatively spliced. They were associated with upstream intronic deletions, increased nucleosome occupancy, and RNA polymerase II pausing. Genes containing new internal exons had increased gene expression, but only in tissues in which the exon was included. Increased expression correlated with the level of exon inclusion, promoter proximity, and signatures of cotranscriptional splicing. Altogether, these findings suggest that increased splicing at the 5' ends of genes enhances expression and that changes in 5' end splicing alter gene expression between tissues and between species.
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Affiliation(s)
- Jason J Merkin
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Ping Chen
- Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, University of Helsinki, 00014 Helsinki, Finland
| | - Maria S Alexis
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sampsa K Hautaniemi
- Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, University of Helsinki, 00014 Helsinki, Finland
| | - Christopher B Burge
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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207
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Myosin VI regulates gene pairing and transcriptional pause release in T cells. Proc Natl Acad Sci U S A 2015; 112:E1587-93. [PMID: 25770220 DOI: 10.1073/pnas.1502461112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Naive CD4 T cells differentiate into several effector lineages, which generate a stronger and more rapid response to previously encountered immunological challenges. Although effector function is a key feature of adaptive immunity, the molecular basis of this process is poorly understood. Here, we investigated the spatiotemporal regulation of cytokine gene expression in resting and restimulated effector T helper 1 (Th1) cells. We found that the Lymphotoxin (LT)/TNF alleles, which encode TNF-α, were closely juxtaposed shortly after T-cell receptor (TCR) engagement, when transcription factors are limiting. Allelic pairing required a nuclear myosin, myosin VI, which is rapidly recruited to the LT/TNF locus upon restimulation. Furthermore, transcription was paused at the TNF locus and other related genes in resting Th1 cells and released in a myosin VI-dependent manner following activation. We propose that homologous pairing and myosin VI-mediated transcriptional pause release account for the rapid and efficient expression of genes induced by an external stimulus.
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208
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Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions. Proc Natl Acad Sci U S A 2015; 112:3841-6. [PMID: 25755260 DOI: 10.1073/pnas.1502971112] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
More than a thousand proteins are thought to contribute to mammalian chromatin and its regulation, but our understanding of the genomic occupancy and function of most of these proteins is limited. Here we describe an approach, which we call "chromatin proteomic profiling," to identify proteins associated with genomic regions marked by specifically modified histones. We used ChIP-MS to identify proteins associated with genomic regions marked by histones modified at specific lysine residues, including H3K27ac, H3K4me3, H3K79me2, H3K36me3, H3K9me3, and H4K20me3, in ES cells. We identified 332 known and 114 novel proteins associated with these histone-marked genomic segments. Many of the novel candidates have been implicated in various diseases, and their chromatin association may provide clues to disease mechanisms. More than 100 histone modifications have been described, so similar chromatin proteomic profiling studies should prove to be valuable for identifying many additional chromatin-associated proteins in a broad spectrum of cell types.
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209
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Jonkers I, Lis JT. Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2015; 16:167-77. [PMID: 25693130 PMCID: PMC4782187 DOI: 10.1038/nrm3953] [Citation(s) in RCA: 572] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances in sequencing techniques that measure nascent transcripts and that reveal the positioning of RNA polymerase II (Pol II) have shown that the pausing of Pol II in promoter-proximal regions and its release to initiate a phase of productive elongation are key steps in transcription regulation. Moreover, after the release of Pol II from the promoter-proximal region, elongation rates are highly dynamic throughout the transcription of a gene, and vary on a gene-by-gene basis. Interestingly, Pol II elongation rates affect co-transcriptional processes such as splicing, termination and genome stability. Increasing numbers of factors and regulatory mechanisms have been associated with the steps of transcription elongation by Pol II, revealing that elongation is a highly complex process. Elongation is thus now recognized as a key phase in the regulation of transcription by Pol II.
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Affiliation(s)
- Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, 416 Biotechnology Building, 14853, Ithaca, New York, USA
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210
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A role for the serine/arginine-rich (SR) protein B52/SRSF6 in cell growth and myc expression in Drosophila. Genetics 2015; 199:1201-11. [PMID: 25680814 PMCID: PMC4391563 DOI: 10.1534/genetics.115.174391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/11/2015] [Indexed: 11/18/2022] Open
Abstract
Serine-/arginine-rich (SR) proteins are RNA-binding proteins that are primarily involved in alternative splicing. Expression of some SR proteins is frequently upregulated in tumors, and previous reports have demonstrated that these proteins can directly participate in cell transformation. Identifying factors that can rescue the effects of SR overexpression in vivo is, therefore, of potential therapeutic interest. Here, we analyzed phenotypes induced by overexpression of the SR protein B52 during Drosophila development and identified several proteins that can rescue these phenotypes. Using the mechanosensory bristle lineage as a developmental model, we show that B52 expression level influences cell growth, but not differentiation, in this lineage. In particular, B52 overexpression increases cell growth, upregulates myc transcription, and gives rise to flies lacking thoracic bristles. Using a genetic screen, we identified several suppressors of the phenotypes induced by overexpression of B52 in vivo in two different organs. We show that upregulation of brain tumor (brat), a tumor suppressor and post-transcriptional repressor of myc, and downregulation of lilliputian (lilli), a subunit of the superelongation complex involved in transcription elongation, efficiently rescue the phenotypes induced by B52 overexpression. Our results demonstrate a role of this SR protein in cell growth and identify candidate proteins that may overcome the effects of SR protein overexpression in mammals.
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211
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Mo S, Ji X, Fu XD. Unique role of SRSF2 in transcription activation and diverse functions of the SR and hnRNP proteins in gene expression regulation. Transcription 2015; 4:251-9. [PMID: 24406341 DOI: 10.4161/trns.26932] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcription pause release from gene promoters has been recognized to be a critical point for transcriptional regulation in higher eukaryotes. Recent studies suggest that regulatory RNAs are extensively involved in transcriptional control, which may enlist various RNA binding proteins. We recently showed a key role of SRSF2, a member of the SR family of splicing regulators, in binding to promoter-associated small RNA to mediate transcription pause release, a regulatory strategy akin to the function of the HIV Tat protein via binding to the TAR element in nascent RNA to activate transcription. In this report, we further dissect the structural requirement for SRSF2 to function as a transcription activator and extend the analysis to multiple SR and hnRNP proteins by using the MS2 tethering strategy. Our results reveal that SRSF2 is a unique SR protein that activates transcription in a position-dependent manner while three other SR proteins enhance translation in a position-independent fashion. In contrast, multiple hnRNP proteins appear to negatively influence mRNA levels, especially when tethered in the gene body. These findings suggest broad participation of RNA binding proteins in diverse aspects of regulated gene expression at both the transcriptional and posttranscriptional levels in mammalian cells.
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212
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Fujinaga K, Luo Z, Peterlin BM. Genetic analysis of the structure and function of 7SK small nuclear ribonucleoprotein (snRNP) in cells. J Biol Chem 2015; 289:21181-90. [PMID: 24917669 DOI: 10.1074/jbc.m114.557751] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The positive transcription elongation factor b (P-TEFb), comprised of cyclin-dependent kinase 9 (CDK9) and cyclins T1 (CycT1) or T2 (CycT2), activates eukaryotic transcription elongation. In growing cells, P-TEFb exists in active and inactive forms. In the latter, it is incorporated into the 7SK small nuclear ribonucleoprotein, which contains hexamethylene bisacetamide-induced proteins (HEXIM) 1 or 2, La-related protein 7 (LaRP7), methyl phosphate capping enzyme, and 7SK small nuclear RNA (7SK). HEXIM1 inhibits the kinase activity of CDK9 via interactions between 7SK, HEXIM1, and CycT1. LaRP7 and methyl phosphate capping enzyme interact with 7SK independently of HEXIM1 and P-TEFb. To analyze genetic interactions between HEXIM1 and/or LaRP7 and 7SK using a cell-based system, we established artificial heterologous RNA tethering assays in which reporter gene expression depended on interactions between selected regions of 7SK and its cognate binding partners fused to a strong activator. This system enabled us to map the HEXIM1- and LaRP7- binding regions of 7SK. Assays with various mutant 7SK plasmid targets revealed that the 5'U-Ubulge and central loop of stem-loop I or RNA motif 3 of 7SK are required for transactivation, suggesting that HEXIM1 and CycT1 form a combinatorial binding surface for 7SK. Moreover, a region in HEXIM1 C-terminal to its previously mapped RNA-binding motif was also required for interactions between HEXIM1 and 7SK. Finally, a tyrosine-to-alanine mutation in HEXIM1, which is critical for its inhibitory effect on CDK9, changed HEXIM1 into an activator. These cell-based assays elucidate this important aspect of transcription elongation in vivo.
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213
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Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, Zhu P, Chang Z, Wu Q, Zhao Y, Jia Y, Xu P, Liu H, Shan G. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol 2015; 22:256-64. [PMID: 25664725 DOI: 10.1038/nsmb.2959] [Citation(s) in RCA: 2029] [Impact Index Per Article: 225.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/19/2014] [Indexed: 02/06/2023]
Abstract
Noncoding RNAs (ncRNAs) have numerous roles in development and disease, and one of the prominent roles is to regulate gene expression. A vast number of circular RNAs (circRNAs) have been identified, and some have been shown to function as microRNA sponges in animal cells. Here, we report a class of circRNAs associated with RNA polymerase II in human cells. In these circRNAs, exons are circularized with introns 'retained' between exons; we term them exon-intron circRNAs or EIciRNAs. EIciRNAs predominantly localize in the nucleus, interact with U1 snRNP and promote transcription of their parental genes. Our findings reveal a new role for circRNAs in regulating gene expression in the nucleus, in which EIciRNAs enhance the expression of their parental genes in cis, and highlight a regulatory strategy for transcriptional control via specific RNA-RNA interaction between U1 snRNA and EIciRNAs.
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Affiliation(s)
- Zhaoyong Li
- 1] School of Life Sciences, University of Science and Technology of China, Hefei, China. [2] Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China
| | - Chuan Huang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chun Bao
- 1] School of Life Sciences, University of Science and Technology of China, Hefei, China. [2] Department of Physics, Central China Normal University, Wuhan, China. [3] Institute of Biophysics, Central China Normal University, Wuhan, China
| | - Liang Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Mei Lin
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaolin Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Guolin Zhong
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Bin Yu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wanchen Hu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Limin Dai
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Pengfei Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhaoxia Chang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Ya Jia
- 1] Department of Physics, Central China Normal University, Wuhan, China. [2] Institute of Biophysics, Central China Normal University, Wuhan, China
| | - Ping Xu
- National Center for Protein Sciences, Beijing, China
| | - Huijie Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ge Shan
- 1] School of Life Sciences, University of Science and Technology of China, Hefei, China. [2] Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China
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214
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Xue F, Li X, Zhao X, Wang L, Liu M, Shi R, Zheng J. SRSF1 facilitates cytosolic DNA-induced production of type I interferons recognized by RIG-I. PLoS One 2015; 10:e0115354. [PMID: 25658361 PMCID: PMC4319963 DOI: 10.1371/journal.pone.0115354] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Evidence has shown that psoriasis is closely associated with infection; however, the mechanism of this association remains unclear. In mammalian cells, viral or bacterial infection is accompanied by the release of cytosolic DNA, which in turn triggers the production of type-I interferons (IFNs). Type I IFNs and their associated genes are significantly upregulated in psoriatic lesions. RIG-I is also highly upregulated in psoriatic lesions and is responsible for IFN production. However, RIG-I mediated regulatory signaling in psoriasis is poorly understood. METHODS We screened a cDNA library and identified potential RIG-I interacting partners that may play a role in psoriasis. RESULTS We found that serine/arginine-rich splicing factor 1 (SRSF1) could specifically interact with RIG-I to facilitate RIG-I mediated production of type-I IFN that is triggered by cytosolic DNA. We found SRSF1 associates with RNA polymerase III and RIG-I in a DNA-dependent manner. In addition, treatment with a TNFα inhibitor downregulated SRSF1 expression in peripheral blood mononuclear cells (PBMCs) from psoriasis vulgaris patients. DISCUSSION Based on the abundance of pathogenic cytosolic DNA that is detected in psoriatic lesions, our finding that RIG-I interacts with SRSF1 to regulate type-I IFN production reveals a critical link regarding how cytosolic DNA specifically activates aberrant IFN expression. These data may provide new therapeutic targets for the treatment of psoriasis.
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Affiliation(s)
- Feng Xue
- Laboratory of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Li
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqing Zhao
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanqi Wang
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Min Liu
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruofei Shi
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Zheng
- Laboratory of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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215
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Sei E, Wang T, Hunter OV, Xie Y, Conrad NK. HITS-CLIP analysis uncovers a link between the Kaposi's sarcoma-associated herpesvirus ORF57 protein and host pre-mRNA metabolism. PLoS Pathog 2015; 11:e1004652. [PMID: 25710169 PMCID: PMC4339584 DOI: 10.1371/journal.ppat.1004652] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/02/2015] [Indexed: 11/19/2022] Open
Abstract
The Kaposi's sarcoma associated herpesvirus (KSHV) is an oncogenic virus that causes Kaposi's sarcoma, primary effusion lymphoma (PEL), and some forms of multicentric Castleman's disease. The KSHV ORF57 protein is a conserved posttranscriptional regulator of gene expression that is essential for virus replication. ORF57 is multifunctional, but most of its activities are directly linked to its ability to bind RNA. We globally identified virus and host RNAs bound by ORF57 during lytic reactivation in PEL cells using high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP). As expected, ORF57-bound RNA fragments mapped throughout the KSHV genome, including the known ORF57 ligand PAN RNA. In agreement with previously published ChIP results, we observed that ORF57 bound RNAs near the oriLyt regions of the genome. Examination of the host RNA fragments revealed that a subset of the ORF57-bound RNAs was derived from transcript 5' ends. The position of these 5'-bound fragments correlated closely with the 5'-most exon-intron junction of the pre-mRNA. We selected four candidates (BTG1, EGR1, ZFP36, and TNFSF9) and analyzed their pre-mRNA and mRNA levels during lytic phase. Analysis of both steady-state and newly made RNAs revealed that these candidate ORF57-bound pre-mRNAs persisted for longer periods of time throughout infection than control RNAs, consistent with a role for ORF57 in pre-mRNA metabolism. In addition, exogenous expression of ORF57 was sufficient to increase the pre-mRNA levels and, in one case, the mRNA levels of the putative ORF57 targets. These results demonstrate that ORF57 interacts with specific host pre-mRNAs during lytic reactivation and alters their processing, likely by stabilizing pre-mRNAs. These data suggest that ORF57 is involved in modulating host gene expression in addition to KSHV gene expression during lytic reactivation.
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Affiliation(s)
- Emi Sei
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tao Wang
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Olga V. Hunter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yang Xie
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nicholas K. Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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216
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Mauger O, Klinck R, Chabot B, Muchardt C, Allemand E, Batsché E. Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions. Nucleic Acids Res 2015; 43:1869-82. [PMID: 25605796 PMCID: PMC4330376 DOI: 10.1093/nar/gkv013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Alternative splicing is the main source of proteome diversity. Here, we have investigated how alternative splicing affects the function of two human histone methyltransferases (HMTase): G9A and SUV39H2. We show that exon 10 in G9A and exon 3 in SUV39H2 are alternatively included in a variety of tissues and cell lines, as well as in a different species. The production of these variants is likely tightly regulated because both constitutive and alternative splicing factors control their splicing profiles. Based on this evidence, we have assessed the link between the inclusion of these exons and the activity of both enzymes. We document that these HMTase genes yield several protein isoforms, which are likely issued from alternative splicing regulation. We demonstrate that inclusion of SUV39H2 exon 3 is a determinant of the stability, the sub-nuclear localization, and the HMTase activity. Genome-wide expression analysis further revealed that alternative inclusion of SUV39H2 exon 3 differentially modulates the expression of target genes. Our data also suggest that a variant of G9A may display a function that is independent of H3K9 methylation. Our work emphasizes that expression and function of genes are not collinear; therefore alternative splicing must be taken into account in any functional study.
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Affiliation(s)
- Oriane Mauger
- Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 6, IFD, 4 Place Jussieu, 75252 PARIS cedex 05, France Institut Pasteur, Département de Biologie du Développement et Cellules Souches, CNRS URA2578, Unité de Régulation Epigénétique, 25 rue du Docteur Roux, Paris, 75015, France
| | - Roscoe Klinck
- Laboratory of Functional Genomics of the Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Benoit Chabot
- Laboratory of Functional Genomics of the Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke. Québec, J1E 4K8, Canada
| | - Christian Muchardt
- Institut Pasteur, Département de Biologie du Développement et Cellules Souches, CNRS URA2578, Unité de Régulation Epigénétique, 25 rue du Docteur Roux, Paris, 75015, France
| | - Eric Allemand
- Institut Pasteur, Département de Biologie du Développement et Cellules Souches, CNRS URA2578, Unité de Régulation Epigénétique, 25 rue du Docteur Roux, Paris, 75015, France
| | - Eric Batsché
- Institut Pasteur, Département de Biologie du Développement et Cellules Souches, CNRS URA2578, Unité de Régulation Epigénétique, 25 rue du Docteur Roux, Paris, 75015, France
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217
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Bradley T, Cook ME, Blanchette M. SR proteins control a complex network of RNA-processing events. RNA (NEW YORK, N.Y.) 2015; 21:75-92. [PMID: 25414008 PMCID: PMC4274639 DOI: 10.1261/rna.043893.113] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 10/15/2014] [Indexed: 05/23/2023]
Abstract
SR proteins are a well-conserved class of RNA-binding proteins that are essential for regulation of splice-site selection, and have also been implicated as key regulators during other stages of RNA metabolism. For many SR proteins, the complexity of the RNA targets and specificity of RNA-binding location are poorly understood. It is also unclear if general rules governing SR protein alternative pre-mRNA splicing (AS) regulation uncovered for individual SR proteins on few model genes, apply to the activity of all SR proteins on endogenous targets. Using RNA-seq, we characterize the global AS regulation of the eight Drosophila SR protein family members. We find that a majority of AS events are regulated by multiple SR proteins, and that all SR proteins can promote exon inclusion, but also exon skipping. Most coregulated targets exhibit cooperative regulation, but some AS events are antagonistically regulated. Additionally, we found that SR protein levels can affect alternative promoter choices and polyadenylation site selection, as well as overall transcript levels. Cross-linking and immunoprecipitation coupled with high-throughput sequencing (iCLIP-seq), reveals that SR proteins bind a distinct and functionally diverse class of RNAs, which includes several classes of noncoding RNAs, uncovering possible novel functions of the SR protein family. Finally, we find that SR proteins exhibit positional RNA binding around regulated AS events. Therefore, regulation of AS by the SR proteins is the result of combinatorial regulation by multiple SR protein family members on most endogenous targets, and SR proteins have a broader role in integrating multiple layers of gene expression regulation.
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Affiliation(s)
- Todd Bradley
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Malcolm E Cook
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Marco Blanchette
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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218
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Stubbs SH, Conrad NK. Depletion of REF/Aly alters gene expression and reduces RNA polymerase II occupancy. Nucleic Acids Res 2014; 43:504-19. [PMID: 25477387 PMCID: PMC4288173 DOI: 10.1093/nar/gku1278] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pre-mRNA processing is mechanistically linked to transcription with RNA pol II serving as a platform to recruit RNA processing factors to nascent transcripts. The TREX complex member, REF/Aly, has been suggested to play roles in transcription and nuclear RNA stability in addition to its more broadly characterized role in mRNA export. We employed RNA-seq to identify a subset of transcripts with decreased expression in both nuclear and cytoplasmic fractions upon REF/Aly knockdown, which implies that REF/Aly affects their expression upstream of its role in mRNA export. Transcription inhibition experiments and metabolic labeling assays argue that REF/Aly does not affect stability of selected candidate transcripts. Instead, ChIP assays and nuclear run-on analysis reveal that REF/Aly depletion diminishes the transcription of these candidate genes. Furthermore, we determined that REF/Aly binds directly to candidate transcripts, supporting a direct effect of REF/Aly on candidate gene transcription. Taken together, our data suggest that the importance of REF/Aly is not limited to RNA export, but that REF/Aly is also critical for gene expression at the level of transcription. Our data are consistent with the model that REF/Aly is involved in linking splicing with transcription efficiency.
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Affiliation(s)
- Sarah H Stubbs
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9048, USA
| | - Nicholas K Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9048, USA
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219
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Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature 2014; 518:249-53. [PMID: 25470060 DOI: 10.1038/nature13923] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 10/06/2014] [Indexed: 12/19/2022]
Abstract
DEAD-box RNA helicases are vital for the regulation of various aspects of the RNA life cycle, but the molecular underpinnings of their involvement, particularly in mammalian cells, remain poorly understood. Here we show that the DEAD-box RNA helicase DDX21 can sense the transcriptional status of both RNA polymerase (Pol) I and II to control multiple steps of ribosome biogenesis in human cells. We demonstrate that DDX21 widely associates with Pol I- and Pol II-transcribed genes and with diverse species of RNA, most prominently with non-coding RNAs involved in the formation of ribonucleoprotein complexes, including ribosomal RNA, small nucleolar RNAs (snoRNAs) and 7SK RNA. Although broad, these molecular interactions, both at the chromatin and RNA level, exhibit remarkable specificity for the regulation of ribosomal genes. In the nucleolus, DDX21 occupies the transcribed rDNA locus, directly contacts both rRNA and snoRNAs, and promotes rRNA transcription, processing and modification. In the nucleoplasm, DDX21 binds 7SK RNA and, as a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, is recruited to the promoters of Pol II-transcribed genes encoding ribosomal proteins and snoRNAs. Promoter-bound DDX21 facilitates the release of the positive transcription elongation factor b (P-TEFb) from the 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes. Our results uncover the multifaceted role of DDX21 in multiple steps of ribosome biogenesis, and provide evidence implicating a mammalian RNA helicase in RNA modification and Pol II elongation control.
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Affiliation(s)
- Eliezer Calo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ryan A Flynn
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lance Martin
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Robert C Spitale
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Joanna Wysocka
- 1] Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA [2] Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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220
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Abstract
Sequence-specific RNA-binding proteins (RBPs) bind to pre-mRNA to control alternative splicing, but it is not yet possible to read the 'splicing code' that dictates splicing regulation on the basis of genome sequence. Each alternative splicing event is controlled by multiple RBPs, the combined action of which creates a distribution of alternatively spliced products in a given cell type. As each cell type expresses a distinct array of RBPs, the interpretation of regulatory information on a given RNA target is exceedingly dependent on the cell type. RBPs also control each other's functions at many levels, including by mutual modulation of their binding activities on specific regulatory RNA elements. In this Review, we describe some of the emerging rules that govern the highly context-dependent and combinatorial nature of alternative splicing regulation.
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Affiliation(s)
- Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic, Medicine, University of California San Diego, La Jolla, California 92093–0651, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, and Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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221
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Abstract
The ability to distinguish self from non-self nucleic acids enables eukaryotes to suppress mobile elements and maintain genome integrity. In organisms from protist to human, this function is performed by RNA silencing pathways. There have been major advances in our understanding of the RNA silencing machinery, but the mechanisms by which these pathways distinguish self from non-self remain unclear. Recent studies in the yeast C. neoformans indicate that transposon-derived transcripts encode suboptimal introns and tend to stall in spliceosomes, which promotes the biogenesis of siRNA that targets these transcripts. These findings identify gene expression signal strength as a metric by which a foreign element can be distinguished from a host gene, and reveal a new function for introns and the spliceosome in genome defense. Anticipating that these principles may apply to RNA silencing in other systems, we discuss strong hints in the literature suggesting that the spliceosome may guide small RNA biogenesis in the siRNA and piRNA pathways of plants and animals.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
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222
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Moon H, Cho S, Loh TJ, Oh HK, Jang HN, Zhou J, Kwon YS, Liao DJ, Jun Y, Eom S, Ghigna C, Biamonti G, Green MR, Zheng X, Shen H. SRSF2 promotes splicing and transcription of exon 11 included isoform in Ron proto-oncogene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1132-40. [PMID: 25220236 DOI: 10.1016/j.bbagrm.2014.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 08/21/2014] [Accepted: 09/02/2014] [Indexed: 02/03/2023]
Abstract
The product of proto-oncogene Ron is a human receptor for the macrophage-stimulating protein (MSP). Upon activation, Ron is able to induce cell dissociation, migration and matrix invasion. Exon 11 skipping of Ron pre-mRNA produces Ron△165 protein that is constitutively active even in the absence of its ligand. Here we show that knockdown of SRSF2 promotes the decrease of exon 11 inclusion, whereas overexpression of SRSF2 promotes exon 11 inclusion. We demonstrate that SRSF2 promotes exon 11 inclusion through splicing and transcription procedure. We also present evidence that reduced expression of SRSF2 induces a decrease in the splicing of both introns 10 and 11; by contrast, overexpression of SRSF2 induces an increase in the splicing of introns 10 and 11. Through mutation analysis, we show that SRSF2 functionally targets and physically interacts with CGAG sequence on exon 11. In addition, we reveal that the weak strength of splice sites of exon 11 is not required for the function of SRSF2 on the splicing of Ron exon 11. Our results indicate that SRSF2 promotes exon 11 inclusion of Ron proto-oncogene through targeting exon 11. Our study provides a novel mechanism by which Ron is expressed.
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Affiliation(s)
- Heegyum Moon
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Sunghee Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Tiing Jen Loh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Hyun Kyung Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Ha Na Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Jianhua Zhou
- JiangSu Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
| | - Young-Soo Kwon
- Department of Bioscience & Biotechnology, Sejong University, Seoul 143-747, Republic of Korea
| | - D Joshua Liao
- Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Youngsoo Jun
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Soohyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Claudia Ghigna
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy
| | - Michael R Green
- Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea.
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223
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Howard JM, Sanford JR. The RNAissance family: SR proteins as multifaceted regulators of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:93-110. [PMID: 25155147 DOI: 10.1002/wrna.1260] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Abstract
Serine and arginine-rich (SR) proteins play multiple roles in the eukaryotic gene expression pathway. Initially described as constitutive and alternative splicing factors, now it is clear that SR proteins are key determinants of exon identity and function as molecular adaptors, linking the pre-messenger RNA (pre-mRNA) to the splicing machinery. In addition, now SR proteins are implicated in many aspects of mRNA and noncoding RNA (ncRNA) processing well beyond splicing. These unexpected roles, including RNA transcription, export, translation, and decay, may prove to be the rule rather than the exception. To simply define, this family of RNA-binding proteins as splicing factors belies the broader roles of SR proteins in post-transcriptional gene expression.
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Affiliation(s)
- Jonathan M Howard
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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224
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Regulation of gene expression programmes by serine–arginine rich splicing factors. Semin Cell Dev Biol 2014; 32:11-21. [DOI: 10.1016/j.semcdb.2014.03.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/11/2014] [Indexed: 12/21/2022]
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225
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Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc Natl Acad Sci U S A 2014; 111:10359-64. [PMID: 24982146 DOI: 10.1073/pnas.1409457111] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated hidden treasure 1 (HID1), as a factor promoting photomorphogenesis in continuous red light (cR). We show that HID1 acts through phytochrome-interacting factor 3 (PIF3), which encodes a basic helix-loop-helix transcription factor known to be a key repressor of photomorphogenesis. Knockdown of HID1 in hid1 mutants leads to a significant increase in the expression of PIF3, which in turn drives the development of elongated hypocotyls in cR. We identified two major stem-loops in HID1 that are essential for its modulation of hypocotyl growth in cR-grown seedlings. Furthermore, our data reveal that HID1 is assembled into large nuclear protein-RNA complex(es) and that it associates with the chromatin of the first intron of PIF3 to repress its transcription. Strikingly, phylogenetic analysis reveals that many land plants have conserved homologs of HID1 and that its rice homolog can rescue the mutant phenotype when expressed in Arabidopsis hid1 mutants. We thus concluded that HID1 is a previously uncharacterized noncoding RNA whose function represents another layer of regulation in the precise control of seedling photomorphogenesis.
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226
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Heim A, Grimm C, Müller U, Häußler S, Mackeen MM, Merl J, Hauck SM, Kessler BM, Schofield CJ, Wolf A, Böttger A. Jumonji domain containing protein 6 (Jmjd6) modulates splicing and specifically interacts with arginine-serine-rich (RS) domains of SR- and SR-like proteins. Nucleic Acids Res 2014; 42:7833-50. [PMID: 24914048 PMCID: PMC4081092 DOI: 10.1093/nar/gku488] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Fe(II) and 2-oxoglutarate dependent oxygenase Jmjd6 has been shown to hydroxylate lysine residues in the essential splice factor U2 auxiliary factor 65 kDa subunit (U2AF65) and to act as a modulator of alternative splicing. We describe further evidence for the role of Jmjd6 in the regulation of pre-mRNA processing including interactions of Jmjd6 with multiple arginine–serine-rich (RS)-domains of SR- and SR-related proteins including U2AF65, Luc7-like protein 3 (Luc7L3), SRSF11 and Acinus S′, but not with the bona fide RS-domain of SRSF1. The identified Jmjd6 target proteins are involved in different mRNA processing steps and play roles in exon dependent alternative splicing and exon definition. Moreover, we show that Jmjd6 modifies splicing of a constitutive splice reporter, binds RNA derived from the reporter plasmid and punctually co-localises with nascent RNA. We propose that Jmjd6 exerts its splice modulatory function by interacting with specific SR-related proteins during splicing in a RNA dependent manner.
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Affiliation(s)
- Astrid Heim
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Christina Grimm
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Udo Müller
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Simon Häußler
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Mukram M Mackeen
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK Research Unit Protein Science, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Juliane Merl
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Stefanie M Hauck
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Benedikt M Kessler
- School of Chemical Science, Faculty of Science and Technology, and Institute of Systems Biology (INBIOSIS) Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Darul Ehsan, Malaysia
| | - Christopher J Schofield
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Alexander Wolf
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Angelika Böttger
- Department of Biology II, Ludwig Maximilians University, Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
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227
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Bowman EA, Kelly WG. RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases. Nucleus 2014; 5:224-36. [PMID: 24879308 DOI: 10.4161/nucl.29347] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The transition between initiation and productive elongation during RNA Polymerase II (Pol II) transcription is a well-appreciated point of regulation across many eukaryotes. Elongating Pol II is modified by phosphorylation of serine 2 (Ser2) on its carboxy terminal domain (CTD) by two kinases, Bur1/Ctk1 in yeast and Cdk9/Cdk12 in metazoans. Here, we discuss the roles and regulation of these kinases and their relationship to Pol II elongation control, and focus on recent data from work in C. elegans that point out gaps in our current understand of transcription elongation.
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Affiliation(s)
- Elizabeth A Bowman
- National Institute of Environmental Health Sciences; Research Triangle Park, NC USA
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228
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Affiliation(s)
- Kamaleldin E Elagib
- Department of Pathology; University of Virginia School of Medicine; Charlottesville, VA USA
| | - Adam N Goldfarb
- Department of Pathology; University of Virginia School of Medicine; Charlottesville, VA USA
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229
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Itzen F, Greifenberg AK, Bösken CA, Geyer M. Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation. Nucleic Acids Res 2014; 42:7577-90. [PMID: 24860166 PMCID: PMC4081074 DOI: 10.1093/nar/gku449] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The bromodomain protein Brd4 regulates the transcription of signal-inducible genes. This is achieved by recruiting the positive transcription elongation factor P-TEFb to promoters by its P-TEFb interaction domain (PID). Here we show that Brd4 stimulates the kinase activity of P-TEFb for phosphorylation of the C-terminal domain (CTD) of RNA polymerase II over basal levels. The CTD phosphorylation saturation levels, the preferences for pre-phosphorylated substrates, and the phosphorylation specificity for Ser5 of the CTD however remain unchanged. Inhibition of P-TEFb by Hexim1 is relieved by Brd4, although no mutual displacement with the Cyclin T-binding domain of Hexim1 was observed. Brd4 PID shows a surprising sequence motif similarity to the trans-activating Tat protein from HIV-1, which includes a core RxL motif, a polybasic cluster known as arginine-rich motif, and a C-terminal leucine motif. Mutation of these motifs to alanine significantly diminished the stimulatory effect of Brd4 and fully abrogated its activation potential in presence of Hexim1. Yet the protein was not found to bind Cyclin T1 as Tat, but only P-TEFb with a dissociation constant of 0.5 μM. Our data suggest a model where Brd4 acts on the kinase subunit of P-TEFb to relieve inhibition and stimulate substrate recognition.
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Affiliation(s)
- Friederike Itzen
- Max Planck Institute of Molecular Physiology, Department of Physical Biochemistry, 44227 Dortmund, Germany
| | - Ann Katrin Greifenberg
- Max Planck Institute of Molecular Physiology, Department of Physical Biochemistry, 44227 Dortmund, Germany Center of Advanced European Studies and Research (caesar), Group Physical Biochemistry, 53175 Bonn, Germany
| | - Christian A Bösken
- Max Planck Institute of Molecular Physiology, Department of Physical Biochemistry, 44227 Dortmund, Germany Center of Advanced European Studies and Research (caesar), Group Physical Biochemistry, 53175 Bonn, Germany
| | - Matthias Geyer
- Max Planck Institute of Molecular Physiology, Department of Physical Biochemistry, 44227 Dortmund, Germany Center of Advanced European Studies and Research (caesar), Group Physical Biochemistry, 53175 Bonn, Germany
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230
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Koga M, Satoh T, Takasaki I, Kawamura Y, Yoshida M, Kaida D. U2 snRNP is required for expression of the 3' end of genes. PLoS One 2014; 9:e98015. [PMID: 24845214 PMCID: PMC4028248 DOI: 10.1371/journal.pone.0098015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 04/28/2014] [Indexed: 01/05/2023] Open
Abstract
Pre-mRNA in eukaryotes is subjected to mRNA processing, which includes capping, polyadenylation, and splicing. Transcription and mRNA processing are coupled, and this coupling stimulates mRNA processing; however, the effects of mRNA processing on transcription are not fully understood. In this study, we found that inhibition of U2 snRNP by a splicing inhibitor, spliceostatin A (SSA), or by an antisense oligonucleotide to U2 snRNA, caused gene-specific 3′-end down-regulation. Removal of SSA from the culture media restored expression of the 3′ ends of genes, suggesting that U2 snRNP is required for expression of the 3′ end of genes. Finally, we found that SSA treatment caused accumulation of Pol II near the 5′ end of 3′-end down regulated genes, such as CDK6, SMEK2 and EGFR, indicating that SSA treatment led to transcription elongation arrest on these genes. These findings suggest that U2 snRNP is important for production of full length mRNA probably through regulation of transcription elongation, and that a novel checkpoint mechanism prevents pre-mRNA from accumulating as a result of splicing deficiencies, and thereby prevents production of aberrant proteins that might be translated from pre-mRNAs through the arrest of transcription elongation.
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Affiliation(s)
- Mitsunori Koga
- Frontier Research Core for Life Sciences, University of Toyama, Toyama, Japan
| | - Takayuki Satoh
- Frontier Research Core for Life Sciences, University of Toyama, Toyama, Japan
| | - Ichiro Takasaki
- Division of Molecular Genetics Research, Life Science Research Center, University of Toyama, Toyama, Japan
| | - Yumi Kawamura
- Molecular Ligand Target Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN, Wako, Saitama, Japan
- JST, CREST, Kawaguchi, Saitama, Japan
| | - Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, Toyama, Japan
- * E-mail:
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231
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Abstract
A striking finding in the past decade is the production of numerous non-coding RNAs (ncRNAs) from mammalian genomes. While it is entirely possible that many of those ncRNAs are transcription noises or by-products of RNA processing, increasing evidence suggests that a large fraction of them are functional and provide various regulatory activities in the cell. Thus, functional genomics and proteomics are incomplete without understanding functional ribonomics. As has been long suggested by the 'RNA world' hypothesis, many ncRNAs have the capacity to act like proteins in diverse biochemical processes. The enormous amount of information residing in the primary sequences and secondary structures of ncRNAs makes them particularly suited to function as scaffolds for molecular interactions. In addition, their functions appear to be stringently controlled by default via abundant nucleases when not engaged in specific interactions. This review focuses on the functional properties of regulatory ncRNAs in comparison with proteins and emphasizes both the opportunities and challenges in future ncRNA research.
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Affiliation(s)
- Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
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232
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Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. Nat Methods 2014; 11:683-8. [PMID: 24809628 PMCID: PMC4073888 DOI: 10.1038/nmeth.2970] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/28/2014] [Indexed: 12/19/2022]
Abstract
RNA-protein interactions have critical roles in gene regulation. However, high-throughput methods to quantitatively analyze these interactions are lacking. We adapted an Illumina GAIIx sequencer to make several million such measurements with a High-Throughput Sequencing – RNA Affinity Profiling (HiTS-RAP) assay. Millions of cDNAs are sequenced, bound by the E. coli replication terminator protein Tus, and transcribed in situ, whereupon Tus halts transcription leaving RNA stably attached to its template DNA. The binding of fluorescently-labeled protein is then quantified in the sequencer. We used HiTS-RAP to measure the affinity of mutagenized libraries of GFP-binding and NELF-E binding aptamers to their respective targets and thereby identified regions in both aptamers that are critical for their RNA-protein interaction. We show that mutations additively affect binding affinity of the NELF-E binding aptamer, whose interaction depends mainly on a single-stranded RNA motif, but not that of the GFP aptamer, whose interaction depends primarily on secondary structure.
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233
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Khanna N, Hu Y, Belmont AS. HSP70 transgene directed motion to nuclear speckles facilitates heat shock activation. Curr Biol 2014; 24:1138-44. [PMID: 24794297 DOI: 10.1016/j.cub.2014.03.053] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/14/2014] [Accepted: 03/19/2014] [Indexed: 10/25/2022]
Abstract
Association and disassociation of gene loci with respect to specific nuclear compartments accompany changes in gene expression, yet little is known concerning the mechanisms by which this occurs or its functional consequences. Previously, we showed that tethering acidic activators to a peripheral chromosome site led to movement of the chromosome site away from the nuclear periphery, but the physiological relevance of this movement was unclear [1]. Nuclear speckles, or interchromatin granule clusters, are enriched in factors involved in RNA processing [2], and the association of a subset of active genes at their periphery suggests speckles may play a role in gene expression [3, 4]. Here, we show an actin-dependent association of HSP70 transgenes with nuclear speckles after heat shock. We visualized HSP70 transgenes moving curvilinearly toward nuclear speckles over ∼0.5-6 μm distances at velocities of 1-2 μm min(-1). Chromatin stretching in the direction of movement demonstrates a force-generating mechanism. Transcription in nearly all cases increased noticeably only after initial contact with a nuclear speckle. Moreover, blocking new HSP70 transgene/speckle association by actin depolymerization prevented significant heat shock-induced transcriptional activation in transgenes not associated with speckles, although robust transcriptional activation was observed for HSP70 transgenes associated with nuclear speckles. Our results demonstrate the existence of a still-to-be-revealed machinery for moving chromatin in a direct path over long distances toward nuclear speckles in response to transcriptional activation; moreover, this speckle association enhances the heat shock activation of these HSP70 transgenes.
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Affiliation(s)
- Nimish Khanna
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yan Hu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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234
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Abstract
The rapid expansion of genomics methods has enabled developmental biologists to address fundamental questions of developmental gene regulation on a genome-wide scale. These efforts have demonstrated that transcription of developmental control genes by RNA polymerase II (Pol II) is commonly regulated at the transition to productive elongation, resulting in the promoter-proximal accumulation of transcriptionally engaged but paused Pol II prior to gene induction. Here we review the mechanisms and possible functions of Pol II pausing and their implications for development.
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Affiliation(s)
- Bjoern Gaertner
- Stowers Institute for Medical Research, Kansas City, 64110 MO, USA
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235
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Abstract
Discoveries over the past decade portend a paradigm shift in molecular biology. Evidence suggests that RNA is not only functional as a messenger between DNA and protein but also involved in the regulation of genome organization and gene expression, which is increasingly elaborate in complex organisms. Regulatory RNA seems to operate at many levels; in particular, it plays an important part in the epigenetic processes that control differentiation and development. These discoveries suggest a central role for RNA in human evolution and ontogeny. Here, we review the emergence of the previously unsuspected world of regulatory RNA from a historical perspective.
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Affiliation(s)
- Kevin V Morris
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John S Mattick
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; the School of Biotechnology and Biomedical Sciences, and St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
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236
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Molecular basis of mast cell disease. Mol Immunol 2014; 63:55-60. [PMID: 24768320 DOI: 10.1016/j.molimm.2014.03.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 02/18/2014] [Accepted: 03/18/2014] [Indexed: 01/19/2023]
Abstract
Mastocytosis is an incurable and sometimes fatal haematological disorder grossly described as the accumulation of abnormal mast cells in the bone marrow and other organs causing tissue and organ damage. The clinical manifestations of this disease are extremely variable; disease phenotypes range from indolent to aggressive, and often present with associated non-mast cell haematological disorders (AHNMD), mainly myeloproliferative neoplasm and myelodysplastic syndromes. Recent efforts to genetically dissect the mechanisms that define aggressive and non-aggressive mastocytosis have generated a list of recurrent somatic mutations in mastocytosis patients that are associated with and may predict the evolution towards aggressive disease phenotypes. Here we review these mutations and discuss the molecular mechanisms associated with these mutations in an effort to better understand the biology of this disease and to predict its onset and evolution, with the ultimate goal of devising new and improved treatment strategies.
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237
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Both decreased and increased SRPK1 levels promote cancer by interfering with PHLPP-mediated dephosphorylation of Akt. Mol Cell 2014; 54:378-91. [PMID: 24703948 DOI: 10.1016/j.molcel.2014.03.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/24/2014] [Accepted: 02/27/2014] [Indexed: 01/07/2023]
Abstract
Akt activation is a hallmark of human cancers. Here, we report a critical mechanism for regulation of Akt activity by the splicing kinase SRPK1, a downstream Akt target for transducing growth signals to regulate splicing. Surprisingly, we find that SRPK1 has a tumor suppressor function because ablation of SRPK1 in mouse embryonic fibroblasts induces cell transformation. We link the phenotype to constitutive Akt activation from genome-wide phosphoproteomics analysis and discover that downregulated SRPK1 impairs the recruitment of the Akt phosphatase PHLPP1 (pleckstrin homology (PH) domain leucine-rich repeat protein phosphatase) to Akt. Interestingly, SRPK1 overexpression is also tumorigenic because excess SRPK1 squelches PHLPP1. Thus, aberrant SRPK1 expression in either direction induces constitutive Akt activation, providing a mechanistic basis for previous observations that SRPK1 is downregulated in some cancer contexts and upregulated in others.
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238
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Choe SK, Ladam F, Sagerström CG. TALE factors poise promoters for activation by Hox proteins. Dev Cell 2014; 28:203-11. [PMID: 24480644 DOI: 10.1016/j.devcel.2013.12.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 11/08/2013] [Accepted: 12/19/2013] [Indexed: 01/09/2023]
Abstract
Hox proteins form complexes with TALE cofactors from the Pbx and Prep/Meis families to control transcription, but it remains unclear how Hox:TALE complexes function. Examining a Hoxb1b:TALE complex that regulates zebrafish hoxb1a transcription, we find maternally deposited TALE proteins at the hoxb1a promoter already during blastula stages. These TALE factors recruit histone-modifying enzymes to promote an active chromatin profile at the hoxb1a promoter and also recruit RNA polymerase II (RNAPII) and P-TEFb. However, in the presence of TALE factors, RNAPII remains phosphorylated on serine 5 and hoxb1a transcription is inefficient. By gastrula stages, Hoxb1b binds together with TALE factors to the hoxb1a promoter. This triggers P-TEFb-mediated transitioning of RNAPII to the serine 2-phosphorylated form and efficient hoxb1a transcription. We conclude that TALE factors access promoters during early embryogenesis to poise them for activation but that Hox proteins are required to trigger efficient transcription.
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Affiliation(s)
- Seong-Kyu Choe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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239
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Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat. Mol Cell Biol 2014; 34:1911-28. [PMID: 24636995 DOI: 10.1128/mcb.01013-13] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The role of the negative elongation factor (NELF) in maintaining HIV latency was investigated following small hairpin RNA (shRNA) knockdown of the NELF-E subunit, a condition that induced high levels of proviral transcription in latently infected Jurkat T cells. Chromatin immunoprecipitation (ChIP) assays showed that latent proviruses accumulate RNA polymerase II (RNAP II) on the 5' long terminal repeat (LTR) but not on the 3' LTR. NELF colocalizes with RNAP II, and its level increases following proviral induction. RNAP II pause sites on the HIV provirus were mapped to high resolution by ChIP with high-throughput sequencing (ChIP-Seq). Like cellular promoters, RNAP II accumulates at around position +30, but HIV also shows additional pausing at +90, which is immediately downstream of a transactivation response (TAR) element and other distal sites on the HIV LTR. Following NELF-E knockdown or tumor necrosis factor alpha (TNF-α) stimulation, promoter-proximal RNAP II levels increase up to 3-fold, and there is a dramatic increase in RNAP II levels within the HIV genome. These data support a kinetic model for proviral transcription based on continuous replacement of paused RNAP II during both latency and productive transcription. In contrast to most cellular genes, HIV is highly activated by the combined effects of NELF-E depletion and activation of initiation by TNF-α, suggesting that opportunities exist to selectively activate latent HIV proviruses.
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240
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Eilebrecht S, Le Douce V, Riclet R, Targat B, Hallay H, Van Driessche B, Schwartz C, Robette G, Van Lint C, Rohr O, Benecke AG. HMGA1 recruits CTIP2-repressed P-TEFb to the HIV-1 and cellular target promoters. Nucleic Acids Res 2014; 42:4962-71. [PMID: 24623795 PMCID: PMC4005653 DOI: 10.1093/nar/gku168] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Active positive transcription elongation factor b (P-TEFb) is essential for cellular and human immunodeficiency virus type 1 (HIV-1) transcription elongation. CTIP2 represses P-TEFb activity in a complex containing 7SK RNA and HEXIM1. Recently, the inactive 7SK/P-TEFb small nuclear RNP (snRNP) has been detected at the HIV-1 core promoter as well as at the promoters of cellular genes, but a recruiting mechanism still remains unknown to date. Here we show global synergy between CTIP2 and the 7SK-binding chromatin master-regulator HMGA1 in terms of P-TEFb–dependent endogenous and HIV-1 gene expression regulation. While CTIP2 and HMGA1 concordingly repress the expression of cellular 7SK-dependent P-TEFb targets, the simultaneous knock-down of CTIP2 and HMGA1 also results in a boost in Tat-dependent and independent HIV-1 promoter activity. Chromatin immunoprecipitation experiments reveal a significant loss of CTIP2/7SK/P-TEFb snRNP recruitment to cellular gene promoters and the HIV-1 promoter on HMGA1 knock-down. Our findings not only provide insights into a recruiting mechanism for the inactive 7SK/P-TEFb snRNP, but may also contribute to a better understanding of viral latency.
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Affiliation(s)
- Sebastian Eilebrecht
- Vaccine Research Institute, INSERM U955, Institut Mondor de Recherche Biomédicale, 8 rue du général Sarrail, 94011 Créteil, France, Institut des Hautes Études Scientifiques-Centre National de la Recherche Scientifique, 35 route de Chartres, 91440 Bures sur Yvette, France, Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, University of Strasbourg, 3 rue Koeberlé, 67000 Strasbourg, France, IUT Louis Pasteur, 1 Allée d'Athénes, 67300 Schiltigheim, France, Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium, Institut Universitaire de France-IUF, Paris, France and CNRS UMR 7224, Université Pierre et Marie Curie, 7 quai Saint Bernard, 75005 Paris, France
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241
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Adenovirus E1A recruits the human Paf1 complex to enhance transcriptional elongation. J Virol 2014; 88:5630-7. [PMID: 24600005 DOI: 10.1128/jvi.03518-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED During infection by human adenovirus (HAdV), the proteins encoded by the early region 1A (E1A) gene bind and appropriate components of the cellular transcriptional machinery to activate the transcription of viral early genes. Previously, we identified roles for the human Bre1 (hBre1) and hPaf1 complexes in E1A-mediated transcriptional activation of HAdV early genes. Here we show that E1A binds hBre1 directly and that this complex targets the hPaf1 complex via the Rtf1 subunit. Depletion of hPaf1 reduces E1A-dependent activation of transcription from the E2e, E3, and E4 viral transcription units, and this does not result from a reduced ability of RNA polymerase II to be recruited to the promoter-proximal regions of these genes. In contrast, depletion of hPaf1 reduces the occupancy of RNA polymerase II across these transcription units. This is accompanied by reductions in the level of H3K36 trimethylation, a posttranslational histone modification associated with efficient transcriptional elongation, and the number of full-length transcripts from these genes. Together, these results indicate that E1A uses hBre1 to recruit the hPaf1 complex in order to optimally activate viral early transcription by enhancing transcriptional elongation. IMPORTANCE This work provides the mechanism by which the hPaf1 complex contributes to E1A-dependent activation of early gene transcription. The work also demonstrates that E1A induces gene expression by stimulating transcriptional elongation, in addition to its better-characterized effects on transcriptional initiation.
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242
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Mbonye U, Karn J. Transcriptional control of HIV latency: cellular signaling pathways, epigenetics, happenstance and the hope for a cure. Virology 2014; 454-455:328-39. [PMID: 24565118 DOI: 10.1016/j.virol.2014.02.008] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 01/23/2014] [Accepted: 02/07/2014] [Indexed: 02/06/2023]
Abstract
Replication-competent latent HIV-1 proviruses that persist in the genomes of a very small subset of resting memory T cells in infected individuals under life-long antiretroviral therapy present a major barrier towards viral eradication. Multiple molecular mechanisms are required to repress the viral trans-activating factor Tat and disrupt the regulatory Tat feedback circuit leading to the establishment of the latent viral reservoir. In particular, latency is due to a combination of transcriptional silencing of proviruses via host epigenetic mechanisms and restrictions on the expression of P-TEFb, an essential co-factor for Tat. Induction of latent proviruses in the presence of antiretroviral therapy is expected to enable clearance of latently infected cells by viral cytopathic effects and host antiviral immune responses. An in-depth comprehensive understanding of the molecular control of HIV-1 transcription should inform the development of optimal combinatorial reactivation strategies that are intended to purge the latent viral reservoir.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States.
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243
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A splicing-dependent transcriptional checkpoint associated with prespliceosome formation. Mol Cell 2014; 53:779-90. [PMID: 24560925 PMCID: PMC3988880 DOI: 10.1016/j.molcel.2014.01.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 11/26/2013] [Accepted: 01/17/2014] [Indexed: 11/21/2022]
Abstract
There is good evidence for functional interactions between splicing and transcription in eukaryotes, but how and why these processes are coupled remain unknown. Prp5 protein (Prp5p) is an RNA-stimulated adenosine triphosphatase (ATPase) required for prespliceosome formation in yeast. We demonstrate through in vivo RNA labeling that, in addition to a splicing defect, the prp5-1 mutation causes a defect in the transcription of intron-containing genes. We present chromatin immunoprecipitation evidence for a transcriptional elongation defect in which RNA polymerase that is phosphorylated at Ser5 of the largest subunit’s heptad repeat accumulates over introns and that this defect requires Cus2 protein. A similar accumulation of polymerase was observed when prespliceosome formation was blocked by a mutation in U2 snRNA. These results indicate the existence of a transcriptional elongation checkpoint that is associated with prespliceosome formation during cotranscriptional spliceosome assembly. We propose a role for Cus2p as a potential checkpoint factor in transcription. Transcriptional elongation is inhibited when prespliceosome formation is blocked The defect is characterized by RNA polymerase accumulation on introns This checkpoint can be triggered by mutations in either PRP5 or U2 snRNA The U2-associated Cus2 protein is a candidate checkpoint factor
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244
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Bentley DL. Coupling mRNA processing with transcription in time and space. Nat Rev Genet 2014; 15:163-75. [PMID: 24514444 DOI: 10.1038/nrg3662] [Citation(s) in RCA: 544] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Maturation of mRNA precursors often occurs simultaneously with their synthesis by RNA polymerase II (Pol II). The co-transcriptional nature of mRNA processing has permitted the evolution of coupling mechanisms that coordinate transcription with mRNA capping, splicing, editing and 3' end formation. Recent experiments using sophisticated new methods for analysis of nascent RNA have provided important insights into the relative amount of co-transcriptional and post-transcriptional processing, the relationship between mRNA elongation and processing, and the role of the Pol II carboxy-terminal domain (CTD) in regulating these processes.
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Affiliation(s)
- David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, MS8101, PO BOX 6511, Aurora, Colorado 80045, USA
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245
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Giraud M, Jmari N, Du L, Carallis F, Nieland TJF, Perez-Campo FM, Bensaude O, Root DE, Hacohen N, Mathis D, Benoist C. An RNAi screen for Aire cofactors reveals a role for Hnrnpl in polymerase release and Aire-activated ectopic transcription. Proc Natl Acad Sci U S A 2014; 111:1491-6. [PMID: 24434558 PMCID: PMC3910647 DOI: 10.1073/pnas.1323535111] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Aire induces the expression of a large set of autoantigen genes in the thymus, driving immunological tolerance in maturing T cells. To determine the full spectrum of molecular mechanisms underlying the Aire transactivation function, we screened an AIRE-dependent gene-expression system with a genome-scale lentiviral shRNA library, targeting factors associated with chromatin architecture/function, transcription, and mRNA processing. Fifty-one functional allies were identified, with a preponderance of factors that impact transcriptional elongation compared with initiation, in particular members of the positive transcription elongation factor b (P-TEFb) involved in the release of "paused" RNA polymerases (CCNT2 and HEXIM1); mRNA processing and polyadenylation factors were also highlighted (HNRNPL/F, SFRS1, SFRS3, and CLP1). Aire's functional allies were validated on transfected and endogenous target genes, including the generation of lentigenic knockdown (KD) mice. We uncovered the effect of the splicing factor Hnrnpl on Aire-induced transcription. Transcripts sensitive to the P-TEFb inhibitor flavopiridol were reduced by Hnrnpl knockdown in thymic epithelial cells, independently of their dependence on Aire, therefore indicating a general effect of Hnrnpl on RNA elongation. This conclusion was substantiated by demonstration of HNRNPL interactions with P-TEFb components (CDK9, CCNT2, HEXIM1, and the small 7SK RNA). Aire-containing complexes include 7SK RNA, the latter interaction disrupted by HNRNPL knockdown, suggesting that HNRNPL may partake in delivering inactive P-TEFb to Aire. Thus, these results indicate that mRNA processing factors cooperate with Aire to release stalled polymerases and to activate ectopic expression of autoantigen genes in the thymus.
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Affiliation(s)
- Matthieu Giraud
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
- Department of Immunology, Institut Cochin, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Université Paris Descartes, 75014 Paris, France
| | - Nada Jmari
- Department of Immunology, Institut Cochin, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Université Paris Descartes, 75014 Paris, France
| | - Lina Du
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Floriane Carallis
- Department of Immunology, Institut Cochin, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Université Paris Descartes, 75014 Paris, France
| | | | - Flor M. Perez-Campo
- Department of Internal Medicine, Hospital U.M. Valdecilla-Instituto de Formación e Investigación Marqués de Valdecilla, University of Cantabria, 39008 Santander, Spain; and
| | - Olivier Bensaude
- Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, INSERM U1024, 75005 Paris, France
| | - David E. Root
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Nir Hacohen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
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246
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Pagano JM, Kwak H, Waters CT, Sprouse RO, White BS, Ozer A, Szeto K, Shalloway D, Craighead HG, Lis JT. Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions. PLoS Genet 2014; 10:e1004090. [PMID: 24453987 PMCID: PMC3894171 DOI: 10.1371/journal.pgen.1004090] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/22/2013] [Indexed: 11/22/2022] Open
Abstract
The four-subunit Negative Elongation Factor (NELF) is a major regulator of RNA Polymerase II (Pol II) pausing. The subunit NELF-E contains a conserved RNA Recognition Motif (RRM) and is proposed to facilitate Poll II pausing through its association with nascent transcribed RNA. However, conflicting ideas have emerged for the function of its RNA binding activity. Here, we use in vitro selection strategies and quantitative biochemistry to identify and characterize the consensus NELF-E binding element (NBE) that is required for sequence specific RNA recognition (NBE: CUGAGGA(U) for Drosophila). An NBE-like element is present within the loop region of the transactivation-response element (TAR) of HIV-1 RNA, a known regulatory target of human NELF-E. The NBE is required for high affinity binding, as opposed to the lower stem of TAR, as previously claimed. We also identify a non-conserved region within the RRM that contributes to the RNA recognition of Drosophila NELF-E. To understand the broader functional relevance of NBEs, we analyzed promoter-proximal regions genome-wide in Drosophila and show that the NBE is enriched +20 to +30 nucleotides downstream of the transcription start site. Consistent with the role of NELF in pausing, we observe a significant increase in NBEs among paused genes compared to non-paused genes. In addition to these observations, SELEX with nuclear run-on RNA enrich for NBE-like sequences. Together, these results describe the RNA binding behavior of NELF-E and supports a biological role for NELF-E in promoter-proximal pausing of both HIV-1 and cellular genes. RNA polymerase II (Pol II) is a molecular machine that is responsible for transcribing all protein coding genes in the eukaryotic genome. Transcription by Pol II is a highly regulated process consisting of several rate-limiting steps. During transcription elongation, a number of transcription factors are essential to modulate Pol II activity. One of these factors is the Negative Elongation Factor (NELF), and it plays a major role in promoter-proximal pausing, a widespread phenomenon during early transcription elongation. NELF-E, a protein subunit of the NELF complex contains a conserved RNA binding domain that is thought to regulate transcription through its interaction with newly transcribed RNA made by Pol II. However, the function of the RNA binding activity of NELF-E remains unresolved due to prior conflicting studies. Here, we clarify the RNA binding properties of NELF-E and provide insight into how this protein might facilitate promoter-proximal pausing of Pol II in transcription. Moreover, we identify the precise region of NELF-E binding in one of its known regulatory targets, HIV-1. Taken together, the results presented indicate a dynamic interplay between NELF and specific RNA sequences around the promoter pause region to modulate early transcription elongation.
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Affiliation(s)
- John M Pagano
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Rebekka O Sprouse
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Brian S White
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Harold G Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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Hanssens K, Brenet F, Agopian J, Georgin-Lavialle S, Damaj G, Cabaret L, Chandesris MO, de Sepulveda P, Hermine O, Dubreuil P, Soucie E. SRSF2-p95 hotspot mutation is highly associated with advanced forms of mastocytosis and mutations in epigenetic regulator genes. Haematologica 2014; 99:830-5. [PMID: 24389310 DOI: 10.3324/haematol.2013.095133] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mastocytosis is a rare and chronic disease with phenotypes ranging from indolent to severe. Prognosis for this disease is variable and very few biomarkers to predict disease evolution or outcome are currently known. We have performed comprehensive screening in our large cohort of mastocytosis patients for mutations previously found in other myeloid diseases and that could serve as prognostic indicators. KIT, SRSF2-P95 and TET2 mutations were by far the most frequent, detected in 81%, 24% and 21% of patients, respectively. Where TET2 and SRSF2-P95 mutation both correlated with advanced disease phenotypes, SRSF2-P95 hotspot mutation was found almost exclusively in patients diagnosed with associated clonal hematologic non-mast cell disease. Statistically, TET2 and SRSF2-P95 mutations were highly associated, suggesting a mechanistic link between these two factors. Finally, analysis of both clonal and sorted cell populations from patients confirms the presence of these mutations in the mast cell component of the disease, suggests an ontological mutation hierarchy and provides evidence for the expansion of multiple clones. This highlights the prognostic potential of such approaches, if applied systematically, for delineating the roles of specific mutations in predisposing and/or driving distinct disease phenotypes.
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248
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Giudice J, Cooper TA. RNA-binding proteins in heart development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:389-429. [PMID: 25201112 DOI: 10.1007/978-1-4939-1221-6_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA-binding proteins (RBPs) are key players of posttranscriptional regulation occurring during normal tissue development. All tissues examined thus far have revealed the importance of RBPs in the regulation of complex networks involved in organ morphogenesis, maturation, and function. They are responsible for controlling tissue-specific gene expression by regulating alternative splicing, mRNA stability, translation, and poly-adenylation. The heart is the first organ form during embryonic development and is also the first to acquire functionality. Numerous remodeling processes take place during late cardiac development since fetal heart first adapts to birth and then undergoes a transition to adult functionality. This physiological remodeling involves transcriptional and posttranscriptional networks that are regulated by RBPs. Disruption of the normal regulatory networks has been shown to cause cardiomyopathy in humans and animal models. Here we review the complexity of late heart development and the current information regarding how RBPs control aspects of postnatal heart development. We also review how activities of RBPs are modulated adding complexity to the regulation of developmental networks.
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Affiliation(s)
- Jimena Giudice
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA,
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249
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Transcription factors mediate the enzymatic disassembly of promoter-bound 7SK snRNP to locally recruit P-TEFb for transcription elongation. Cell Rep 2013; 5:1256-68. [PMID: 24316072 DOI: 10.1016/j.celrep.2013.11.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/02/2013] [Accepted: 11/02/2013] [Indexed: 12/19/2022] Open
Abstract
The transition from transcription initiation into elongation is controlled by transcription factors, which recruit positive transcription elongation factor b (P-TEFb) to promoters to phosphorylate RNA polymerase II. A fraction of P-TEFb is recruited as part of the inhibitory 7SK small nuclear ribonucleoprotein particle (snRNP), which inactivates the kinase and prevents elongation. However, it is unclear how P-TEFb is captured from the promoter-bound 7SK snRNP to activate elongation. Here, we describe a mechanism by which transcription factors mediate the enzymatic release of P-TEFb from the 7SK snRNP at promoters to trigger activation in a gene-specific manner. We demonstrate that Tat recruits PPM1G/PP2Cγ to locally disassemble P-TEFb from the 7SK snRNP at the HIV promoter via dephosphorylation of the kinase T loop. Similar to Tat, nuclear factor (NF)-κB recruits PPM1G in a stimulus-dependent manner to activate elongation at inflammatory-responsive genes. Recruitment of PPM1G to promoter-assembled 7SK snRNP provides a paradigm for rapid gene activation through transcriptional pause release.
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250
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Allison KA, Kaikkonen MU, Gaasterland T, Glass CK. Vespucci: a system for building annotated databases of nascent transcripts. Nucleic Acids Res 2013; 42:2433-47. [PMID: 24304890 PMCID: PMC3936758 DOI: 10.1093/nar/gkt1237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the unique problem of identifying transcriptional units de novo from short reads located all across the genome. Here, we present a novel algorithm for de novo transcript identification from GRO-sequencing data, along with a system that determines transcript regions, stores them in a relational database and associates them with known reference annotations. We use this method to analyze GRO-sequencing data from primary mouse macrophages and derive novel quantitative insights into the extent and characteristics of non-coding transcription in mammalian cells. In doing so, we demonstrate that Vespucci expands existing annotations for mRNAs and lincRNAs by defining the primary transcript beyond the polyadenylation site. In addition, Vespucci generates assemblies for un-annotated non-coding RNAs such as those transcribed from enhancer-like elements. Vespucci thereby provides a robust system for defining, storing and analyzing diverse classes of primary RNA transcripts that are of increasing biological interest.
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Affiliation(s)
- Karmel A Allison
- Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA, Department of Bioinformatics and Systems Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA, San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375, USA, A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, P.O. Box 1627, 70120 Kuopio, Finland, Institute for Genomic Medicine and Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA and Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
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