151
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Cinquin O. Repressor dimerization in the zebrafish somitogenesis clock. PLoS Comput Biol 2007; 3:e32. [PMID: 17305423 PMCID: PMC1797823 DOI: 10.1371/journal.pcbi.0030032] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 01/02/2007] [Indexed: 11/18/2022] Open
Abstract
The oscillations of the somitogenesis clock are linked to the fundamental process of vertebrate embryo segmentation, yet little is known about their generation. In zebrafish, it has been proposed that Her proteins repress the transcription of their own mRNA. However, in its simplest form, this model is incompatible with the fact that morpholino knockdown of Her proteins can impair expression of their mRNA. Simple self-repression models also do not account for the spatiotemporal pattern of gene expression, with waves of gene expression shrinking as they propagate. Here we study computationally the networks generated by the wealth of dimerization possibilities amongst transcriptional repressors in the zebrafish somitogenesis clock. These networks can reproduce knockdown phenotypes, and strongly suggest the existence of a Her1–Her7 heterodimer, so far untested experimentally. The networks are the first reported to reproduce the spatiotemporal pattern of the zebrafish somitogenesis clock; they shed new light on the role of Her13.2, the only known link between the somitogenesis clock and positional information in the paraxial mesoderm. The networks can also account for perturbations of the clock by manipulation of FGF signaling. Achieving an understanding of the interplay between clock oscillations and positional information is a crucial first step in the investigation of the segmentation mechanism. Vertebrate embryos acquire a segmented structure along the anteroposterior axis. Segmentation is critical for patterning of other structures (such as nerves, vertebrae, muscles, and blood vessels) and occurs by the rhythmic separation of balls of cells, called somites, from the anterior end of their precursor tissue, called the presomitic mesoderm. These rhythmic events are associated with oscillatory gene expression in the presomitic mesoderm: waves of gene expression originate at the posterior end and spread anteriorly. When a wave reaches the anterior end, a pair of new somites detaches. The set of genes whose expression oscillates is termed the “somitogenesis clock.” Even though the zebrafish somitogenesis clock has been the subject of intensive study, it is not clear how its oscillations are generated. It has been proposed that the mechanism involves a simple negative feedback loop, with proteins of the Her family periodically repressing their own expression. However, this is incompatible with some experimental results and does not explain how the spatiotemporal pattern of gene expression is generated. Here I propose a model—based on physical interactions between Her proteins—that is compatible with experimental results, and that explains how positional information is used to generate the spatiotemporal pattern of gene expression.
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Affiliation(s)
- Olivier Cinquin
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, United Kingdom.
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152
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Zaichuk T, Ivancic D, Scholtens D, Schiller C, Khan SA. Tissue-specific transcripts of human steroid sulfatase are under control of estrogen signaling pathways in breast carcinoma. J Steroid Biochem Mol Biol 2007; 105:76-84. [PMID: 17596930 DOI: 10.1016/j.jsbmb.2006.12.101] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 12/18/2006] [Indexed: 11/30/2022]
Abstract
Steroid sulfatase (STS) increases the pool of precursors of biologically active steroids, thereby playing an important role in breast cancer development. Mechanisms that control STS expression remain poorly understood. In present study we investigated alterations in the 5' region of STS gene to gain insight into the mechanism(s) that regulates its expression in mammary epithelial cells. We found that at least four alternatively spliced transcripts of STS gene can be produced from at least four different leader exons. Distinct expression patterns of the STS variants were observed in human tissues. Expression profiles of estrogen receptor alpha (ERalpha)-positive and ERalpha-negative breast carcinomas showed that these two categories of tumors and their adjacent benign tissues display remarkably different expression of STS isoforms. Coexpression of STS isoforms with ER isotypes suggests their cell-type specific coregulation. In addition, we identified ERalpha as essential regulator of STS transcription and provide evidence of direct estradiol-dependent binding of ERalpha to multiple STS cis-regulatory regions in vivo. Our results indicate that STS isoforms are under control of estrogen signaling pathways and their differential expression may play a significant role in breast cancer biology.
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Affiliation(s)
- Tetiana Zaichuk
- Department of Surgery, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
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153
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Ferreira EN, Galante PAF, Carraro DM, de Souza SJ. Alternative splicing: a bioinformatics perspective. MOLECULAR BIOSYSTEMS 2007; 3:473-7. [PMID: 17579772 DOI: 10.1039/b702485c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The degree of diversity at the transcriptome and proteome levels generated by alternative splicing is astonishing. In this review, we discuss several issues related to alternative splicing with a special emphasis on identification strategies based on bioinformatics.
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154
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hnRNP E1 and E2 have distinct roles in modulating HIV-1 gene expression. Retrovirology 2007; 4:28. [PMID: 17451601 PMCID: PMC1863430 DOI: 10.1186/1742-4690-4-28] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 04/23/2007] [Indexed: 11/10/2022] Open
Abstract
Pre-mRNA processing, including 5' end capping, splicing, and 3' end cleavage/polyadenylation, are events coordinated by transcription that can influence the subsequent export and translation of mRNAs. Coordination of RNA processing is crucial in retroviruses such as HIV-1, where inefficient splicing and the export of intron-containing RNAs are required for expression of the full complement of viral proteins. RNA processing can be affected by both viral and cellular proteins, and in this study we demonstrate that a member of the hnRNP E family of proteins can modulate HIV-1 RNA metabolism and expression. We show that hnRNP E1/E2 are able to interact with the ESS3a element of the bipartite ESS in tat/rev exon 3 of HIV-1 and that modulation of hnRNP E1 expression alters HIV-1 structural protein synthesis. Overexpression of hnRNP E1 leads to a reduction in Rev, achieved in part through a decrease in rev mRNA levels. However, the reduction in Rev levels cannot fully account for the effect of hnRNP E1, suggesting that hmRNP E1 might also act to suppress viral RNA translation. Deletion mutagenesis determined that the C-terminal end of hnRNP E1 was required for the reduction in Rev expression and that replacing this portion of hnRNP E1 with that of hnRNP E2, despite the high degree of conservation, could not rescue the loss of function.
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155
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Nojima T, Hirose T, Kimura H, Hagiwara M. The interaction between cap-binding complex and RNA export factor is required for intronless mRNA export. J Biol Chem 2007; 282:15645-51. [PMID: 17363367 DOI: 10.1074/jbc.m700629200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA export factor (REF) is a component of the exon junction complex (EJC) that is deposited on mRNA in a splicing-dependent manner, and targets spliced mRNA for export. In this study, analysis of the RNA-binding protein complexes revealed that REF associates with beta-globin mRNA at the region other than the EJC deposition site. Comparison between RNA polymerase II and T7 transcription and further analysis showed that the deposition of REF apart from the EJC is dependent on the 5' cap structure, but not splicing. Excess amounts of m(7)GpppG cap analog reduced REF binding to intronless mRNA, and a co-immunoprecipitation experiment revealed that REF interacts with the cap-binding protein CBP20. The export of Cy3-labeled intronless beta-globin mRNA from nuclei of HeLa cells was enhanced by co-injection of CBP20 and REF. Thus, REF recruited by CBP20 may play a stimulatory role to export the capped intronless mRNAs.
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Affiliation(s)
- Takayuki Nojima
- Laboratory of Gene Expression, School of Biomedical Science, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Japan
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156
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Luo Z, Chen Z. Improperly terminated, unpolyadenylated mRNA of sense transgenes is targeted by RDR6-mediated RNA silencing in Arabidopsis. THE PLANT CELL 2007; 19:943-58. [PMID: 17384170 PMCID: PMC1867362 DOI: 10.1105/tpc.106.045724] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
RNA silencing can be induced by highly transcribed transgenes through a pathway dependent on RNA-DEPENDENT RNA POLYMERASE6 (RDR6) and may function as a genome protection mechanism against excessively expressed genes. Whether all transcripts or just aberrant transcripts activate this protection mechanism is unclear. Consistent RNA silencing induced by a transgene with three direct repeats of the beta-glucuronidase (GUS) open reading frame (ORF) is associated with high levels of truncated, unpolyadenylated transcripts, probably from abortive transcription elongation. Truncated, unpolyadenylated transcripts from triple GUS ORF repeats were degraded in the wild type but accumulated in an rdr6 mutant, suggesting targeting for degradation by RDR6-mediated RNA silencing. A GUS transgene without a 3' transcription terminator produced unpolyadenylated readthrough mRNA and consistent RDR6-dependent RNA silencing. Both GUS triple repeats and terminator-less GUS transgenes silenced an expressed GUS transgene in trans in the wild type but not in the rdr6 mutant. Placing two 3' terminators in the GUS transgene 3' reduced mRNA 3' readthrough, decreased GUS-specific small interfering RNA accumulation, and enhanced GUS gene expression. Moreover, RDR6 was localized in the nucleus. We propose that improperly terminated, unpolyadenylated mRNA from transgene transcription is subject to RDR6-mediated RNA silencing, probably by acting as templates for the RNA polymerase, in Arabidopsis thaliana.
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Affiliation(s)
- Zhenghua Luo
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907-2054, USA
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157
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Yang Q, Lucas A, Son S, Chang LJ. Overlapping enhancer/promoter and transcriptional termination signals in the lentiviral long terminal repeat. Retrovirology 2007; 4:4. [PMID: 17241475 PMCID: PMC1802088 DOI: 10.1186/1742-4690-4-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Accepted: 01/22/2007] [Indexed: 12/14/2022] Open
Abstract
Oncoretrovirus, but not lentivirus, displays a high transcriptional readthrough activity in the 3' long terminal repeat (LTR) (Zaiss et al. J. Virol. 76, 7209–7219, 2002). However, the U3-deleted, self-inactivating (SIN) lentiviral LTR also exhibits high transcriptional readthrough activity. Since the canonical "core" polyadenylation signal (AAUAAA) of the lentivirus is located in the R-U5 region, the above finding suggests that additional RNA termination signals must be present in the U3 region. Insertion of alternative termination signals including panhuman T cell leukemia virus type I polyadenylation signal, a 3' end small intron, and a tertiary tRNA motif into the lentiviral SIN LTR did not restore the transcriptional termination function. Functional dissection of the U3 region revealed that 70–80% of the termination signals reside in the transcriptional control region within 124 nt overlapping NFκB, Sp1 and TATA binding sites. Serial deletion analysis of the transcriptional control region indicates that the lentiviral enhancer/promoter elements are essential to the RNA termination function. These results characterize the mechanism of lentiviral transcriptional readthrough, which addresses important fundamental and practical issue of RNA readthrough influencing lentiviral gene function and vector safety.
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Affiliation(s)
- Qing Yang
- Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center and McKnight Brain Institute, University of Florida, College of Medicine, Gainesville, Florida 32606, USA
| | - Aurore Lucas
- Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center and McKnight Brain Institute, University of Florida, College of Medicine, Gainesville, Florida 32606, USA
| | - Sodany Son
- Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center and McKnight Brain Institute, University of Florida, College of Medicine, Gainesville, Florida 32606, USA
| | - Lung-Ji Chang
- Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center and McKnight Brain Institute, University of Florida, College of Medicine, Gainesville, Florida 32606, USA
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158
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159
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Matlin AJ, Moore MJ. Spliceosome assembly and composition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:14-35. [PMID: 18380338 DOI: 10.1007/978-0-387-77374-2_2] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cells control alternative splicing by modulating assembly of the pre-mRNA splicing machinery at competing splice sites. Therefore, a working knowledge of spliceosome assembly is essential for understanding how alternative splice site choices are achieved. In this chapter, we review spliceosome assembly with particular emphasis on the known steps and factors subject to regulation during alternative splice site selection in mammalian cells. We also review recent advances regarding similarities and differences between the in vivo and in vitro assembly pathways, as well as proofreading mechanisms contributing to the fidelity of splice site selection.
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Affiliation(s)
- Arianne J Matlin
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
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160
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Kornblihtt AR. Coupling Transcription and Alternative Splicing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:175-89. [DOI: 10.1007/978-0-387-77374-2_11] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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161
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Tardiff DF, Lacadie SA, Rosbash M. A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. Mol Cell 2006; 24:917-29. [PMID: 17189193 PMCID: PMC1828117 DOI: 10.1016/j.molcel.2006.12.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 11/01/2006] [Accepted: 12/06/2006] [Indexed: 09/30/2022]
Abstract
Recent ChIP experiments indicate that spliceosome assembly and splicing can occur cotranscriptionally in S. cerevisiae. However, only a few genes have been examined, and all have long second exons. To extend these studies, we analyzed intron-containing genes with different second exon lengths by using ChIP as well as whole-genome tiling arrays (ChIP-CHIP). The data indicate that U1 snRNP recruitment is independent of exon length. Recursive splicing constructs, which uncouple U1 recruitment from transcription, suggest that cotranscriptional U1 recruitment contributes to optimal splicing efficiency. In contrast, U2 snRNP recruitment, as well as cotranscriptional splicing, is deficient on short second exon genes. We estimate that > or =90% of endogenous yeast splicing is posttranscriptional, consistent with an analysis of posttranscriptional snRNP-associated pre-mRNA.
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Affiliation(s)
- Daniel F. Tardiff
- Howard Hughes Medical Institute, Biology Department MS008, Brandeis University, 415 South Street Waltham, Massachusetts 02454
| | - Scott A. Lacadie
- Howard Hughes Medical Institute, Biology Department MS008, Brandeis University, 415 South Street Waltham, Massachusetts 02454
| | - Michael Rosbash
- Howard Hughes Medical Institute, Biology Department MS008, Brandeis University, 415 South Street Waltham, Massachusetts 02454
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162
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Jackson SA, Koduvayur S, Woodson SA. Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast. RNA (NEW YORK, N.Y.) 2006; 12:2149-59. [PMID: 17135489 PMCID: PMC1664722 DOI: 10.1261/rna.184206] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Stable RNAs must form specific three-dimensional structures, yet many RNAs become kinetically trapped in misfolded conformations. To understand the factors that control the accuracy of RNA folding in the cell, the self-splicing activity of the Tetrahymena group I intron was compared in different genetic contexts in budding yeast. The extent of splicing was 98% when the intron was placed in its natural rDNA context, but only 3% when the intron was expressed in an exogenous pre-mRNA. Further experiments showed that the probability of forming the active intron structure depends on local sequence context and transcription by Pol I. Pre-rRNAs decayed at similar rates, whether the intron was wild type or inactivated by an internal deletion, suggesting that most of the unreacted pre-rRNA is incompetent to splice. Northern blots and complementation assays showed that mutations that destabilize the intron tertiary structure inhibited self-splicing and processing of internal transcribed spacer 2. The data are consistent with partitioning of pre-rRNAs into active and inactive populations. The misfolded RNAs are sequestered and degraded without refolding to a significant extent. Thus, the initial fidelity of folding can dictate the intracellular fate of transcripts containing this group I intron.
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Affiliation(s)
- Scott A Jackson
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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163
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Moore MJ, Schwartzfarb EM, Silver PA, Yu MC. Differential Recruitment of the Splicing Machinery during Transcription Predicts Genome-Wide Patterns of mRNA Splicing. Mol Cell 2006; 24:903-15. [PMID: 17189192 DOI: 10.1016/j.molcel.2006.12.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Revised: 11/30/2006] [Accepted: 12/11/2006] [Indexed: 11/23/2022]
Abstract
The splicing machinery associates with genes to facilitate efficient cotranscriptional mRNA processing. We have mapped these associations by genome localization analysis to ascertain how splicing is achieved and regulated on a system-wide scale. Our data show that factors important for intron recognition sample nascent mRNAs and are retained specifically at intron-containing genes via RNA-dependent interactions. Spliceosome assembly proceeds cotranscriptionally but completes posttranscriptionally in most cases. Some intron-containing genes were not bound by the spliceosome, including several developmentally regulated genes. On this basis, we predicted and verified regulated splicing and observed a role for nuclear mRNA surveillance in monitoring those events. Finally, we present evidence that cotranscriptional processing events determine the recruitment of specific mRNA export factors. Broadly, our results provide mechanistic insights into the coordinated regulation of transcription, mRNA processing, and nuclear export in executing complex gene expression programs.
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Affiliation(s)
- Michael J Moore
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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164
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Gómez E, Caamaño JN, Rodríguez A, De Frutos C, Facal N, Díez C. Bovine Early Embryonic Development and Vitamin A. Reprod Domest Anim 2006; 41 Suppl 2:63-71. [PMID: 16984470 DOI: 10.1111/j.1439-0531.2006.00770.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Vitamin A and its derivatives, collectively termed as retinoids, have been paid attention in recent years because of their effects in bovine reproduction. However, the role of retinoids in the pre-implantation period continues to be largely unexplored, in contrast to later stages of development. Retinoids control cell growth, differentiation and death through binding to specific nuclear receptors by retinoic acid and other active metabolites. This paper reviews how retinoids can influence early embryonic development in cattle through their influence on the follicle, the extrafollicular oocyte and the pre-implantation embryo itself.
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Affiliation(s)
- E Gómez
- Servicio Regional de Investigación y Desarrollo Agroalimentario, (SERIDA), Area de Genética y Reproducción, SERIDA, Asturias, Spain.
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165
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Listerman I, Sapra AK, Neugebauer KM. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nat Struct Mol Biol 2006; 13:815-22. [PMID: 16921380 DOI: 10.1038/nsmb1135] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 07/24/2006] [Indexed: 01/09/2023]
Abstract
Coupling between transcription and RNA processing is a key gene regulatory mechanism. Here we use chromatin immunoprecipitation to detect transcription-dependent accumulation of the precursor mRNA (pre-mRNA) splicing factors hnRNP A1, U2AF65 and U1 and U5 snRNPs on the intron-containing human FOS gene. These factors were poorly detected on intronless heat-shock and histone genes, a result that opposes direct recruitment by RNA polymerase II (Pol II) or the cap-binding complex in vivo. However, an observed RNA-dependent interaction between U2AF65 and active forms of Pol II may stabilize U2AF65 binding to intron-containing nascent RNA. We establish chromatin-RNA immunoprecipitation and show that FOS pre-mRNA is cotranscriptionally spliced. Notably, the topoisomerase I inhibitor camptothecin, which stalls elongating Pol II, increased cotranscriptional splicing factor accumulation and splicing in parallel. This provides direct evidence for a kinetic link between transcription, splicing factor recruitment and splicing catalysis.
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Affiliation(s)
- Imke Listerman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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166
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Shav-Tal Y, Darzacq X, Singer RH. Gene expression within a dynamic nuclear landscape. EMBO J 2006; 25:3469-79. [PMID: 16900099 PMCID: PMC1538565 DOI: 10.1038/sj.emboj.7601226] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 06/07/2006] [Indexed: 01/01/2023] Open
Abstract
Molecular imaging in living cells or organisms now allows us to observe macromolecular assemblies with a time resolution sufficient to address cause-and-effect relationships on specific molecules. These emerging technologies have gained much interest from the scientific community since they have been able to reveal novel concepts in cell biology, thereby changing our vision of the cell. One main paradigm is that cells stochastically vary, thus implying that population analysis may be misleading. In fact, cells should be analyzed within time-resolved single-cell experiments rather than being compared to other cells within a population. Technological imaging developments as well as the stochastic events present in gene expression have been reviewed. Here, we discuss how the structural organization of the nucleus is revealed using noninvasive single-cell approaches, which ultimately lead to the resolution required for the analysis of highly controlled molecular processes taking place within live cells. We also describe the efforts being made towards physiological approaches within the context of living organisms.
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Affiliation(s)
- Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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167
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Hicks MJ, Yang CR, Kotlajich MV, Hertel KJ. Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns. PLoS Biol 2006; 4:e147. [PMID: 16640457 PMCID: PMC1450099 DOI: 10.1371/journal.pbio.0040147] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 03/09/2006] [Indexed: 11/19/2022] Open
Abstract
RNA processing is carried out in close proximity to the site of transcription, suggesting a regulatory link between transcription and pre-mRNA splicing. Using an in vitro transcription/splicing assay, we demonstrate that an association of RNA polymerase II (Pol II) transcription and pre-mRNA splicing is required for efficient gene expression. Pol II-synthesized RNAs containing functional splice sites are protected from nuclear degradation, presumably because the local concentration of the splicing machinery is sufficiently high to ensure its association over interactions with nucleases. Furthermore, the process of transcription influences alternative splicing of newly synthesized pre-mRNAs. Because other RNA polymerases do not provide similar protection from nucleases, and their RNA products display altered splicing patterns, the link between transcription and RNA processing is RNA Pol II-specific. We propose that the connection between transcription by Pol II and pre-mRNA splicing guarantees an extended half-life and proper processing of nascent pre-mRNAs. A novel in vitro method to study transcription and splicing leads to the proposal that linking transcription by Pol II and pre-mRNA splicing guarantees an extended half-life and proper processing of nascent pre-mRNAs.
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Affiliation(s)
- Martin J Hicks
- 1Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Chin-Rang Yang
- 1Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
- 2Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
| | - Matthew V Kotlajich
- 1Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Klemens J Hertel
- 1Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
- 2Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, California, United States of America
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168
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Ling Y, Smith AJ, Morgan GT. A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear targeting by human TFIIS. Nucleic Acids Res 2006; 34:2219-29. [PMID: 16648364 PMCID: PMC1450333 DOI: 10.1093/nar/gkl239] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The three structural domains of transcription elongation factor TFIIS are conserved from yeast to human. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified previously in other transcription factors. We found this conserved sequence, the LW motif, in another three human proteins that are predominantly nuclear localized. We investigated two examples to determine whether the LW motif is actually a dedicated nuclear targeting signal. However, in one of the newly identified proteins, hIWS1 (human Iws1), a region containing classic nuclear localization signals (NLS) rather than the LW motif was necessary and sufficient for nuclear targeting in HeLa cells. In contrast, human TFIIS does not possess an NLS and only constructs containing the LW motif were efficiently targeted to nuclei. Moreover, mutations in the motif could cause cytoplasmic accumulation of TFIIS and enabled a structure/function assay for the domain based on the efficiency of nuclear targeting. Finally, GST pull-down assays showed that the LW motif is part of a protein-binding domain. We suggest that the targeting role the LW motif plays in TFIIS arises from its more general function as a protein interaction domain, enabling TFIIS to bind a carrier protein(s) that accomplishes nuclear import.
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Affiliation(s)
| | | | - Garry T. Morgan
- To whom correspondence should be addressed. Tel: +44 115 823 0390; Fax: +44 115 823 0313;
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169
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Gullerova M, Barta A, Lorkovic ZJ. AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II. RNA (NEW YORK, N.Y.) 2006; 12:631-43. [PMID: 16497658 PMCID: PMC1421086 DOI: 10.1261/rna.2226106] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
AtCyp59 and its orthologs from different organisms belong to a family of modular proteins consisting of a peptidyl-prolyl cis-trans isomerase (PPIase) domain, followed by an RNA recognition motif (RRM), and a C-terminal domain enriched in charged amino acids. AtCyp59 was identified in a yeast two-hybrid screen as an interacting partner of the Arabidopsis SR protein SCL33/SR33. The interaction with SCL33/SR33 and with a majority of Arabidopsis SR proteins was confirmed by in vitro pull-down assays. Consistent with these interactions, AtCyp59 localizes to the cell nucleus, but it does not significantly colocalize with SR proteins in nuclear speckles. Rather, it shows a punctuate localization pattern resembling transcription sites. Indeed, by using yeast two-hybrid, in vitro pull-down, and immunoprecipitation assays, we found that AtCyp59 interacts with the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. Ectopic expression of the tagged protein in Arabidopsis cell suspension resulted in highly reduced growth that is most probably due to reduced phosphorylation of the CTD. Together our data suggest a possible function of AtCyp59 in activities connecting transcription and pre-mRNA processing. We discuss our data in the context of a dynamic interplay between transcription and pre-mRNA processing.
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Affiliation(s)
- Monika Gullerova
- Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Department of Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9/3, A-1030 Vienna, Austria
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170
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Stanek D, Neugebauer KM. The Cajal body: a meeting place for spliceosomal snRNPs in the nuclear maze. Chromosoma 2006; 115:343-54. [PMID: 16575476 DOI: 10.1007/s00412-006-0056-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 01/27/2006] [Accepted: 01/29/2006] [Indexed: 10/24/2022]
Abstract
Spliceosomal small nuclear ribonucleoprotein particles (snRNPs) are essential pre-mRNA splicing factors that consist of small nuclear RNAs (snRNAs) complexed with specific sets of proteins. A considerable body of evidence has established that snRNP assembly is accomplished after snRNA synthesis in the nucleus through a series of steps involving cytoplasmic and nuclear phases. Recent work indicates that snRNPs transiently localize to the Cajal body (CB), a nonmembrane-bound inclusion present in the nuclei of most cells, for the final steps in snRNP maturation, including snRNA base modification, U4/U6 snRNA annealing, and snRNA-protein assembly. Here, we review these findings that suggest a crucial role for CBs in the spliceosome cycle in which production of new snRNPs--and perhaps regenerated snRNPs after splicing--is promoted by the concentration of substrates in this previously mysterious subnuclear organelle. These insights allow us to speculate on the role of nuclear bodies in regulating the dynamics of RNP assembly to maintain a functional pool of factors available for key steps in gene expression.
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Affiliation(s)
- David Stanek
- Department of Cellular Biology and Pathology, First Medical Faculty, Institute of Physiology, Charles University, Academy of Sciences of the Czech Republic, Albertov 4, Prague 2, 128 00, Czech Republic.
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171
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Le Texier V, Riethoven JJ, Kumanduri V, Gopalakrishnan C, Lopez F, Gautheret D, Thanaraj TA. AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics 2006; 7:169. [PMID: 16556303 PMCID: PMC1435940 DOI: 10.1186/1471-2105-7-169] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 03/23/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect data & annotation individually for each of these variants. It is important to take an integrated view of these data sets and to derive a data set of alternate transcripts along with consolidated annotation. We have been developing in the past computational pipelines that generate value-added data at genome-scale on individual variant types; these include AltSplice on splicing and AltPAS on polyadenylation. We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants. DESCRIPTION The AltSplice pipeline examines gene-transcript alignments and delineates alternative splice events and splice patterns; this pipeline is extended as AltTrans to delineate isoform transcript patterns for each of which both introns/exons and 'terminating' polyA site are delineated; EST/mRNA sequences that qualify the transcript pattern confirm both the underlying splicing and polyadenylation. The AltPAS pipeline examines gene-transcript alignments and delineates all potential polyA sites irrespective of underlying splicing patterns. Resultant polyA sites from both AltTrans and AltPAS are merged. The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features. The data (named as integrated AltTrans data) generated for both the organisms of human and mouse is made available through the Alternate Transcript Diversity web site at http://www.ebi.ac.uk/atd/. CONCLUSION The reported data set presents alternate transcript patterns that are annotated for both alternative splicing and alternative polyadenylation. Results based on current transcriptome data indicate that the contribution of alternative splicing is larger than that of alternative polyadenylation.
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Affiliation(s)
- Vincent Le Texier
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jean-Jack Riethoven
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- 18 Crispin Close, Haverhill, Suffolk, CB9 9PT, UK
| | - Vasudev Kumanduri
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Chellappa Gopalakrishnan
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Fabrice Lopez
- INSERM ERM206, Université de la Méditerranée, Luminy case 928 – 13 288 Marseille Cedex 09, France
| | - Daniel Gautheret
- INSERM ERM206, Université de la Méditerranée, Luminy case 928 – 13 288 Marseille Cedex 09, France
| | - Thangavel Alphonse Thanaraj
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- 4 Copperfields, Saffron Walden, Essex, CB11 4FG, UK
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172
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Vargovic P, Pokorný R, Hölker U, Hofer M, Varecka L. Light accelerates the splicing of srh1 homologue gene transcripts in aerial mycelia of Trichoderma viride. FEMS Microbiol Lett 2006; 254:240-4. [PMID: 16445751 DOI: 10.1111/j.1574-6968.2005.00047.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The expression of the Tvsrh1 gene encoding conidial hydrophobin was investigated during the development of surface-cultivated Trichoderma viride mycelia under different illumination regimes. Three transcripts of the whole gene amplified from the total mRNA were found with lengths of 400, 323 and 272 bp. The 400-bp transcript was slowly converted to the shorter forms in the dark. Light-pulse dramatically increased the rate of conversion, and a permanent illumination of mycelia was most efficient in this process. The sequencing of transcripts revealed that the 400 bp transcript contains two introns, whereas the intermediate one contains only one intron located distally from the 5'-end. The shortest transcript was without introns. The sum of all transcripts remained almost unchanged in the dark and increased upon the light pulse but decreased during development under permanent illumination. The appearance of conidia coincided with the complete conversion of the transcripts. The results showed that the splicing of the two introns was not random but sequential, and that it did not follow the cotranscriptional mechanism. Furthermore, they suggested that mRNA processing could represent another regulation level of gene expression by light during the photo-induced conidiation in T. viride.
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Affiliation(s)
- Peter Vargovic
- Department of Biochemistry and Microbiology, Slovak University of Technology, Bratislava, Slovakia
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173
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Yilmaz A, Fernandez S, Lairmore MD, Boris-Lawrie K. Coordinate enhancement of transgene transcription and translation in a lentiviral vector. Retrovirology 2006; 3:13. [PMID: 16480517 PMCID: PMC1388234 DOI: 10.1186/1742-4690-3-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Accepted: 02/15/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coordinate enhancement of transgene transcription and translation would be a potent approach to significantly improve protein output in a broad array of viral vectors and nonviral expression systems. Many vector transgenes are complementary DNA (cDNA). The lack of splicing can significantly reduce the efficiency of their translation. Some retroviruses contain a 5' terminal post-transcriptional control element (PCE) that facilitates translation of unspliced mRNA. Here we evaluated the potential for spleen necrosis virus PCE to stimulate protein production from HIV-1 based lentiviral vector by: 1) improving translation of the internal transgene transcript; and 2) functionally synergizing with a transcriptional enhancer to achieve coordinate increases in RNA synthesis and translation. RESULTS Derivatives of HIV-1 SIN self-inactivating lentiviral vector were created that contain PCE and cytomegalovirus immediate early enhancer (CMV IE). Results from transfected cells and four different transduced cell types indicate that: 1) PCE enhanced transgene protein synthesis; 2) transcription from the internal promoter is enhanced by CMV IE; 3) PCE and CMV IE functioned synergistically to significantly increase transgene protein yield; 4) the magnitude of translation enhancement by PCE was similar in transfected and transduced cells; 5) differences were observed in steady state level of PCE vector RNA in transfected and transduced cells; 6) the lower steady state was not attributable to reduced RNA stability, but to lower cytoplasmic accumulation in transduced cells. CONCLUSION PCE is a useful tool to improve post-transcriptional expression of lentiviral vector transgene. Coordinate enhancement of transcription and translation is conferred by the combination of PCE with CMV IE transcriptional enhancer and increased protein yield up to 11 to 17-fold in transfected cells. The incorporation of the vector provirus into chromatin correlated with reduced cytoplasmic accumulation of PCE transgene RNA. We speculate that epigenetic modulation of promoter activity altered cotranscriptional recruitment of RNA processing factors and reduced the availability of fully processed transcript or the efficiency of export from the nucleus. Our results provide an example of the dynamic interplay between the transcription and post-transcription steps of gene expression and document that introduction of heterologous gene expression signals can yield disparate effects in transfected versus transduced cells.
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Affiliation(s)
- Alper Yilmaz
- Center for Retrovirus Research and Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
- Molecular, Cellular & Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Soledad Fernandez
- Center for Biostatistics, The Ohio State University, Columbus, OH, 43210, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael D Lairmore
- Center for Retrovirus Research and Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
- Department of Molecular Virology, Immunology & Medical Genetics, The Ohio State University, Columbus, OH, 43210, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
- Molecular, Cellular & Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Kathleen Boris-Lawrie
- Center for Retrovirus Research and Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
- Department of Molecular Virology, Immunology & Medical Genetics, The Ohio State University, Columbus, OH, 43210, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
- Molecular, Cellular & Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
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174
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Abstract
The mammalian nucleus is arguably the most complex cellular organelle. It houses the vast majority of an organism's genetic material and is the site of all major genome regulatory processes. Reductionist approaches have been spectacularly successful at dissecting at the molecular level many of the key processes that occur within the nucleus, particularly gene expression. At the same time, the limitations of analyzing single nuclear processes in spatial and temporal isolation and the validity of generalizing observations of single gene loci are becoming evident. The next level of understanding of genome function is to integrate our knowledge of their sequences and the molecular mechanisms involved in nuclear processes with our insights into the spatial and temporal organization of the nucleus and to elucidate the interplay between protein and gene networks in regulatory circuits. To do so, catalogues of genomes and proteomes as well as a precise understanding of the behavior of molecules in living cells are required. Converging technological developments in genomics, proteomics, dynamics and computation are now leading towards such an integrated biological understanding of genome biology and nuclear function.
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Affiliation(s)
- Stanislaw Gorski
- National Cancer Institute, NIH, 41 Library Drive, Bethesda, MD 20892, USA.
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175
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Penheiter KL, Washburn TM, Porter SE, Hoffman MG, Jaehning JA. A posttranscriptional role for the yeast Paf1-RNA polymerase II complex is revealed by identification of primary targets. Mol Cell 2006; 20:213-23. [PMID: 16246724 DOI: 10.1016/j.molcel.2005.08.023] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/03/2005] [Accepted: 08/22/2005] [Indexed: 11/22/2022]
Abstract
The yeast Paf1 complex (Paf1C: Paf1, Cdc73, Ctr9, Rtf1, and Leo1) is associated with RNA Polymerase II (Pol II) at promoters and coding regions of transcriptionally active genes, but transcript abundance for only a small subset of genes is altered by loss of Paf1. By using conditional and null alleles of PAF1 and microarrays, we determined the identity of both primary and secondary targets of the Paf1C. Neither primary nor secondary Paf1C target promoters were responsive to loss of Paf1. Instead, Paf1 loss altered poly(A) site utilization of primary target genes SDA1 and MAK21, resulting in increased abundance of 3'-extended mRNAs. The 3'-extended MAK21 RNA is sensitive to nonsense-mediated decay (NMD), as revealed by its increased abundance in the absence of Upf1. Therefore, although the Paf1C is associated with Pol II at initiation and during elongation, these critical Paf1-dependent changes in transcript abundance are due to alterations in posttranscriptional processing.
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Affiliation(s)
- Kristi L Penheiter
- Department of Biochemistry and Molecular Genetics and Molecular Biology Program, University of Colorado, Denver, USA
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176
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Jeffares DC, Mourier T, Penny D. The biology of intron gain and loss. Trends Genet 2006; 22:16-22. [PMID: 16290250 DOI: 10.1016/j.tig.2005.10.006] [Citation(s) in RCA: 195] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 09/02/2005] [Accepted: 10/25/2005] [Indexed: 12/21/2022]
Abstract
Intron density in eukaryote genomes varies by more than three orders of magnitude, so there must have been extensive intron gain and/or intron loss during evolution. A favored and partial explanation for this range of intron densities has been that introns have accumulated stochastically in large eukaryote genomes during their evolution from an intron-poor ancestor. However, recent studies have shown that some eukaryotes lost many introns, whereas others accumulated and/or gained many introns. In this article, we discuss the growing evidence that these differences are subject to selection acting on introns depending on the biology of the organism and the gene involved.
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Affiliation(s)
- Daniel C Jeffares
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, CB10 1SA.
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177
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Azubel M, Habib N, Sperling R, Sperling J. Native spliceosomes assemble with pre-mRNA to form supraspliceosomes. J Mol Biol 2005; 356:955-66. [PMID: 16386271 DOI: 10.1016/j.jmb.2005.11.078] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 11/28/2005] [Accepted: 11/28/2005] [Indexed: 11/16/2022]
Abstract
Regulation of eukaryotic gene expression is achieved at different levels, which require accurate coordination. Macromolecular assemblies that exist as pre-formed entities can account for such coordination. Processing of pre-mRNA represents one step in this cascade of regulatory events but, moreover, provides explanation for protein versatility. The cellular machine where splicing of pre-mRNA, as well as additional processing events, take place in vivo is termed the supraspliceosome. Here, we show that the supraspliceosome is composed of four active spliceosomes, termed native spliceosomes, connected to each other by the pre-mRNA. Cleavage of pre-mRNA shows that its integrity is essential for the stability of the supraspliceosome. Furthermore, supraspliceosomes can be reconstituted in vitro, from purified native spliceosomes by addition of synthetic pre-mRNAs, providing further support to the supraspliceosome as a preassembled biological complex. The internal setting of the native spliceosomes within the supraspliceosome is most suitable to enable the communication between these structures, which is crucial in order to achieve regulated splicing.
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Affiliation(s)
- Maia Azubel
- Deptartment of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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178
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Meyer IM, Miklós I. Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucleic Acids Res 2005; 33:6338-48. [PMID: 16275783 PMCID: PMC1278941 DOI: 10.1093/nar/gki923] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes for evolutionarily conserved secondary structure elements using RNA-Decoder, a comparative secondary structure prediction program that is capable of explicitly taking the known protein-coding context of the mRNA sequences into account. We detect well-defined, conserved RNA secondary structure elements in the coding regions of the mRNA sequences and show that base-paired codons strongly correlate with sparse codons. We also investigate the role of repetitive elements in the formation of secondary structure and explain the use of alternate start codons in the caveolin-1 gene by a conserved secondary structure element overlapping the nominal start codon. We discuss the functional roles of our novel findings in regulating the gene expression on mRNA level. We also investigate the role of secondary structure on the correct splicing of the human CFTR gene. We study the wild-type version of the pre-mRNA as well as 29 variants with synonymous mutations in exon 12. By comparing our predicted secondary structures to the experimentally determined splicing efficiencies, we find with weak statistical significance that pre-mRNAs with high-splicing efficiencies have different predicted secondary structures than pre-mRNAs with low-splicing efficiencies.
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Affiliation(s)
- Irmtraud M Meyer
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.
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179
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Fededa JP, Petrillo E, Gelfand MS, Neverov AD, Kadener S, Nogués G, Pelisch F, Baralle FE, Muro AF, Kornblihtt AR. A polar mechanism coordinates different regions of alternative splicing within a single gene. Mol Cell 2005; 19:393-404. [PMID: 16061185 DOI: 10.1016/j.molcel.2005.06.035] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 03/14/2005] [Accepted: 06/30/2005] [Indexed: 11/20/2022]
Abstract
Alternative splicing plays a key role in generating protein diversity. Transfections with minigenes revealed coordination between two distant, alternatively spliced exons in the same gene. Mutations that either inhibit or stimulate inclusion of the upstream alternative exon deeply affect inclusion of the downstream one. However, similar mutations at the downstream alternative exon have little effect on the upstream one. This polar effect is promoter specific and is enhanced by inhibition of transcriptional elongation. Consistently, cells from mutant mice with either constitutive or null inclusion of a fibronectin alternative exon revealed coordination with a second alternative splicing region, located far downstream. Using allele-specific RT-PCR, we demonstrate that this coordination occurs in cis and is also affected by transcriptional elongation rates. Bioinformatics supports the generality of these findings, indicating that 25% of human genes contain multiple alternative splicing regions and identifying several genes with nonrandom distribution of mRNA isoforms at two alternative regions.
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Affiliation(s)
- Juan P Fededa
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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180
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Lin JC, Tarn WY. Exon selection in alpha-tropomyosin mRNA is regulated by the antagonistic action of RBM4 and PTB. Mol Cell Biol 2005; 25:10111-21. [PMID: 16260624 PMCID: PMC1280272 DOI: 10.1128/mcb.25.22.10111-10121.2005] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 07/05/2005] [Accepted: 08/19/2005] [Indexed: 12/26/2022] Open
Abstract
RNA-binding motif protein 4 (RBM4) has been implicated in the regulation of precursor mRNA splicing. Using differential display analysis, we identified mRNAs that associate with RBM4-containing messenger RNPs in vivo. Among these mRNAs, alpha-tropomyosin (alpha-TM) is known to exhibit a muscle cell type-specific splicing pattern. The level of the skeletal muscle-specific alpha-TM mRNA isoform partially correlated with that of RBM4 in human tissues examined and could be modulated by ectopic overexpression or suppression of RBM4. These results indicated that RBM4 directly influences the expression of the skeletal muscle-specific alpha-TM isoform. Using minigenes, we demonstrated that RBM4 can activate the selection of skeletal muscle-specific exons, possibly via binding to intronic pyrimidine-rich elements. By contrast, the splicing regulator polypyrimidine tract binding protein (PTB) excluded these exons; moreover, RBM4 antagonized this PTB-mediated exon exclusion likely by competing with PTB for binding to a CU-rich element. This study suggests a possible mechanism underlying the regulated alternative splicing of alpha-TM by the antagonistic splicing regulators RBM4 and PTB.
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Affiliation(s)
- Jung-Chun Lin
- Institute of Biomedical Sciences, Academia Sinica, 128 Academy Road Section 2, Nankang, Taipei 11529, Taiwan
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181
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Abstract
mRNAs are transported from the nucleus to the cytoplasm by a machinery conserved from yeast to humans. Previous studies showed that mRNA export factors are loaded on nascent mRNAs during elongation, coupling transcription to export. More recently identified mRNA export factors connect transcription initiation to the export machinery associated with nuclear pores, and potentially tether active genes to the nuclear periphery. Furthermore, a newly identified link between the nuclear exosome and the transcription, 3'-end formation and export machineries suggests that early messenger ribonucleoprotein complex (mRNP) assembly is co-transcriptionally monitored. Moreover, inefficient mRNP assembly impairs transcription elongation, indicating tight interdependence of these processes. Finally, nuclear retention of unspliced mRNAs by the perinuclear Mlp proteins reveals a novel mechanism of mRNP surveillance prior to export.
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Affiliation(s)
- Patrizia Vinciguerra
- Department of Cell Biology, University of Geneva, Sciences III, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland
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182
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Mabon SA, Misteli T. Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo. PLoS Biol 2005; 3:e374. [PMID: 16231974 PMCID: PMC1262628 DOI: 10.1371/journal.pbio.0030374] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2005] [Accepted: 09/07/2005] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing in mammalian cells has been suggested to be largely controlled by combinatorial binding of basal splicing factors to pre-mRNA templates. This model predicts that distinct sets of pre-mRNA splicing factors are associated with alternatively spliced transcripts. However, no experimental evidence for differential recruitment of splicing factors to transcripts with distinct splicing fates is available. Here we have used quantitative single-cell imaging to test this key prediction in vivo. We show that distinct combinations of splicing factors are recruited to sites of alternatively spliced transcripts in intact cells. While a subset of serine/arginine protein splicing factors, including SF2/ASF, SC35, and SRp20, is efficiently recruited to the tau gene when exon 10 is included, these factors are less frequently associated with tau transcription sites when exon 10 is excluded. In contrast, the frequency of recruitment of several other splicing factors is independent of splicing outcome. Mutation analysis of SF2/ASF shows that both protein–protein as well as protein–RNA interactions are required for differential recruitment. The differential behavior of the various splicing factors provides the basis for combinatorial occupancy at pre-mRNAs. These observations represent the first in vivo evidence for differential association of pre-mRNA splicing factors with alternatively spliced transcripts. They confirm a key prediction of a stochastic model of alternative splicing, in which distinct combinatorial sets of generic pre-mRNA splicing factors contribute to splicing outcome. Quantitative single-cell imaging reveals distinct combinations of splicing factors recruited to sites of alternatively spliced transcripts in intact cells.
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Affiliation(s)
- Stephen A Mabon
- 1National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tom Misteli
- 1National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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183
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Aiyar S, Sun JL, Li R. BRCA1: a locus-specific "liaison" in gene expression and genetic integrity. J Cell Biochem 2005; 94:1103-11. [PMID: 15723343 DOI: 10.1002/jcb.20386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutations in BRCA1 predominantly lead to elevated risks of breast and ovarian cancers. In contrast to the tissue-specific nature of BRCA1tumors, the normal BRCA1 gene product functions in diverse nuclear events including transcription, DNA repair, and DNA damage checkpoint. Recent findings of physical and functional associations between BRCA1 and the RNA polymerase II (RNAPII)-dependent transcription machinery may shed some light on this longstanding paradox of BRCA1 biology. Eukaryotic gene expression is now known to be a continuous process, whereby each step is physically and functionally connected to the next. In particular, RNAPII plays a pivotal role in coordinating transcription with various pre-mRNA processing events and stress response. Interestingly, BRCA1 preferentially interacts with the processive form of RNAPII and proteins that regulate RNAPII activity and movement during transcription elongation. In response to DNA damage, BRCA1 dissociates from RNAPII and localizes to DNA damage sites. We propose that BRCA1 may coordinate multiple steps in gene expression, including transcription initiation, elongation, and pre-mRNA processing via its interactions with the transcription machinery at selected gene loci. The same BRCA1-associated transcription apparatus may serve as a sensor for stress signals and facilitate the transition from a transcription state to checkpoint/DNA repair state. Such a coordinating role of BRCA1 in gene expression may ensure the appropriate quantity and quality of the mature transcripts for certain breast and ovarian cancer-related genes, as well as the genetic integrity of the breast and ovary tissues.
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Affiliation(s)
- Sarah Aiyar
- Department of Biochemistry and Molecular Genetics, School of Medicine, P.O. Box 800733, University of Virginia, Charlottesville, Virginia 22908-0733, USA
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184
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Chapman RD, Conrad M, Eick D. Role of the mammalian RNA polymerase II C-terminal domain (CTD) nonconsensus repeats in CTD stability and cell proliferation. Mol Cell Biol 2005; 25:7665-74. [PMID: 16107713 PMCID: PMC1190292 DOI: 10.1128/mcb.25.17.7665-7674.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The C-terminal domain (CTD) of mammalian RNA polymerase II (Pol II) consists of 52 repeats of the consensus heptapeptide YSPTSPS and links transcription to the processing of pre-mRNA. The length of the CTD and the number of repeats diverging from the consensus sequence have increased through evolution, but their functional importance remains unknown. Here, we show that the deletion of repeats 1 to 3 or 52 leads to cleavage and degradation of the CTD from Pol II in vivo. Including these repeats, however, allowed the construction of stable, synthetic CTDs. To our surprise, polymerases consisting of just consensus repeats could support normal growth and viability of cells. We conclude that all other nonconsensus CTD repeats are dispensable for the transcription and pre-mRNA processing of genes essential for proliferation.
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Affiliation(s)
- Rob D Chapman
- GSF-Research Centre for Environment and Health, Institute for Clinical Molecular Biology and Tumour Genetics, Munich, Germany.
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185
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Sjölinder M, Björk P, Söderberg E, Sabri N, Farrants AKO, Visa N. The growing pre-mRNA recruits actin and chromatin-modifying factors to transcriptionally active genes. Genes Dev 2005; 19:1871-84. [PMID: 16103215 PMCID: PMC1186187 DOI: 10.1101/gad.339405] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In the dipteran Chironomus tentans, actin binds to hrp65, a nuclear protein associated with mRNP complexes. Disruption of the actin-hrp65 interaction in vivo by the competing peptide 65-2CTS reduces transcription drastically, which suggests that the actin-hrp65 interaction is required for transcription. We show that the inhibitory effect of the 65-2CTS peptide on transcription is counteracted by trichostatin A, a drug that inhibits histone deacetylation. We also show that actin and hrp65 are associated in vivo with p2D10, an evolutionarily conserved protein with histone acetyltransferase activity that acts on histone H3. p2D10 is recruited to class II genes in a transcription-dependent manner. We show, using the Balbiani ring genes of C. tentans as a model system, that p2D10 is cotranscriptionally associated with the growing pre-mRNA. We also show that experimental disruption of the actin-hrp65 interaction by the 65-2CTS peptide in vivo results in the release of p2D10 from the transcribed genes, reduced histone H3 acetylation, and a lower level of transcription activity. Furthermore, antibodies against p2D10 inhibit run-on elongation. Our results suggest that actin, hrp65, and p2D10 are parts of a positive feedback mechanism that contributes to maintaining the active transcription state of a gene by recruiting HATs at the RNA level.
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Affiliation(s)
- Mikael Sjölinder
- Department of Molecular Biology and Functional Genomics, The Wenner-Gren Institute, Stockholm University, Sweden
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186
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Abstract
From the very beginning, mRNAs have a complex existence. They are transcribed, capped, spliced, modified at the 3'end, exported from the nucleus, translated, and eventually degraded. These many events not only affect the overall survival and properties of an mRNA, but are also carefully co-ordinated and integrated with quality control mechanisms that function to ensure that only 'proper' mRNAs are translated at the correct developmental time and place. This does not mean that all mRNAs follow a single or uniform path from synthesis to death. Instead, there are diverse means by which the activities of specific mRNAs are regulated, and these controls often depend upon multiple events in the mRNA's life. mRNAs are not found naked in the cell, instead they are part of complex RNPs (ribonucleoproteins) that consist of many factors. These RNPs are highly dynamic structures that change during the lifetime of a given RNA; linking events such as synthesis and processing to the final fate of the mRNA. Here, we will discuss what is known of the assembly of RNPs in general, with specific reference to the myriad of connections between different nuclear events and the cytoplasmic activity of an mRNA. Due to space limitations this review is not comprehensive, instead we focus on specific examples to illustrate these emerging themes in gene expression.
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Affiliation(s)
- Scott Kuersten
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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187
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Abstract
The universal pre-mRNA processing events of 5' end capping, splicing, and 3' end formation by cleavage/polyadenylation occur co-transcriptionally. As a result, the substrate for mRNA processing factors is a nascent RNA chain that is being extruded from the RNA polymerase II exit channel at 10-30 bases per second. How do processing factors find their substrate RNAs and complete most mRNA maturation before transcription is finished? Recent studies suggest that this task is facilitated by a combination of protein-RNA and protein-protein interactions within a 'mRNA factory' that comprises the elongating RNA polymerase and associated processing factors. This 'factory' undergoes dynamic changes in composition as it traverses a gene and provides the setting for regulatory interactions that couple processing to transcriptional elongation and termination.
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Affiliation(s)
- David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Aurora, Colorado 80045, USA.
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188
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Abstract
Recent findings justify a renewed interest in alternative splicing (AS): the process is more a rule than an exception as it affects the expression of 60% of human genes; it explains how a vast mammalian proteomic complexity is achieved with a limited number of genes; and mutations in AS regulatory sequences are a widespread source of human disease. AS regulation not only depends on the interaction of splicing factors with their target sequences in the pre-mRNA but is coupled to transcription. A clearer picture is emerging of the mechanisms by which transcription affects AS through promoter identity and occupation. These mechanisms involve the recruitment of factors with dual functions in transcription and splicing (i.e. that contain both functional domains and hence link the two processes) and the control of RNA polymerase II elongation.
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Affiliation(s)
- Alberto R Kornblihtt
- Laboratorio de Fisiologia y Biologia Molecular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon 2, 2 piso, C1428EHA Buenos Aires, Argentina.
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189
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Zhu B, Mandal SS, Pham AD, Zheng Y, Erdjument-Bromage H, Batra SK, Tempst P, Reinberg D. The human PAF complex coordinates transcription with events downstream of RNA synthesis. Genes Dev 2005; 19:1668-73. [PMID: 16024656 PMCID: PMC1176003 DOI: 10.1101/gad.1292105] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The yeast PAF (yPAF) complex interacts with RNA polymerase II and coordinates the setting of histone marks associated with active transcription. We report the isolation and functional characterization of the human PAF (hPAF) complex. hPAF shares four subunits with yPAF (hCtr9, hPaf1, hLeo1, and hCdc73), but contains a novel higher eukaryotic-specific subunit, hSki8. RNAi against hSki8 or hCtr9 reduces the cellular levels of other hPAF subunits and of mono- and trimethylated H3-Lys 4 and dimethylated H3-Lys 79. The hSki8 subunit is also a component of the human SKI (hSKI) complex. Yeast SKI complex is cytoplasmic and together with Exosome mediates 3'-5' mRNA degradation. However, hSKI complex localizes to both nucleus and cytoplasm. Immunoprecipitation experiments revealed that hPAF and hSKI complexes interact, and ChIP experiments demonstrated that hSKI associates with transcriptionally active genes dependent on the presence of hPAF. Thus, in addition to coordinating events during transcription (initiation, promoter clearance, and elongation), hPAF also coordinates events in RNA quality control.
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Affiliation(s)
- Bing Zhu
- Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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190
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Görnemann J, Kotovic KM, Hujer K, Neugebauer KM. Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell 2005; 19:53-63. [PMID: 15989964 DOI: 10.1016/j.molcel.2005.05.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 04/05/2005] [Accepted: 05/09/2005] [Indexed: 10/25/2022]
Abstract
Coupling between transcription and pre-mRNA splicing is a key regulatory mechanism in gene expression. Here, we investigate cotranscriptional spliceosome assembly in yeast, using in vivo crosslinking to determine the distribution of spliceosome components along intron-containing genes. Accumulation of the U1, U2, and U5 small nuclear ribonucleoprotein particles (snRNPs) and the 3' splice site binding factors Mud2p and BBP was detected in patterns indicative of progressive and complete spliceosome assembly; recruitment of the nineteen complex (NTC) component Prp19p suggests that splicing catalysis is also cotranscriptional. The separate dynamics of the U1, U2, and U5 snRNPs are consistent with stepwise recruitment of individual snRNPs rather than a preformed "penta-snRNP", as recently proposed. Finally, we show that the cap binding complex (CBC) is necessary, but not sufficient, for cotranscriptional spliceosome assembly. Thus, the demonstration of an essential link between CBC and spliceosome assembly in vivo indicates that 5' end capping couples pre-mRNA splicing to transcription.
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Affiliation(s)
- Janina Görnemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
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191
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Lacadie SA, Rosbash M. Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5'ss base pairing in yeast. Mol Cell 2005; 19:65-75. [PMID: 15989965 DOI: 10.1016/j.molcel.2005.05.006] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 04/05/2005] [Accepted: 05/09/2005] [Indexed: 11/16/2022]
Abstract
To investigate the mechanism of spliceosome assembly in vivo, we performed chromatin immunoprecipitation (ChIP) analysis of U1, U2, and U5 small nuclear ribonucleoprotein particles (snRNPs) to intron-containing yeast (S. cerevisiae) genes. The snRNPs display patterns that indicate a cotranscriptional assembly model: U1 first, then U2, and the U4/U6*U5 tri-snRNP followed by U1 destabilization. cis-splicing mutations also support a role of U2 and/or the tri-snRNP in U1 destabilization. Moreover, they indicate that splicing efficiency has a major impact on cotranscriptional snRNP recruitment and suggest that cotranscriptional recruitment of U2 or the tri-snRNP is required to commit the pre-mRNA to splicing. Branchpoint (BP) mutations had a major effect on the U1 pattern, whereas 5' splice site (5'ss) mutations had a stronger effect on the U2 pattern. A 5'ss-U1 snRNA complementation experiment suggests that pairing between U1 and the 5'ss occurs after U1 recruitment and contributes to a specific U1:substrate conformation required for efficient U2 and tri-snRNP recruitment.
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Affiliation(s)
- Scott A Lacadie
- Howard Hughes Medical Institute, Biology Department MS008, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA
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192
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Ballarino M, Morlando M, Pagano F, Fatica A, Bozzoni I. The cotranscriptional assembly of snoRNPs controls the biosynthesis of H/ACA snoRNAs in Saccharomyces cerevisiae. Mol Cell Biol 2005; 25:5396-403. [PMID: 15964797 PMCID: PMC1156983 DOI: 10.1128/mcb.25.13.5396-5403.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The carboxy-terminal domain (CTD) of RNA polymerase II large subunit acts as a platform to assemble the RNA processing machinery in a controlled way throughout the transcription cycle. In yeast, recent findings revealed a physical connection between phospho-CTD, generated by the Ctk1p kinase, and protein factors having a function in small nucleolar RNA (snoRNA) biogenesis. The snoRNAs represent a large family of polymerase II noncoding transcripts that are associated with highly conserved polypeptides to form stable ribonucleoprotein particles (snoRNPs). In this work, we have studied the biogenesis of the snoRNPs belonging to the box H/ACA class. We report that the assembly factor Naf1p and the core components Cbf5p and Nhp2p are recruited on H/ACA snoRNA genes very early during transcription. We also show that the cotranscriptional recruitment of Naf1p and Cbf5p is Ctk1p dependent and that Ctk1p and Cbf5p are required for preventing the readthrough into the snoRNA downstream genes. All these data suggest that proper cotranscriptional snoRNP assembly controls 3'-end formation of snoRNAs and, consequently, the release of a functional particle.
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Affiliation(s)
- Monica Ballarino
- Institute Pasteur Fondazione Cenci-Bolognetti, Department of Genetics and Molecular Biology, University La Sapienza, P.le A. Moro 5, 00185 Rome, Italy
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193
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Abstract
Production of mature mRNAs that encode functional proteins consists of a highly complex pathway of synthesis, processing and export. Along this pathway, the mRNA transcript is scrutinized by quality control machinery at numerous steps. Such extensive RNA surveillance ensures that only correctly processed mature mRNAs are translated and precludes production of aberrant transcripts that could encode mutant or possibly deleterious proteins.
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Affiliation(s)
- Milo B Fasken
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, NE, Atlanta, Georgia 30322, USA
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194
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Gomez E, Rodríguez A, Goyache F, Díez C, José Royo L, Moreira PN, Néstor Caamaño J, Morán E, Gutiérrez-Adán A. Retinoid-dependent mRNA expression and poly-(A) contents in bovine oocytes meiotically arrested and/or matured in vitro. Mol Reprod Dev 2005; 69:101-8. [PMID: 15278910 DOI: 10.1002/mrd.20154] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The presence of retinoic acid (RA) during in vitro maturation (IVM) improves bovine oocyte quality and developmental potential. In this work, we investigated the underlying molecular mechanisms. Cumulus-oocyte complexes were meiotically arrested by roscovitine and/or matured in defined medium containing RA, 1% ethanol (vehicle), or no additives. Cumulus-free oocytes were analyzed for poly-(A) mRNA contents and relative mRNA expression of genes involved in cell cycle regulation (cyclin B1 and H1) and antioxidative defence (Mn-superoxide dismutase and glucose-6-phosphate dehydrogenase). Poly-(A) mRNA increased after meiotic inhibition and decreased with IVM completion, both in meiotically arrested and permissively matured oocytes, i.e., matured without previous meiotic arrest. RA dramatically increased poly-(A) mRNA in meiotically arrested oocytes, but more than half of the poly-(A) mRNA disappeared during maturation. Irrespective of oocyte origin, transcripts were detected for all the genes analyzed. IVM, with or without previous meiotic inhibition, increased expression of cyclin B1 and glucose-6-phosphate dehydrogenase, and decreased cyclin H1 and Mn-superoxide dismutase. Except for a decreasing of Mn-superoxide dismutase in meiotically arrested and matured oocytes, RA did not affect mRNA expression. Ethanol led to an abnormal poly-(A) mRNA profile and expression of all the genes analyzed. RA does not modify expression of cyclin B1 and HI genes in the bovine oocyte, and probably does not generate oxidative stress. In addition, RA enhanced mRNA amount as measured by poly-(A) mRNA contents.
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Affiliation(s)
- Enrique Gomez
- Servicio Regional de Investigación y Desarrollo Agroalimentario, Area de Genética y Reproducción Animal, Camino de los Claveles, 604-Somio, Gijón 33203, Asturias, Spain.
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195
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196
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Auboeuf D, Dowhan DH, Dutertre M, Martin N, Berget SM, O'Malley BW. A subset of nuclear receptor coregulators act as coupling proteins during synthesis and maturation of RNA transcripts. Mol Cell Biol 2005; 25:5307-16. [PMID: 15964789 PMCID: PMC1156981 DOI: 10.1128/mcb.25.13.5307-5316.2005] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Didier Auboeuf
- INSERM U685/AVENIR, Centre G. Hayem, Hôpital Saint Louis, Paris, France.
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197
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Belostotsky DA, Rose AB. Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events. TRENDS IN PLANT SCIENCE 2005; 10:347-53. [PMID: 15951220 DOI: 10.1016/j.tplants.2005.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 04/20/2005] [Accepted: 05/26/2005] [Indexed: 05/02/2023]
Abstract
The extensive mechanistic and regulatory interconnections between the various events of mRNA biogenesis are now recognized as a fundamental principle of eukaryotic gene expression, yet the specific details of the coupling between the various steps of mRNA biogenesis do differ, and sometimes dramatically, between the different kingdoms. In this review, we emphasize examples where plants must differ in this respect from other eukaryotes, and highlight a recurring trend of recruiting the conserved, versatile functional modules, which have evolved to support the general mRNA biogenesis reactions, for plant-specific functions. We also argue that elucidating the inner workings of the plant 'mRNA factory' is essential for accomplishing the ambitious goal of building the 'virtual plant'.
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Affiliation(s)
- Dmitry A Belostotsky
- Department of Biological Sciences, State University of New York at Albany, 1400 Washington Ave, Albany, NY 12222, USA.
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198
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Abstract
Although it is frequently assumed that translation does not occur in eukaryotic nuclei, recent evidence suggests that some translation can take place and that it is closely coupled to transcription. The first evidence concerns the destruction of nuclear mRNAs containing premature termination codons by nonsense-mediated decay (NMD). Only ribosomes can detect termination codons, and as some NMD occurs within the nuclear fraction, active nuclear ribosomes could perform the required detection. The second evidence is the demonstration that tagged amino acids are incorporated into nascent polypeptides in a nuclear process coupled to transcription. The third evidence is that components involved in translation, NMD and transcription colocalize, coimmunoprecipitate and co-purify. All these results are simply explained if nuclear ribosomes scan nascent transcripts for premature termination codons at the site of transcription. Alternatively, the scanning needed for NMD might take place at the nuclear membrane, and contaminating cytoplasmic ribosomes might give the appearance of some nuclear translation. We argue, however, that the balance of evidence favours bona fide nuclear translation.
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Affiliation(s)
- Francisco J Iborra
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
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199
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Durand LO, Advani SJ, Poon APW, Roizman B. The carboxyl-terminal domain of RNA polymerase II is phosphorylated by a complex containing cdk9 and infected-cell protein 22 of herpes simplex virus 1. J Virol 2005; 79:6757-62. [PMID: 15890914 PMCID: PMC1112163 DOI: 10.1128/jvi.79.11.6757-6762.2005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The infected-cell protein 22 (ICP22), a regulatory protein encoded by the alpha22 gene of herpes simplex virus 1, is required for the optimal expression of a set of late viral proteins that includes the products of the U(S)11, U(L)38, and U(L)41 genes. ICP22 has two activities. Thus, ICP22 and the U(L)13 protein kinase mediate the activation of cdc2 and degradation of its partners, cyclins A and B. cdc2 and its new partner, the DNA polymerase accessory factor (U(L)42), bind topoisomerase IIalpha in an ICP22-dependent manner. In addition, ICP22 and U(L)13 mediate an intermediate phosphorylation of the carboxyl terminus of RNA polymerase II (RNA POL II). Here we report another function of ICP22. Thus, ICP22 physically interacts with cdk9, a constitutively active cyclin-dependent kinase involved in transcriptional regulation. A protein complex containing ICP22 and cdk9 phosphorylates in vitro the carboxyl-terminal domain of RNA POL II in a viral U(S)3 protein kinase-dependent fashion. Finally, the carboxyl-terminal domain of RNA POL II fused to glutathione S-transferase is phosphorylated in reaction mixtures containing complexes pulled down with ICP22 or cdk9 immune precipitated from lysates of wild-type parent virus or deltaU(L)13 but not deltaU(S)3 mutant-infected cells. The experiments described here place ICP22 and cdk9 in a complex with the carboxyl-terminal domain of RNA POL II. At the same time we confirm the requirement of ICP22 and the U(L)13 protein kinase in the posttranslational modification of RNA POL II that alters its electrophoretic mobility, although U(S)3 kinase appears to play a role in a cell-type-dependent fashion.
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Affiliation(s)
- Lizette O Durand
- The Marjorie B. Kovler Viral Oncology Laboratories, The University of Chicago, 910 East 58th Street, Chicago, IL 60637, USA
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200
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Abstract
Pre-messenger RNA (pre-mRNA) splicing is a central step in gene expression. Lying between transcription and protein synthesis, pre-mRNA splicing removes sequences (introns) that would otherwise disrupt the coding potential of intron-containing transcripts. This process takes place in the nucleus, catalyzed by a large RNA-protein complex called the spliceosome. Prp8p, one of the largest and most highly conserved of nuclear proteins, occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there. Recently, Prp8p has also come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa.Prp8 is unique, having no obvious homology to other proteins; however, using bioinformatical analysis we reveal the presence of a conserved RNA recognition motif (RRM), an MPN/JAB domain and a putative nuclear localization signal (NLS). Here, we review biochemical and genetical data, mostly related to the human and yeast proteins, that describe Prp8's central role within the spliceosome and its molecular interactions during spliceosome formation, as splicing proceeds, and in post-splicing complexes.
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Affiliation(s)
- Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
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