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Lesman D, Rodriguez Y, Rajakumar D, Wein N. U7 snRNA, a Small RNA with a Big Impact in Gene Therapy. Hum Gene Ther 2021; 32:1317-1329. [PMID: 34139889 DOI: 10.1089/hum.2021.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The uridine-rich 7 (U7) small nuclear RNA (snRNA) is a component of a small nuclear ribonucleoprotein (snRNP) complex. U7 snRNA naturally contains an antisense sequence that identifies histone premessenger RNAs (pre-mRNAs) and is involved in their 3' end processing. By altering this antisense sequence, researchers have turned U7 snRNA into a versatile tool for targeting pre-mRNAs and modifying splicing. Encapsulating a modified U7 snRNA into a viral vector such as adeno-associated virus (also referred as vectorized exon skipping/inclusion, or VES/VEI) enables the delivery of this highly efficacious splicing modulator into a range of cell lines, primary cells, and tissues. In addition, and in contrast to antisense oligonucleotides, viral delivery of U7 snRNA enables long-term expression of antisense sequences in the nucleus as part of a stable snRNP complex. As a result, VES/VEI has emerged as a promising therapeutic platform for treating a large variety of human diseases caused by errors in pre-mRNA splicing or its regulation. Here we provide an overview of U7 snRNA's natural function and its applications in gene therapy.
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Affiliation(s)
- Daniel Lesman
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Yacidzohara Rodriguez
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Dhanarajan Rajakumar
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Nicolas Wein
- Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatric, The Ohio State University, Columbus, Ohio, USA
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2
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Heyn P, Salmonowicz H, Rodenfels J, Neugebauer KM. Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos. RNA Biol 2016; 14:752-760. [PMID: 27858508 DOI: 10.1080/15476286.2016.1255397] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Nuclear bodies are cellular compartments that lack lipid bilayers and harbor specific RNAs and proteins. Recent proposals that nuclear bodies form through liquid-liquid phase separation leave the question of how different nuclear bodies maintain their distinct identities unanswered. Here we investigate Cajal bodies (CBs), histone locus bodies (HLBs) and nucleoli - involved in assembly of the splicing machinery, histone mRNA 3' end processing, and rRNA processing, respectively - in the embryos of the zebrafish, Danio rerio. We take advantage of the transcriptional silence of the 1-cell embryo and follow nuclear body appearance as zygotic transcription becomes activated. CBs are present from fertilization onwards, while HLB and nucleolar components formed foci several hours later when histone genes and rDNA became active. HLB formation was blocked by transcription inhibition, suggesting nascent histone transcripts recruit HLB components like U7 snRNP. Surprisingly, we found that U7 base-pairing with nascent histone transcripts was not required for localization to HLBs. Rather, the type of Sm ring assembled on U7 determined its targeting to HLBs or CBs; the spliceosomal Sm ring targeted snRNAs to CBs while the specialized U7 Sm-ring localized to HLBs, demonstrating the contribution of protein constituents to the distinction among nuclear bodies. Thus, nucleolar, HLB, and CB components can mix in early embryogenesis when transcription is naturally or artificially silenced. These data support a model in which transcription of specific gene loci nucleates nuclear body components with high specificity and fidelity to perform distinct regulatory functions.
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Affiliation(s)
- Patricia Heyn
- a Max Planck Institute of Molecular Cell Biology and Genetics , Dresden , Germany
| | - Hanna Salmonowicz
- a Max Planck Institute of Molecular Cell Biology and Genetics , Dresden , Germany
| | - Jonathan Rodenfels
- b Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA
| | - Karla M Neugebauer
- b Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA
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3
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Somatic Therapy of a Mouse SMA Model with a U7 snRNA Gene Correcting SMN2 Splicing. Mol Ther 2016; 24:1797-1805. [PMID: 27456062 PMCID: PMC5112044 DOI: 10.1038/mt.2016.152] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/18/2016] [Indexed: 12/12/2022] Open
Abstract
Spinal Muscular Atrophy is due to the loss of SMN1 gene function. The duplicate gene SMN2 produces some, but not enough, SMN protein because most transcripts lack exon 7. Thus, promoting the inclusion of this exon is a therapeutic option. We show that a somatic gene therapy using the gene for a modified U7 RNA which stimulates this splicing has a profound and persistent therapeutic effect on the phenotype of a severe Spinal Muscular Atrophy mouse model. To this end, the U7 gene and vector and the production of pure, highly concentrated self-complementary (sc) adenovirus-associated virus 9 vector particles were optimized. Introduction of the functional vector into motoneurons of newborn Spinal Muscular Atrophy mice by intracerebroventricular injection led to a highly significant, dose-dependent increase in life span and improvement of muscle functions. Besides the central nervous system, the therapeutic U7 RNA was expressed in the heart and liver which may additionally have contributed to the observed therapeutic efficacy. This approach provides an additional therapeutic option for Spinal Muscular Atrophy and could also be adapted to treat other diseases of the central nervous system with regulatory small RNA genes.
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Ruepp MD, Schümperli D, Barabino SML. mRNA 3' end processing and more--multiple functions of mammalian cleavage factor I-68. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 2:79-91. [PMID: 21956970 DOI: 10.1002/wrna.35] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The formation of defined 3(') ends is an important step in the biogenesis of mRNAs. In eukaryotic cells, all mRNA 3(') ends are generated by endonucleolytic cleavage of primary transcripts in reactions that are essentially posttranscriptional. Nevertheless, 3(') end formation is tightly connected to transcription in vivo, and a link with mRNA export to the cytoplasm has been postulated. Here, we briefly review the current knowledge about the two types of mRNA 3(') end processing reactions, cleavage/polyadenylation and histone RNA processing. We then focus on factors shared between these two reactions. In particular, we discuss evidence for new functions of the mammalian cleavage factor I subunit CF I(m) 68 in histone RNA 3(') processing and in the export of mature mRNAs from the nucleus to the cytoplasm.
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Affiliation(s)
- Marc-David Ruepp
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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5
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Marz M, Mosig A, Stadler BMR, Stadler PF. U7 snRNAs: a computational survey. GENOMICS PROTEOMICS & BIOINFORMATICS 2008; 5:187-95. [PMID: 18267300 PMCID: PMC5054213 DOI: 10.1016/s1672-0229(08)60006-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.
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Affiliation(s)
- Manja Marz
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig D-04107, Germany
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6
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Hernandez G, Valafar F, Stumph WE. Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity. Nucleic Acids Res 2006; 35:21-34. [PMID: 17148477 PMCID: PMC1761439 DOI: 10.1093/nar/gkl982] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In animals, most small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II (Pol II), but U6 snRNA is synthesized by RNA polymerase III (Pol III). In Drosophila melanogaster, the promoters for the Pol II-transcribed snRNA genes consist of approximately 21 bp PSEA and approximately 8 bp PSEB. U6 genes utilize a PSEA but have a TATA box instead of the PSEB. The PSEAs of the two classes of genes bind the same protein complex, DmSNAPc. However, the PSEAs that recruit Pol II and Pol III differ in sequence at a few nucleotide positions that play an important role in determining RNA polymerase specificity. We have now performed a bioinformatic analysis to examine the conservation and divergence of the snRNA gene promoter elements in other species of insects. The 5' half of the PSEA is well-conserved, but the 3' half is divergent. Moreover, within each species positions exist where the PSEAs of the Pol III-transcribed genes differ from those of the Pol II-transcribed genes. Interestingly, the specific positions vary among species. Nevertheless, we speculate that these nucleotide differences within the 3' half of the PSEA act similarly to induce conformational alterations in DNA-bound SNAPc that result in RNA polymerase specificity.
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Affiliation(s)
- Genaro Hernandez
- Department of Chemistry and Biochemistry, San Diego State University5500 Campanile Drive, San Diego, CA 92182-1030, USA
- Department of Computer Science, San Diego State University5500 Campanile Drive, San Diego, CA 92182-1030, USA
| | - Faramarz Valafar
- Department of Computer Science, San Diego State University5500 Campanile Drive, San Diego, CA 92182-1030, USA
| | - William E. Stumph
- Department of Chemistry and Biochemistry, San Diego State University5500 Campanile Drive, San Diego, CA 92182-1030, USA
- To whom correspondence should be addressed. Tel: +1 619 594 5575; Fax: +1 619 594-4634;
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7
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Dominski Z, Yang XC, Purdy M, Marzluff WF. Cloning and characterization of the Drosophila U7 small nuclear RNA. Proc Natl Acad Sci U S A 2003; 100:9422-7. [PMID: 12872004 PMCID: PMC170934 DOI: 10.1073/pnas.1533509100] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Base pairing between the 5' end of U7 small nuclear RNA (snRNA) and the histone downstream element (HDE) in replication-dependent histone pre-mRNAs is the key event in 3'-end processing that leads to generation of mature histone mRNAs. We have cloned the Drosophila U7 snRNA and demonstrated that it is required for histone pre-mRNA 3'-end processing in a Drosophila nuclear extract. The 71-nt Drosophila U7 snRNA is encoded by a single gene that is embedded in the direct orientation in an intron of the Eip63E gene. The U7 snRNA gene contains conserved promoter elements typical of other Drosophila snRNA genes, and the coding sequence is followed by a 3' box indicating that the Drosophila U7 snRNA gene is an independent transcription unit. Drosophila U7 snRNA contains a trimethyl-guanosine cap at the 5' end and a putative Sm-binding site similar to the unique Sm-binding site found in other U7 snRNAs. Drosophila U7 snRNA is approximately 10 nt longer than mammalian U7 snRNAs because of an extended 5' sequence and has only a limited potential to form a stem-loop structure near the 3' end. The extended 5' end of Drosophila U7 snRNA can base pair with the HDE in all five Drosophila histone pre-mRNAs. Blocking the 5' end of the U7 snRNA with a complementary oligonucleotide specifically blocks processing of a Drosophila histone pre-mRNA. Changes in the HDE that abolish or decrease processing efficiency result in a reduced ability to recruit U7 snRNA to the pre-mRNA.
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Affiliation(s)
- Zbigniew Dominski
- Department of Biochemistry and Biophysics and Program in Molecular Biology and Biotechnology, University of North Carolina, Chapel Hill, NC 27599, USA.
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8
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Dominski Z, Erkmann JA, Yang X, Sànchez R, Marzluff WF. A novel zinc finger protein is associated with U7 snRNP and interacts with the stem-loop binding protein in the histone pre-mRNP to stimulate 3'-end processing. Genes Dev 2002; 16:58-71. [PMID: 11782445 PMCID: PMC155312 DOI: 10.1101/gad.932302] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The stem-loop binding protein (SLBP) is the posttranscriptional regulator of histone mRNA in metazoan cells. SLBP binds histone pre-mRNAs and facilitates 3'-end processing by promoting stable association of U7 snRNP with the pre-mRNA. To identify other factors involved in histone pre-mRNA processing, we used a modified yeast two-hybrid assay in which SLBP and its RNA target were coexpressed as bait. A novel zinc finger protein, hZFP100, which interacts with the SLBP/RNA complex but not with free SLBP, was cloned. The interaction requires regions of SLBP that are important for histone pre-mRNA processing. Antibodies to hZFP100 precipitate U7 snRNA, and expression of hZFP100 in Xenopus oocytes stimulates processing of histone pre-mRNA, showing that hZFP100 is a component of the processing machinery.
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Affiliation(s)
- Zbigniew Dominski
- Department of Biochemistry and Biophysics, Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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9
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Gorman L, Mercatante DR, Kole R. Restoration of correct splicing of thalassemic beta-globin pre-mRNA by modified U1 snRNAs. J Biol Chem 2000; 275:35914-9. [PMID: 10969081 DOI: 10.1074/jbc.m006259200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The T-->G mutation at nucleotide 705 in the second intron of the beta-globin gene creates an aberrant 5' splice site and activates a 3' cryptic splice site upstream from the mutation. As a result, the IVS2-705 pre-mRNA is spliced via the aberrant splice sites leading to a deficiency of beta-globin mRNA and protein and to the genetic blood disorder thalassemia. We have shown previously that in cell culture models of thalassemia, aberrant splicing of beta-thalassemic IVS2-705 pre-mRNA was permanently corrected by a modified murine U7 snRNA that incorporated sequences antisense to the splice sites activated by the mutation. To explore the possibility of using other snRNAs as vectors for antisense sequences, U1 snRNA was modified in a similar manner. Replacement of the U1 9-nucleotide 5' splice site recognition sequence with nucleotides complementary to the aberrant 5' splice site failed to correct splicing of IVS2-705 pre-mRNA. In contrast, U1 snRNA targeted to the cryptic 3' splice site was effective. A hybrid with a modified U7 snRNA gene under the control of the U1 promoter and terminator sequences resulted in the highest levels of correction (up to 70%) in transiently and stably transfected target cells.
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Affiliation(s)
- L Gorman
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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10
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Lück R, Gräf S, Steger G. ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure. Nucleic Acids Res 1999; 27:4208-17. [PMID: 10518612 PMCID: PMC148695 DOI: 10.1093/nar/27.21.4208] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A tool for prediction of conserved secondary structure of a set of homologous single-stranded RNAs is presented. For each RNA of the set the structure distribution is calculated and stored in a base pair probability matrix. Gaps, resulting from a multiple sequence alignment of the RNA set, are introduced into the individual probability matrices. These 'aligned' probability matrices are summed up to give a consensus probability matrix emphasizing the conserved structural elements of the RNA set. Because the multiple sequence alignment is independent of any structural constraints, such an alignment may result in introduction of gaps into the homologous probability matrices that disrupt a common consensus structure. By use of its graphical user interface the presented tool allows the removal of such misalignments, which are easily recognized, from the individual probability matrices by optimizing the sequence alignment with respect to a structural alignment. From the consensus probability matrix a consensus structure is extracted, which is viewable in three different graphical representations. The functionality of the tool is demonstrated using a small set of U7 RNAs, which are involved in 3'-end processing of histone mRNA precursors. Supplementary Material lists further results obtained. Advantages and drawbacks of the tool are discussed in comparison to several other algorithms.
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Affiliation(s)
- R Lück
- Institut für Physikalische Biologie, Geb. 26.12.U1, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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11
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Abstract
All metazoan messenger RNAs, with the exception of the replication-dependent histone mRNAs, terminate at the 3' end with a poly(A) tail. Replication-dependent histone mRNAs end instead in a conserved 26-nucleotide sequence that contains a 16-nucleotide stem-loop. Formation of the 3' end of histone mRNA occurs by endonucleolytic cleavage of pre-mRNA releasing the mature mRNA from the chromatin template. Cleavage requires several trans-acting factors, including a protein, the stem-loop binding protein (SLBP), which binds the 26-nucleotide sequence; and a small nuclear RNP, U7 snRNP. There are probably additional factors also required for cleavage. One of the functions of the SLBP is to stabilize binding of the U7 snRNP to the histone pre-mRNA. In the nucleus, both U7 snRNP and SLBP are present in coiled bodies, structures that are associated with histone genes and may play a direct role in histone pre-mRNA processing in vivo. One of the major regulatory events in the cell cycle is regulation of histone pre-mRNA processing, which is at least partially mediated by cell-cycle regulation of the levels of the SLBP protein.
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Affiliation(s)
- Z Dominski
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill 27599, USA
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12
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Mostardini M, Appierto V, Pergolizzi R, Zucchi I, Mumm S, DeBellis G, Milanesi L, Rogozin IB, Biunno I. Identification of a U7snRNA homologue mapping to the human Xq27.1 region, between the DXS1232 and DXS119 loci. Gene 1997; 187:221-4. [PMID: 9099884 DOI: 10.1016/s0378-1119(96)00754-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
To contribute to the identification and analysis of novel genes, we undertook the study of a cosmid clone in the Xq27 region of human DNA. The cloned fragment was previously observed to have a high number of evolutionarily conserved sequences. In this genomic stretch of DNA we have identified sequence homologous to the U7 RNA gene including its potential regulatory elements. This paper describes the genomic organisation of this gene and its mapping to the Xq27.1 genomic sub-interval between the DXS1232 and DXS119 loci.
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Affiliation(s)
- M Mostardini
- Istituto Tecnologie Biomediche Avanzate, CNR, Milano, Italy
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13
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Stefanovic B, Hackl W, Lührmann R, Schümperli D. Assembly, nuclear import and function of U7 snRNPs studied by microinjection of synthetic U7 RNA into Xenopus oocytes. Nucleic Acids Res 1995; 23:3141-51. [PMID: 7667090 PMCID: PMC307171 DOI: 10.1093/nar/23.16.3141] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In Xenopus oocytes in vitro transcribed mouse U7 RNA is assembled into small nuclear ribonucleoproteins (snRNPs) that are functional in histone RNA 3' processing. If the special Sm binding site of U7 (AAUUUGUCUAG, U7 Sm WT) is converted into the canonical Sm sequence derived from the major snRNAs (AAUUUUUGGAG, U7 Sm OPT) the RNA assembles into a particle which accumulates more efficiently in the nucleus, but which is non-functional. U7 RNA with a heavily mutated Sm binding site (AACGCGUCAUG, U7 Sm MUT) is deficient in nuclear accumulation and function. By UV cross-linking U7 Sm WT RNA can be linked to three proteins, i.e. the common snRNP proteins G and B/B' and an apparently U7-specific protein of 40 kDa. As a result of altering the Sm binding site, U7 Sm OPT RNA cannot be cross-linked to the 40 kDa protein and no cross-links are obtained with U7 Sm MUT RNA. The fact that the Sm site also interacts with at least one U7-specific protein is so far unique to U7 RNA and may provide an explanation for the atypical sequence of this site. All described RNA-protein interactions, including that with the 40 kDa protein, already occur in the cytoplasm. An additional cytoplasmic photoadduct obtained with U7 Sm WT and U7 Sm OPT, but not U7 Sm MUT, RNAs is indicative of a protein of 60-80 kDa. The m7G cap structure of U7 Sm WT and U7 Sm OPT RNA becomes hypermethylated. However, the 3mG cap enhances, but is not required for, nuclear accumulation. Finally, U7 Sm WT RNA is functional in histone RNA processing even when bearing an ApppG cap.
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Affiliation(s)
- B Stefanovic
- Abteilung für Entwicklungsbiologie, Universität Bern, Switzerland
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14
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Abstract
A subclone containing a single Xenopus borealis U7 snRNA-encoding gene has been microinjected into X. laevis oocyte nuclei to examine its expression using [32P]GTP as an in vivo label. Only two U7 snRNA bands were detected after incubation, and subsequent fractionation of the oocyte showed that only the larger transcript is present in the nucleus. The sequence of this functional U7 gene shows that, in addition to the coding region, it contains, in the appropriate locations, the 3'-box and proximal sequence element (PSE) which are typical of Pol II-transcribed snRNA genes. Surprisingly, the Xenopus U7 gene contains two adjacent octamer-binding motifs located only 12 and 24 bp upstream from the PSE, instead of the usual location around 150-200 bp upstream. No other cis-acting elements appear to be present. A 5' deletion analysis shows that the transcription level of this U7 gene remains constant if sequences upstream of the two octamer motifs are removed, yet is undetectable when an additional 34 bp containing both octamers and the PSE are removed. This confirms that the Xenopus U7 gene is the most compact snRNA-encoding gene isolated to date. A comparison of U7 sequences shows there is a much greater conservation in the 5' half of the molecule, which contains sequences that base-pair with target pre-mRNA, than in the 3' half which can form a single stem-loop structure that varies in size.
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Affiliation(s)
- N J Watkins
- Department of Biochemistry, University of Liverpool, UK
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15
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Wendelburg BJ, Marzluff WF. Two promoter elements are necessary and sufficient for expression of the sea urchin U1 snRNA gene. Nucleic Acids Res 1992; 20:3743-51. [PMID: 1641340 PMCID: PMC334027 DOI: 10.1093/nar/20.14.3743] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The essential elements of the sea urchin L. variegatus U1 snRNA promoter were mapped by microinjection of a U1 maxigene into sea urchin zygotes. Two elements are required for expression: a distal sequence element (DSE) located between -318 and -300 and a proximal sequence element (PSE) centered at -55. Removal or alteration of other sequences conserved in different sea urchin snRNA U1 genes, including deletion of all sequence between -90 and -273, did not affect the expression. Sequences around the start site were not required for expression. Deletion of nucleotides between the PSE and the start site resulted in initiation inside the U1 coding region, suggesting that the PSE determines the start site of transcription. There is no obvious similarity between the sequences required for the sea urchin U1 snRNA expression and the sequences required for the expression of other sea urchin snRNAs.
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Affiliation(s)
- B J Wendelburg
- Department of Chemistry, Florida State University, Tallahassee 32306
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16
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Abstract
Expression of the U7 gene, encoding mouse U7 snRNA, following microinjection into Xenopus oocytes is both accurate and efficient, giving rise to mature U7 snRNA and a precursor with an 8-nucleotide (nt) 3' extension. The mouse U7 gene promoter, which is similar to that of the vertebrate major U genes comprising a DSE, a PSE and a 3' box, with the same spatial arrangement, is as efficient as the Xenopus U2 gene promoter in this assay. A deletion analysis of the mouse U7 gene identified sequences downstream from the 3' box, within the region (nt +74 to +196), which seem to have a negative regulatory effect upon the frequency of transcription initiation and are also required for accurate 3' end formation. Sequences in the nt -1699 to -431 region also seemed to have a negative effect on the level of transcription. In addition, sequences upstream from the PSE, within the nt -65 to -421 region, are necessary for accurate and efficient synthesis of mature U7 snRNA. Finally, the mouse U7 snRNA may not form a functional snRNP in Xenopus oocytes due to defective snRNP assembly and/or nuclear import.
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Affiliation(s)
- S C Phillips
- Department of Biochemistry, University of Liverpool, UK
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17
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Phillips SC, Birnstiel ML. Analysis of a gene cluster coding for the Xenopus laevis U7 snRNA. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1131:95-8. [PMID: 1374647 DOI: 10.1016/0167-4781(92)90104-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A cluster of Xenopus laevis U7 snRNA genes has been isolated and sequenced. The gene structure is more compact than, but otherwise comparable to, the major U snRNA genes since the distal sequence element (DSE) is located only 4 nt upstream of the PSE. The corresponding RNA is present in the oocyte and accumulates early in oogenesis.
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Affiliation(s)
- S C Phillips
- Research Institute of Molecular Pathology, Vienna, Austria
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18
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Abstract
The rodent 4.5 S RNA is an RNA polymerase III product with a sequence related to the Alu family of interspersed repeated DNA. A previous study identified a tandem array of 4.2-kb repeating units that contain the 4.5 S RNA coding sequence as well as many short repetitive sequences. To understand the genomic organization of this gene family, we have isolated and characterized 4.5 S RNA sequences that are part of the tandem array as well as identified members that are not part of the array. One variant 4.5 S RNA gene family member exhibits length polymorphisms in its minisatellite sites relative to the single previously reported gene. The 4.5 S RNA sequences that are not part of the tandem array possess many of the features of processed pseudogenes and are found adjacent to other interspersed repeated elements. These findings suggest that the mouse 4.5 S RNA can behave as a retroposon, resulting in the accumulation of 4.5 S RNA-like elements at many sites in the genome.
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Affiliation(s)
- R Kraft
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
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