Genomes and Genes
small nuclear rna
Summary: Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
- Wang P, Palfi Z, Preusser C, Lücke S, Lane W, Kambach C, et al. Sm core variation in spliceosomal small nuclear ribonucleoproteins from Trypanosoma brucei. EMBO J. 2006;25:4513-23 pubmed..In sum, we have demonstrated that the heteroheptameric Sm core structure varies between spliceosomal snRNPs, and that modulation of the Sm core composition mediates the recognition of small nuclear RNA-specific Sm sites.
- Madocsai C, Lim S, Geib T, Lam B, Hertel K. Correction of SMN2 Pre-mRNA splicing by antisense U7 small nuclear RNAs. Mol Ther. 2005;12:1013-22 pubmed..These results suggest that modulation of SMN2 pre-mRNA splicing by modified U7 snRNAs provides a promising form of gene therapy for the treatment of SMA. ..
- Frilander M, Meng X. Proximity of the U12 snRNA with both the 5' splice site and the branch point during early stages of spliceosome assembly. Mol Cell Biol. 2005;25:4813-25 pubmed..Thus, no major rearrangements are subsequently needed to position these sites for the first step of catalysis. ..
- Jang M, Mochizuki K, Zhou M, Jeong H, Brady J, Ozato K. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Mol Cell. 2005;19:523-34 pubmed..Together, P-TEFb alternately interacts with Brd4 and the inhibitory subunit to maintain functional equilibrium in the cell. ..
- Juranek S, Rupprecht S, Postberg J, Lipps H. snRNA and heterochromatin formation are involved in DNA excision during macronuclear development in stichotrichous ciliates. Eukaryot Cell. 2005;4:1934-41 pubmed
- Valadkhan S, Mohammadi A, Jaladat Y, Geisler S. Protein-free small nuclear RNAs catalyze a two-step splicing reaction. Proc Natl Acad Sci U S A. 2009;106:11901-6 pubmed publisher..These results prove that the complex formed by U6 and U2 RNAs is a ribozyme and can potentially carry out RNA-based catalysis in the spliceosome. ..
- Cojocaru V, Nottrott S, Klement R, Jovin T. The snRNP 15.5K protein folds its cognate K-turn RNA: a combined theoretical and biochemical study. RNA. 2005;11:197-209 pubmed..Based on these observations, we propose a protein-assisted RNA folding mechanism in which the RNA intrinsic flexibility functions as a catalyst. ..
- Kudo T, Sutou S. Usage of putative chicken U6 promoters for vector-based RNA interference. J Reprod Dev. 2005;51:411-7 pubmed..For the expression of siRNA in mammalian cells, mammalian U6 small nuclear RNA (snRNA) promoters are widely used...
- Lai H, Kang Y, Stumph W. Subunit stoichiometry of the Drosophila melanogaster small nuclear RNA activating protein complex (SNAPc). FEBS Lett. 2008;582:3734-8 pubmed publisherb>Small nuclear RNA activating protein complex (SNAPc) is a multi-subunit transcription factor required for expression of small nuclear RNA genes...
- Egloff S, O Reilly D, Chapman R, Taylor A, Tanzhaus K, Pitts L, et al. Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression. Science. 2007;318:1777-9 pubmed..These findings assign a biological function to this amino acid and highlight a gene type-specific requirement for a residue within the CTD heptapeptide, supporting the existence of a CTD code. ..
- Freund M, Hicks M, Konermann C, Otte M, Hertel K, Schaal H. Extended base pair complementarity between U1 snRNA and the 5' splice site does not inhibit splicing in higher eukaryotes, but rather increases 5' splice site recognition. Nucleic Acids Res. 2005;33:5112-9 pubmed..Although the splicing mechanisms are conserved between human and S.cerevisiae, these results demonstrate that distinct differences exist in the activation of the spliceosome. ..
- McGrail J, Tatum E, O Keefe R. Mutation in the U2 snRNA influences exon interactions of U5 snRNA loop 1 during pre-mRNA splicing. EMBO J. 2006;25:3813-22 pubmed..Our data suggest that U2 aligns the exons with U5 loop 1 for ligation during the second step of pre-mRNA splicing. ..
- Konarska M, Query C. Insights into the mechanisms of splicing: more lessons from the ribosome. Genes Dev. 2005;19:2255-60 pubmed
- Lai H, Chen H, Li C, McNamara Schroeder K, Stumph W. The PSEA promoter element of the Drosophila U1 snRNA gene is sufficient to bring DmSNAPc into contact with 20 base pairs of downstream DNA. Nucleic Acids Res. 2005;33:6579-86 pubmed..However, mutation of the PSEB perturbs the cross-linking pattern. In concordance with these findings, PSEB mutations result in a 2- to 4-fold reduction in U1 promoter activity when assayed by transient transfection. ..
- Denti M, Rosa A, D Antona G, Sthandier O, De Angelis F, Nicoletti C, et al. Chimeric adeno-associated virus/antisense U1 small nuclear RNA effectively rescues dystrophin synthesis and muscle function by local treatment of mdx mice. Hum Gene Ther. 2006;17:565-74 pubmed..in mdx mice by local muscle injection of AAV vectors expressing antisense sequences fused to either U1 or U7 small nuclear RNA (snRNA)...
- Golembe T, Yong J, Dreyfuss G. Specific sequence features, recognized by the SMN complex, identify snRNAs and determine their fate as snRNPs. Mol Cell Biol. 2005;25:10989-1004 pubmed..These findings demonstrate that the SMN complex is the identifier, as well as assembler, of the abundant class of snRNAs in cells because it is able to recognize an snRNP code that they contain...
- Vollmer J, Tluk S, Schmitz C, Hamm S, Jurk M, Forsbach A, et al. Immune stimulation mediated by autoantigen binding sites within small nuclear RNAs involves Toll-like receptors 7 and 8. J Exp Med. 2005;202:1575-85 pubmed..These results demonstrate that a prototype autoantigen, the snRNP, can directly stimulate innate immunity and suggest that autoantibodies against snRNP may initiate SLE by stimulating TLR7/8. ..
- Godfrey A, Kupsco J, Burch B, Zimmerman R, Dominski Z, Marzluff W, et al. U7 snRNA mutations in Drosophila block histone pre-mRNA processing and disrupt oogenesis. RNA. 2006;12:396-409 pubmed..These data suggest that SLBP and U7 snRNP cooperate in the production of histone mRNA in vivo, and that disruption of histone pre-mRNA processing is detrimental to development. ..
- Hinas A, Larsson P, Avesson L, Kirsebom L, Virtanen A, Söderbom F. Identification of the major spliceosomal RNAs in Dictyostelium discoideum reveals developmentally regulated U2 variants and polyadenylated snRNAs. Eukaryot Cell. 2006;5:924-34 pubmed..Expression was verified from 17 small nuclear RNA (snRNA) genes. All these genes are preceded by a putative noncoding RNA gene promoter...
- Barboric M, Kohoutek J, Price J, Blazek D, Price D, Peterlin B. Interplay between 7SK snRNA and oppositely charged regions in HEXIM1 direct the inhibition of P-TEFb. EMBO J. 2005;24:4291-303 pubmed..sequestered into the large complex, P-TEFb kinase activity is inhibited by the coordinate actions of 7SK small nuclear RNA (7SK snRNA) and hexamethylene bisacetamide (HMBA)-induced protein 1 (HEXIM1)...
- Finkel J, Chinchilla K, Ursic D, Culbertson M. Sen1p performs two genetically separable functions in transcription and processing of U5 small nuclear RNA in Saccharomyces cerevisiae. Genetics. 2010;184:107-18 pubmed publisher..The effects of the mutants on the synthesis of U5 small nuclear RNA were analyzed. Two defects were observed, one in transcription termination and one in 3'-end maturation...
- Egloff S, Van Herreweghe E, Kiss T. Regulation of polymerase II transcription by 7SK snRNA: two distinct RNA elements direct P-TEFb and HEXIM1 binding. Mol Cell Biol. 2006;26:630-42 pubmed..The 7SK small nuclear RNA, in cooperation with HEXIM1 protein, functions as a general polymerase II transcription regulator by ..
- Dundr M, Ospina J, Sung M, John S, Upender M, Ried T, et al. Actin-dependent intranuclear repositioning of an active gene locus in vivo. J Cell Biol. 2007;179:1095-103 pubmed..Cajal bodies (CBs) are nuclear suborganelles that nonrandomly associate with small nuclear RNA (snRNA) and histone gene loci in human cells during interphase...
- Schwartz S, Silva J, Burstein D, Pupko T, Eyras E, Ast G. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 2008;18:88-103 pubmed
- Damgaard C, Kahns S, Lykke Andersen S, Nielsen A, Jensen T, Kjems J. A 5' splice site enhances the recruitment of basal transcription initiation factors in vivo. Mol Cell. 2008;29:271-8 pubmed publisher..Our data suggest a model in which a promoter-proximal 5' splice site via its U1 snRNA interaction can feed back to stimulate transcription initiation by enhancing pre-initiation complex assembly. ..
- Ruan J, Ullu E, Tschudi C. Characterization of the Trypanosoma brucei cap hypermethylase Tgs1. Mol Biochem Parasitol. 2007;155:66-9 pubmed
- Russell A, Watanabe Y, Charette J, Gray M. Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya. Nucleic Acids Res. 2005;33:2781-91 pubmed
- Schulte A, Czudnochowski N, Barboric M, Schönichen A, Blazek D, Peterlin B, et al. Identification of a cyclin T-binding domain in Hexim1 and biochemical analysis of its binding competition with HIV-1 Tat. J Biol Chem. 2005;280:24968-77 pubmed..It becomes inactivated when associated in a tetrameric complex with the abundant 7SK small nuclear RNA and the recently identified protein Hexim1...
- Sajic R, Lee K, Asai K, Sakac D, Branch D, Upton C, et al. Use of modified U1 snRNAs to inhibit HIV-1 replication. Nucleic Acids Res. 2007;35:247-55 pubmed..The conserved nature of the sequences targeted and the high efficacy of the constructs suggests that this strategy has significant potential as an HIV therapeutic. ..
- Saayman S, Barichievy S, Capovilla A, Morris K, Arbuthnot P, Weinberg M. The efficacy of generating three independent anti-HIV-1 siRNAs from a single U6 RNA Pol III-expressed long hairpin RNA. PLoS ONE. 2008;3:e2602 pubmed publisher..Although lhRNAs offer advantages for combinatorial RNAi, we show that good silencing efficacy across the span of the lhRNA duplex is difficult to achieve with sequences that encode more than two adjacent independent siRNAs. ..
- Batsche E, Yaniv M, Muchardt C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat Struct Mol Biol. 2006;13:22-9 pubmed
- Fuke H, Ohno M. Role of poly (A) tail as an identity element for mRNA nuclear export. Nucleic Acids Res. 2008;36:1037-49 pubmed..Our results reveal a novel function of the poly (A) tail in mRNA export. ..
- McGrail J, O Keefe R. The U1, U2 and U5 snRNAs crosslink to the 5' exon during yeast pre-mRNA splicing. Nucleic Acids Res. 2008;36:814-25 pubmedActivation of pre-messenger RNA (pre-mRNA) splicing requires 5' splice site recognition by U1 small nuclear RNA (snRNA), which is replaced by U5 and U6 snRNA...
- Palfi Z, Schimanski B, GUNZL A, Lücke S, Bindereif A. U1 small nuclear RNP from Trypanosoma brucei: a minimal U1 snRNA with unusual protein components. Nucleic Acids Res. 2005;33:2493-503 pubmed..These data result in a model of the trypanosome U1 snRNP, which deviates substantially from our classical view of the U1 particle and may reflect the special requirements for splicing of a small set of cis-introns in trypanosomes. ..
- Girard C, Verheggen C, Neel H, Cammas A, Vagner S, Soret J, et al. Characterization of a short isoform of human Tgs1 hypermethylase associating with small nucleolar ribonucleoprotein core proteins and produced by limited proteolytic processing. J Biol Chem. 2008;283:2060-9 pubmed..Together, our results suggest that proteasome maturation constitutes a mechanism regulating Tgs1 function by generating Tgs1 species with different substrate specificities, subcellular localizations, and functions. ..
- Chakrabarti K, Pearson M, Grate L, Sterne Weiler T, Deans J, Donohue J, et al. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA. 2007;13:1923-39 pubmed..These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts. ..
- Kühn Hölsken E, Dybkov O, Sander B, Luhrmann R, Urlaub H. Improved identification of enriched peptide RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry. Nucleic Acids Res. 2007;35:e95 pubmed..Applying our approach to a partial complex of U2 snRNP allowed us to identify the contact site between the U2 snRNP-specific protein p14/SF3b14a and the branch-site interacting region (BSiR) of U2 snRNA. ..
- Konarska M, Vilardell J, Query C. Repositioning of the reaction intermediate within the catalytic center of the spliceosome. Mol Cell. 2006;21:543-53 pubmed..Changes in the relative occupancy of first and second step substrates at the catalytic center alter efficiency of the two steps of splicing, allowing use of suboptimal intron sequences and thereby altering substrate selectivity. ..
- Ambrósio D, Silva M, Cicarelli R. Cloning and molecular characterization of Trypanosoma cruzi U2, U4, U5, and U6 small nuclear RNAs. Mem Inst Oswaldo Cruz. 2007;102:97-105 pubmed..Their respective secondary structures were predicted and compared with known T. brucei structures. In addition, the copy number of each snRNA in the T. cruzi genome was characterized by Southern blotting. ..
- Ma X, Yang C, Alexandrov A, Grayhack E, Behm Ansmant I, Yu Y. Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism. EMBO J. 2005;24:2403-13 pubmedYeast U2 small nuclear RNA (snRNA) contains three pseudouridines (Psi35, Psi42, and Psi44). Pus7p and Pus1p catalyze the formation of Psi35 and Psi44, respectively, but the mechanism of Psi42 formation remains unclear...
- Alioto T. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Res. 2007;35:D110-5 pubmed..Public access to the U12DB is available at http://genome.imim.es/cgi-bin/u12db/u12db.cgi. ..
- Kyriakopoulou C, Larsson P, Liu L, Schuster J, Söderbom F, Kirsebom L, et al. U1-like snRNAs lacking complementarity to canonical 5' splice sites. RNA. 2006;12:1603-11 pubmedWe have detected a surprising heterogeneity among human spliceosomal U1 small nuclear RNA (snRNA)...
- Gruber A, Koper Emde D, Marz M, Tafer H, Bernhart S, Obernosterer G, et al. Invertebrate 7SK snRNAs. J Mol Evol. 2008;66:107-15 pubmed publisher..The additional sequence data confirm the evolutionary conservation and hence functional importance of the previously described 3' and 5' stem-loop motifs, and provide evidence for a third, structurally well-conserved domain. ..
- Valadkhan S. The spliceosome: a ribozyme at heart?. Biol Chem. 2007;388:693-7 pubmed..Of the five spliceosomal RNAs, U2 and U6 are the only ones that are absolutely required for both steps of splicing. These two snRNAs form an elaborate base-paired complex that might in fact constitute the active site of the spliceosome. ..
- Matera A, Terns R, Terns M. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol. 2007;8:209-20 pubmed publisher..The small nuclear and small nucleolar RNPs are two well studied classes of ncRNPs with elaborate assembly and trafficking pathways that provide paradigms for understanding the biogenesis of other ncRNPs. ..
- Matera A. Drosophila Cajal bodies: accessories not included. J Cell Biol. 2006;172:791-3 pubmed..A recent study describes the discovery of the Drosophila Cajal body, revealing some interesting insights into the subnuclear organization of RNA processing machineries among different species...
- Bahia D, Aviñó A, Darzynkiewicz E, Eritja R, Bach Elias M. Trimethylguanosine nucleoside inhibits cross-linking between Snurportin 1 and m3G-CAPPED U1 snRNA. Nucleosides Nucleotides Nucleic Acids. 2006;25:909-23 pubmed..These results indicate that the free nucleoside TMG could be a candidate to be an inhibitor of the interaction between Snurportin 1 and U snRNAs. We also show the behavior of free TMG nucleoside in in vitro U snRNPs nuclear import. ..
- Akashi H, Miyagishi M, Yokota T, Watanabe T, Hino T, Nishina K, et al. Escape from the interferon response associated with RNA interference using vectors that encode long modified hairpin-RNA. Mol Biosyst. 2005;1:382-90 pubmed..Our findings should enhance the exploitation of RNAi in mammalian cells, especially in the field of RNAi therapy against pathogenic viruses. ..
- Schultz A, Nottrott S, Hartmuth K, Luhrmann R. RNA structural requirements for the association of the spliceosomal hPrp31 protein with the U4 and U4atac small nuclear ribonucleoproteins. J Biol Chem. 2006;281:28278-86 pubmed