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Small nuclear RNAs (snRNAs) and other RNA spliceosomal components are involved in neurological and psychiatric disorders. U1 snRNA has recently been demonstrated to be altered in pathology in some neurodegenerative diseases, but whether it has a causative role is not clear. Here we have studied this by overexpressing U1 snRNA in mice and measured their hippocampal oscillatory patterns and brain functions. Novel object recognition test showed that the recognition index was significantly decreased in the U1 snRNA over-expression mice compared to that in the C57BL mice. U1 snRNA over-expression regulated not only the pattern of neural oscillations but also the expression of neuron excitatory and inhibitory proteins. Here we show that U1 snRNA over-expression contains the shrinkage distribution of theta-power, theta-phase lock synchronization, and theta and low-gamma cross-frequency coupling in the hippocampus. The alternations of neuron receptors by the U1 snRNA overexpression also modulated the decreasing of recognition index, the energy distribution of theta power spectrum with the reductions of theta phase synchronization and phase-amplitude coupling between theta and low-gamma. Linking these all together, our results suggest that U1 snRNA overexpression particularly causes a deficit in short-term memory. These findings make a bedrock of our research that U1 snRNA bridges the gap about the mechanism behind short-term memory based on the molecular and mesoscopic level. [ABSTRACT FROM AUTHOR]

U1 small nuclear RNA (snRNA) is selectively enriched in 100% of familial Alzheimer's disease (AD) resulting from presenilin1 (PS1) and amyloid precursor protein (APP) mutations. However, it remains unknown what gene or protein cause the U1 snRNA overexpression and then resulted in AD. Using SH-SY5Y cells, we discovered that PS1 induced the overexpression of U1 snRNA, which increased the production of Aβ. Moreover, the U1 snRNA overexpression induced the upregulation of apoe and clu transcripts. In addition, the levels of phosphorylation of tau protein at Thr212 were significantly elevated in U1 snRNA overexpression cells. Immunofluorescence using antibodies reactive with the phosphorylation of tau at Thr212 site demonstrated the hyperphosphorylated tau localization with α-tubulin, the main component of cytoskeleton. Importantly, the increased levels of Bax, Bcl2, and Bax/Bcl2 ratio showed that the overexpression of U1 snRNA could cause cell apoptosis. Conclusively, these findings suggest that PS1 considerably increases the level of U1snRNA accompanied with the adverse change of Aβ level, AD-related tau cytoskeletal pathology, and cell apoptosis. [ABSTRACT FROM AUTHOR]

draft sequence of the genome of Brachypodium distachyon, the emerging grass model, was recently released. This represents a unique opportunity to determine its functional diversity compared to the genomes of other model species. Using homology mapping of assembled expressed sequence tags with chromosome scale pseudomolecules, we identified 128 alternative splicing events in B. distachyon. Our study identified that retention of introns is the major type of alternative splicing events (53%) in this plant and highlights the prevalence of splicing site recognition for definition of introns in plants. We have analyzed the compositional profiles of exon-intron junctions by base-pairing nucleotides with U1 snRNA which serves as a model for describing the possibility of sequence conservation. The alternative splicing isoforms identified in this study are novel and represent one of the potentially biologically significant means by which B. distachyon controls the function of its genes. Our observations serve as a basis to understand alternative splicing events of cereal crops with more complex genomes, like wheat or barley. [ABSTRACT FROM AUTHOR]

We report the molecular characterization of two splice mutations in two different French families affected with a late onset form of Charcot–Marie–Tooth disease type 1B (CMT1B), an autosomal dominant inherited disorder caused by mutations in the myelin protein zero gene. The first substitution, c.306G>A, located in exon 3, does not change the codon p.Val102Val but is co-transmitted with the disease in the first family. The second substitution, c.675+3dup, is an insertion of a T at position +3 of intron 5. To identify the functional impact of these nucleotide changes on splicing and because no RNA sample was available, we used in silico prediction and in vitro splicing assay. Mutation c.306G>A increases the strength of a preexisting cryptic donor site at position c.304 which becomes stronger than the normal donor site of intron 3. This variation creates a sequence that better matches the U1 small nuclear RNA (snRNA) binding consensus, and HeLa cells, transfected with the mutant minigene, produce a truncated exon 3 messenger RNA (mRNA). Mutation c.675+3dup was predicted to abolish the donor site of intron 5, and, indeed, HeLa cells transfected with the mutant minigene completely skip exon 5 from the transcript. The mutated sequence abolishes U1 snRNA binding and co-transfection of a mutated complementary U1 snRNA restored exon 5 inclusion in the mRNA. This work provides valuable information regarding the molecular basis of two forms of late onset of CMT1B, U1 snRNA mis-binding, and provides more evidence that a “silent” polymorphism may be a disease causing mutation. [ABSTRACT FROM AUTHOR]

Transforming growth factorβ1 (TGFβ1) is known to be intimately involved in many cellular processes. To explore the mechanism of TGFβ1 in these processes, the non-chimeric hammer-head ribozyme and U1 snRNA chimeric ribozyme against TGFβ1 were designed to down-regulate TGFβ1 expression. The activity of non-chimeric ribozyme and U1 snRNA chimeric ribozyme against TGFβ1 in vitro and in activated hepatic stellate cells (HSCs) was detected. Cleavage reactions of both ribozymes in vitro demonstrated that non-chimeric ribozyme possessed better cleavage activity in vitro than U1 snRNA chimeric ribozyme. The further study showed U1 snRNA chimeric ribozyme inhibited TGFβ1 expression more efficiently than non-chimeric ribozyme in transfected HSC cells. So it indicates that the U1 snRNA chimeric ribozyme provides an alternative approach for the research on the precise mechanism of TGFβ1 in many cellular processes and a potential therapeutic candidate for TGFβ1-related diseases. [ABSTRACT FROM AUTHOR]

Peptides that bind either U1 small nuclear RNA (U1 snRNA) or the anticodon stem and loop of yeast tRNAPhe (tRNA) were selected from a random-sequence, 15-amino acid bacteriophage display library. An experimental system, including an affinity selection method, was designed to identify primary RNA-binding peptide sequences without bias to known amino acid sequences and without incorporating nonspecific binding of the anionic RNA backbone. Nitrocellulose binding assays were used to evaluate the binding of RNA by peptide-displaying bacteriophage. Amino acid sequences of RNA-binding bacteriophage were determined from the foreign insert DNA sequences, and peptides corresponding to the RNA-binding bacteriophage inserts were chemically synthesized. Peptide affinities for the RNAs ( Kd ≍ 0.1–5.0 μM) were analyzed successfully using fluorescence and circular dichroism spectroscopies. These methodologies demonstrate the feasibility of rapidly identifying, isolating, and initiating the analyses of small peptides that bind to RNAs in an effort to define better the chemistry, structure, and function of protein–RNA complexes. [ABSTRACT FROM AUTHOR]

In this paper we first show that the primary structure of U1 snRNA is homologous to that of tandem repeated pre-tRNA. Two sets of polymerase III promoter sites (the a and b boxes) are clearly recognisable at the appropriate positions in U1, although neither is functional; these sites occur in a degenerate form and their transcription is initiated by polymerase II. Moreover, several of the conserved subsequences of tRNAs that are not associated with transcription initiation (and supposedly are conserved because of their role in translation) are conserved in U1 as well, one of them being the pattern Py-Py-anticodon-Pu-Pu (for both anticodons of tandem tRNA). Second, we show that the secondary structure of U1 is apparently formed after fixation of the 'B-hairpin loop' by one of the associated proteins. If and only if this hairpin loop is fixed, a consensus secondary structure is produced by the minimisation-of-free-energy technique. Moreover, we show that this B-hairpin loop has been destabilised relatively recently in evolutionary time by deletions (e.g., in the polymerase III box). If we reinsert the deleted bases, the so constructed hypothetical 'ancestral' molecule folds into the consensus secondary structure by unconstrained energy minimisation (i.e., without fixation of the B-loop). Some features of the secondary structure of tandem repeated pre-tRNA are conserved in U1, but the overall structure has changed dramatically. Like tRNA, U1 has a cloverleaf-like structure, but its overall size has doubled. By comparing their secondary structures and by alignment of the sequences, we trace the local events associated with the global change in secondary structure (and apparently in the function of the molecule). Finally, we discuss our results from the perspective of informatic prerequisites for heterarchical multilevel evolution. [ABSTRACT FROM AUTHOR]

As U1 snRNA is produced in all mammalian cell types, antibiotic resistance genes driven by this promoter would be ideally suited as genetic selection markers. However, although the U1 snRNA gene is transcribed by RNA polymerase II, its native product is not a messenger RNA, but a splicing cofactor. To test whether this promoter could nevertheless produce a functional mRNA, sensitive reporter genes expressing resistance to the antibiotics hygromycin-B and bleomycin were constructed with either the U1 snRNA promoter or the SV40 early promoter. Resistant cell lines could only be obtained with constructs equipped with a functional polyadenylation signal. With the U1 snRNA promoter about three times fewer colonies were obtained than with the SV40 early promoter. Another potential advantage of the U1 snRNA promoter is that, in contrast to the promoters commonly used to express genetic selection markers, the enhancer-like element contained in the U1 snRNA promoter had only a minimal stimulative effect, only detectable with the most sensitive methods, on an adjacent mRNA-producing gene. The U1 snRNA promoter was also capable of expressing bleomycin resistance in the context of a self-inactivating retrovirus vector, whereby it was discovered that the mouse 3T3 cells used in this experiment were 10 times more sensitive to bleomycin than human or hamster cell lines. [ABSTRACT FROM AUTHOR]