Prp5 bridges U1 and U2 snRNPs and enables stable U2 snRNP association with intron RNA

Communication between U1 and U2 snRNPs is critical during pre-spliceosome assembly; yet, direct connections have not been observed. To investigate this assembly step, we focused on Prp5, an RNA-dependent ATPase of the DExD/H family. We identified homologs of Saccharomyces cerevisiae Prp5 in humans (hPrp5) and Schizosaccharomyces pombe (SpPrp5), and investigated their interactions and function. Depletion and reconstitution of SpPrp5 from extracts demonstrate that ATP binding and hydrolysis by Prp5 are required for pre-spliceosome complex A formation. hPrp5 and SpPrp5 are each physically associated with both U1 and U2 snRNPs; Prp5 contains distinct U1- and U2-interacting domains that are required for pre-spliceosome assembly; and, we observe a Prp5-associated U1/U2 complex in S. pombe. Together, these data are consistent with Prp5 being a bridge between U1 and U2 snRNPs at the time of pre-spliceosome formation.     

肺癌病人血清中U1-A snRNP自身抗体的发现与鉴定

许多研究表明, 肺癌病人存在自身免疫现象. 为了寻找肺癌病人血清中具有潜在诊断价值的自身抗体, 采用免疫荧光染色, 免疫印迹和蛋白质芯片技术对10例肺癌病人和10例正常人血清进行了检测. 筛选中发现1例来自64岁男性肺鳞癌(Ⅲb期)病人的血清呈现特异性的细胞核染色, 并在31 kD处有一个明显的细胞核蛋白免疫印迹条带. 进而采用该病人的血清进行免疫沉淀, 对所捕获的蛋白组分进行质谱分析和数据库查询后确认31 kD条带为核内小核糖体蛋白U1-A(small nuclear ribonucleoprotein U1-A, U1-A snRNP). 进一步对36例鳞癌、26例腺癌、31例小细胞肺癌和20例健康对照血清样本进行了免疫荧光染色和免疫印迹验证, 结果显示50%的鳞癌、26.9%的腺癌、54.8%的小细胞肺癌病人血清中有抗U1-A snRNP抗体. 上述结果报道了在肺癌病人血清中出现Anti-U1-A snRNP自身抗体.     

A bipartite U1 site represses U1A expression by synergizing with PIE to inhibit nuclear polyadenylation

U1A protein negatively autoregulates itself by polyadenylation inhibition of its own pre-mRNA by binding as two molecules to a 3'UTR-located Polyadenylation Inhibitory Element (PIE). The (U1A)2-PIE complex specifically blocks U1A mRNA biosynthesis by inhibiting polyA tail addition, leading to lower mRNA levels. U1 snRNP bound to a 5'ss-like sequence, which we call a U1 site, in the 3'UTRs of certain papillomaviruses leads to inhibition of viral late gene expression via a similar mechanism. Although such U1 sites can also be artificially used to potently silence reporter and endogenous genes, no naturally occurring U1 sites have been found in eukaryotic genes. Here we identify a conserved U1 site in the human U1A gene that is, unexpectedly, within a bipartite element where the other part represses the U1 site via a base-pairing mechanism. The bipartite element inhibits U1A expression via a synergistic action with the nearby PIE. Unexpectedly, synergy is not based on stabilizing binding of the inhibitory factors to the 3'UTR, but rather is a property of the larger ternary complex. Inhibition targets the biosynthetic step of polyA tail addition rather than altering mRNA stability. This is the first example of a functional U1 site in a cellular gene and of a single gene containing two dissimilar elements that inhibit nuclear polyadenylation. Parallels with other examples where U1 snRNP inhibits expression are discussed. We expect that other cellular genes will harbor functional U1 sites.     

人U_1和U_2snRNA基因定位缺失和取代突变

 用寡聚核苷酸诱导的定位突变法,将人U_1和U_2snRNA基因的5'-端调控区域的一段能与SV_(40)T抗原相结合的DNA删去,造成缺失突变,改变这段DNA核苷酸的排列顺序,造成取代突变。突变株用原位杂交法筛选,由限制性内切酶电泳图谱分析和DNA顺序测定得到证实。突变率约为5％。     

Anti-U1A monoclonal antibodies recognize unique epitope targets of U1A which are involved in the binding of U1 RNA

The U1A (or nRNP A) protein is known to play a critical role in eukaryotic pre-mRNA splicing and polyadenylation. Previous studies revealed that several mouse monoclonal antibodies (MAbs) recognized U1A as part of the U1snRNP, while MAb 12E12 was unique in that it recognized an epitope that is masked when U1A is bound to U1 RNA. In order to further characterize and understand the antigenic targets of these MAbs, we undertook fine specificity epitope mapping studies. Anti-U1A MAbs 12E12 and 10E3 each recognize unique peptides from the U1A protein. Interestingly, these MAbs recognize epitopes which have been shown to be antigenic in human autoimmune diseases. When superimposed on structures of U1A derived from crystal and NMR data, the major epitope recognized by 12E12 (amino acids 103-108) localizes to the surface of the U1A molecule. The 12E12 epitope is immediately adjacent to a helix which probably reacts to U1 RNA binding by undergoing a conformational change. This modification of structure effectively masks the 12E12 epitope, thus preventing binding of the monoclonal to U1A/U1 RNA complexes. These findings suggest that the structure of the U1A protein may be different when not part of the U1snRNP.     

Thermodynamic analyses of the constitutive splicing pathway for ovomucoid pre-mRNA

The ovomucoid pre-mRNA has been folded into mini-hairpins adaptable for the RNA recognition motif (RRM) protein binding. The number of mini-hairpins were 372 for pre-mRNA and 83-86 for mature m RNA The spatial arrangements are, in average, 16 nucleotides per mini-hairpin which includes 7 nt in the stem, 5.6 nt in the loop and 3.7 nt in the inter-hairpin spacer. The constitutive splicing system of ovomucoid-pre-mRNA is characterized by preferred order of intron removal of 5/6 > 7/4 > 2/1 > 3. The 5′ splice sites (5′SS), branch point sequences (BPS) and 3′ splice sites (3′SS) were identified and free energies involved have been estimated in 7 splice sites. Thermodynamic barriers for splice sites from the least (| lowest | -Kcal) were 5,4, 7,6, 2,1, and 3; i.e., −18.7 Kcal, −20.2 Kcal, −21.0 Kcal, −24.0 Kcal, −25.4 Kcal, −26.4 Kcal and −28.2 Kcal respectively. These are parallel to the kinetic data of splicing order reported in the literature. As a result, the preferred order of intron removals can be described by a consideration of free energy changes involved in the spliceosomal assembly pathway. This finding is consistent with the validity of hnRNP formation mechanisms in previous reports.     

Structural basis of the interaction between P-element somatic inhibitor and U1-70k essential for the alternative splicing of P-element transposase

P-element transposition in Drosophila is regulated by tissue-specific alternative splicing of the P-element transposase pre-mRNA. In somatic cells, the P-element somatic inhibitor (PSI) protein binds to exon 3 of the pre-mRNA and recruits U1 small nuclear ribonucleoprotein (snRNP) to the F1 pseudo-splice site. This abrogates binding of U1 snRNP to the genuine 5' splice site, thereby preventing excision of the third intron. Two homologous short sequences, referred to as the A and B boxes, near the C terminus of PSI bind to U1-70k protein within U1 snRNP. We have now mapped the AB box-binding site of U1-70k to a short proline-rich sequence at the C terminus. Our NMR study shows that the B box forms an anti-parallel helical hairpin in which four highly conserved aromatic residues form a cluster on one face of the first helix. This hydrophobic cluster interacts extensively with the proline-rich region of the U1-70k protein.     

Global and local dynamics of the human U1A protein determined by tryptophan fluorescence.

Tryptophan residues have been introduced into two domains of the human U1A protein to probe solution dynamics. The full length protein contains 282 residues, separated into three distinct domains: the N-terminal RBD1 (RNA Binding Domain I), consisting of amino acids 1-101; the C-terminal RBD2, residues 202-282; and the intervening linker region. Tryptophan residues have been substituted for specific phenylalanine residues on the surface of the beta-sheet of either RBD1 or RBD2, thus introducing a single solvent exposed tryptophan as a fluorescence reporter. Both steady-state and time-resolved fluorescence measurements of the isolated RBD domains show that each tryptophan experiences a unique environment on the beta-sheet surface. The spectral properties of each tryptophan in RBD1 and RBD2 are preserved in the context of the U1A protein, indicating these domains do not interact with each other or with the linker region. The rotational correlation times of the isolated RBDs and the whole U1A, determined by dynamic polarization measurements, show that the linker region is highly flexible such that each RBD exhibits uncorrelated motion.     

Primary cilium alterations and expression changes of Patched1 proteins in niemann‐pick type C disease

Niemann‐Pick type C disease (NPC) is a disorder characterized by abnormal intracellular accumulation of unesterified cholesterol and glycolipids. Two distinct disease‐causing genes have been isolated, NPC1 and NPC2. The NPC1 protein is involved in the sorting and recycling of cholesterol and glycosphingolipids in the late endosomal/lysosomal system. It has extensive homology with the Patched1 (Ptc1) receptor, a transmembrane protein localized in the primary cilium, and involved in the Hedgehog signaling (Shh) pathway. We assessed the presence of NPC1 and Ptc1 proteins and evaluated the relative distribution and morphology of primary cilia in fibroblasts from five NPC1 patients and controls, and in normal fibroblasts treated with 3‐ß‐[2‐(diethylamino)ethoxy]androst‐5‐en‐17‐one (U18666A), a cholesterol transport‐inhibiting drug that is widely used to mimic NPC. Immunofluorescence and western blot analyses showed a significant decrease in expression of NPC1 and Ptc1 in NPC1 fibroblasts, while they were normally expressed in U18666A‐treated fibroblasts. Moreover, fibroblasts from NPC1 patients and U18666A‐treated cells showed a lower percentage distribution of primary cilia and a significant reduction in median cilia length with respect to controls. These are the first results demonstrating altered cytoplasmic expression of Ptc1 and reduced number and length of primary cilia, where Ptc1 is located, in fibroblasts from NPC1 patients. We suggest that the alterations in Ptc1 expression in cells from NPC1 patients are closely related to NPC1 expression deficit, while the primary cilia alterations observed in NPC1 and U18666A‐treated fibroblasts may represent a secondary event derived from a defective metabolic pathway.     

Neuromedin U Does Not Act as a Decretin in Rats

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Molecular cloning of cDNAs encoding variants of meiotin-1

Meiotin-1 is a chromatin-associated protein, originally isolated from microsporocytes of Lilium longiflorum, which is found predominantly in cells undergoing meiotic prophase. Chromatin fractionation studies demonstrated that meiotin-1 has an unusual stoichiometry relative to that of histone H1 and the core histones in chromatin fibers. The protein is found less frequently than is histone H1, and appears to be distributed once every 5 to 13 nucleosomes. This distribution may approximate the number of nucleosomes per turn of the chromatin solenoid. A truncated cDNA was identified by immunoscreening of an expression library, and the cDNA was used as a hybridization probe to select a full length cDNA. Variations between the sequence of the predicted polypeptide and sequenced peptides, and variations between the amino acid composition of the protein and the deduced protein indicate that the cDNAs encode minor variants of mature meiotin-1. RNA gel blot hybridization studies reveal that the meiotin-1 mRNA is restricted to anthers in which meiosis is occurring. Computer analysis of the polypeptide deduced from the cDNA indicates that the protein begins with a region highly homologous to the conserved central globular domain of histone H1 molecules. DNA gel blotting experiments demonstrate that homologous sequences exist in the genomes of a fern, a fungus, and both mono-and dicotyledonous plants. Meiotin-1 has been evolutionarily conserved and I propose that it arose from histone H1 to fulfill a role in organizing meiotic chromatin.     

Discovery and identification of anti-U1-A snRNP antibody in lung cancer

There are multiple reports of autoimmune response in patients with lung cancer. To investigate whether a novel autoantibody is present in patients with lung cancer and evaluate its clinical diagnostic and prognostic value, sera from 10 patients with lung cancer and 10 normal individuals were analyzed using immunofluorescence and Western blotting. It was found that one serum sample from the patients with squamous carcinoma gave a fine speckled pattern staining in nucleus and had a high titer antinuclear autoantibody which could recognize 31 kD of nuclear protein isolated from both cancer cells and normal cells. The same patient’s serum was further used to immunoprecipitate the target antigen. The protein bands were excised from the SDS-PAGE gels and were analyzed with a Qstar Pulser I Quadrupole time-flight mass spectrometer, and the 31 kD target antigen was identified as U1-AsnRNP. To test the prevalence of anti-U1-AsnRNP antibody, sera from 93 patients including 36 squmaous carcinomas (SCC), 26 adenocarcinomas (Ad), and 31 small cell carcinomas (SCLC) were screened by Western blotting. The results demonstrated that anti-U1-A snRNP antibody was present in 50% of SCC sera, 26.9% of Ad sera and 54.8% of SCLC sera. In this paper, we report for the first time that anti-U1-AsnRNP antibody could be detected in the patients with lung cancer.     

Interactions of U1 RNP with heterogeneous nuclear RNA in rat Novikoff hepatoma nuclei

Summary The nature of the association of U1 RNA with rapidly sedimenting RNP structures in rat hepatoma nuclei was investigated. The effects of salt and proteinase K treatment on the stability of this bound form of U1 RNA were studied using sucrose density gradient analyses. Quantitation of the amount of U1 RNA remaining associated with large structures after treatment was used to assess the relative contribution of protein-protein(and protein-RNA) versus RNA-RNA interactions. Forty-eight percent of the total nuclear U1 RNA released by sonication was found in a bound form when the sonicate was centrifuged through gradients containing 50 mM NaCl. Fifty percent of this bound U1 RNA remained associated with rapidly sedimenting RNPs when the NaCl concentration was raised to 500 mM. To assess the contribution of protein independent interactions, large RNPs were completely deproteinized and their RNA moieties were then recentrifuged on gradients. By this analysis, 27% of the U1 RNA originally bound to hnRNPs was associated with rapidly sedimenting (>30 S) RNA (at 50 mM NaCl) suggesting their association by RNA-RNA hydrogen bonds. When the concentration of NaCl was 500 mM, 31% of the U1 RNA was associated with large RNA. Hence, approximately 30% of the U1 RNA molecules originally bound (or about 15% of the total nuclear U1 RNA) were found to be associated by RNA-RNA hydrogen bonds while the remainder of the binding of U1 RNP to hnRNP was by protein-protein and/or protein-RNA interactions.     

Current review of in vivo GBM rodent models: emphasis on the CNS-1 tumour model

GBM (glioblastoma multiforme) is a highly aggressive brain tumour with very poor prognosis despite multi-modalities of treatment. Furthermore, recent failure of targeted therapy for these tumours highlights the need of appropriate rodent models for preclinical studies. In this review, we highlight the most commonly used rodent models (U251, U86, GL261, C6, 9L and CNS-1) with a focus on the pathological and genetic similarities to the human disease. We end with a comprehensive review of the CNS-1 rodent model.     

U1 SnRNP association with HnRNP involves an initial non-specific splice-site independent interaction of U1 SnRNP protein with HnRNA

Precursor mRNA is complexed with proteins in the cell nucleus to form heterogeneous nuclear ribonucleoprotein (hnRNP), and these hnRNPs are found associated in vivo with small nuclear RNPs (snRNPs) for the processing of pre-mRNA. In order to better characterize the ATP-independent initial association of U1 snRNP with hnRNP, an important early event in assembly of the spliceosome complex, we have determined some of the components essential to an in vitro reassociation of U1 snRNP with hnRNP. U1 snRNP reassociated in vitro with 40S hnRNP particles from HeLa cells and, similar to the in vivo hnRNP/U1 snRNP association, the in vitro interaction was sensitive to high salt concentrations. U1 snRNP also associated with in vitro reconstituted hnRNP in which bacteriophage MS2 RNA, which lacks introns, was used as the RNA component. Purified snRNA alone would not associate with the MS2 RNA-reconstituted hnRNP, however, intact U1 snRNP did interact with protein-free MS2 RNA. This indicates that the U1 snRNP proteins are required for the hnRNP/U1 snRNP association, but hnRNP proteins are not. Thus, the initial, ATP-independent association of U1 snRNP with hnRNP seems to be mediated by U1 snRNP protein(s) associating with hnRNA without requiring a splice-site sequence. This complex may then be further stabilized by intron-specific interactions and hnRNP proteins, as well as by other snRNPs.