HnRNP L stimulates splicing of the eNOS gene by binding to variable-length CA repeats

In the human genome, dinucleotide repeats are common sequence elements of unknown functional significance. Here we demonstrate that CA repeats in intron 13 of the human endothelial nitric oxide synthase (eNOS) gene function as an unusual intronic splicing enhancer, whose activity depends on the CA repeat number. We identify the 65 kDa heterogenous nuclear ribonucleoprotein (hnRNP) L as the major factor that binds specifically and in a length-dependent manner to the CA-repeat enhancer. In addition, we show that hnRNP L functions as a specific activator of eNOS splicing, providing the first evidence for a role of hnRNP L in the regulation of mRNA splicing. We hypothesize that hnRNP L may be involved in the regulation of many other genes containing CA repeats or A/C-rich enhancers.     

Novel functional role of CA repeats and hnRNP L in RNA stability

CA dinucleotide repeat sequences are very common in the human genome. We have recently demonstrated that the polymorphic CA repeats in intron 13 of the human endothelial nitric oxide synthase (eNOS) gene function as an unusual, length-dependent splicing enhancer. The CA repeat enhancer requires for its activity specific binding of hnRNP L. Here we show that in the absence of bound hnRNP L, the pre-mRNA is cleaved directly upstream of the CA repeats. The addition of recombinant hnRNP L restores RNA stability. CA repeats are both necessary and sufficient for this specific cleavage in the 5' adjacent RNA sequence. We conclude that-in addition to its role as a splicing activator-hnRNP L can act in vitro as a sequence-specific RNA protection factor. Based on the wide abundance of CA repetitive sequences in the human genome, this may represent a novel, generally important role of this abundant hnRNP protein.     

Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing

We have recently identified an intronic polymorphic CA-repeat region in the human endothelial nitric oxide synthase (eNOS) gene as an important determinant of the splicing efficiency, requiring specific binding of hnRNP L. Here, we analyzed the position requirements of this CA-repeat element, which revealed its potential role in alternative splicing. In addition, we defined the RNA binding specificity of hnRNP L by SELEX: not only regular CA repeats are recognized with high affinity but also certain CA-rich clusters. Therefore, we have systematically searched the human genome databases for CA-repeat and CA-rich elements associated with alternative 5' splice sites (5'ss), followed by minigene transfection assays. Surprisingly, in several specific human genes that we tested, intronic CA RNA elements could function either as splicing enhancers or silencers, depending on their proximity to the alternative 5'ss. HnRNP L was detected specifically bound to these diverse CA elements. These data demonstrated that intronic CA sequences constitute novel and widespread regulatory elements of alternative splicing.     

Intein harbouring large tandem repeats in replicative DNA helicase of Trichodesmium erythraeum

Protein splicing inteins can be small as approximately 130 aa or up to approximately 600 aa when harbouring an endonuclease domain. Here we report the identification and characterization of an unusually large intein, 1650 aa long and the largest of known inteins, encoded by the replicative DNA helicase gene dnaB of the oceanic N2-fixing cyanobacterium Trichodesmium erythraeum. This Ter DnaB-1 intein co-exists with a 177-aa mini-intein in the same host protein and harbours large tandem repeats in which an 84-aa sequence is repeated 16 times. Comparison between this tandem repeats and the recently reported tandem repeats of Ter DnaE-1 intein revealed differences and similarities. The two tandem repeats, residing in different inteins of different host proteins, differ by 50% in size and have little sequence similarity. Tandem repeats in the Ter DnaB-1 intein were required for the protein splicing activity when tested in Escherichia coli, in contrast to tandem repeats of the Ter DnaE-1 intein that inhibited protein splicing. On the other hand, tandem repeats of both inteins are located in the same corresponding region of the intein sequence and have the same number of repeating units. These suggest that the two tandem repeats could be related but have diverged greatly in size, sequence and effect on protein splicing. Alternatively, they could have independent origins but evolved certain similarities because of common constraints in structure and maintenance.     

Leishmania major lipophosphoglycan: Discrepancy in toll-like receptor signaling

Lipophosphoglycan (LPG) is structurally characterized by a series of phosphoglycan repeat units. Cellular LPG, isolated from promastigotes, has a very similar structure to culture supernatant LPG, but differs in the average number of phosphorylated oligosaccharide repeat units and in glycan composition. Comparison of these LPGs with capillary electrophoresis and immunoblotting indicate that these molecules are highly conserved structurally and composed of galactosylated Gal-Man repeats but their size and molecular weight are very different which is due to glycan portion. There are 30 and 20 repeat units in sLPG and mLPG, respectively. Both LPGs induced nitric oxide in macrophages cell line while sLPG had the higher stimulatory effect. In the presence of anti-TLR2 nitric oxide stimulated by LPG was reduced to control levels. In addition, in the presence of anti-TLR4, nitric oxide stimulated by LPGs was not affected. We propose that lipophosphoglycan induces nitric oxide production via TLR2 signaling pathway.     

中国人诱导型一氧化氮合酶基因STR多态性研究

一氧化氮（nitric oxide,NO）作为一种可在细胞间自由扩散的信使分子在神经递质传递和血管舒张调节等生理与病理过程中起着重要作用。NO通过一氧化氮合酶（nitric oxide synthase,NOS）催化L-精氨酸的氧化反应而生成。目前在哺乳动物中已发现细胞来源、表达方式和活性调节不同的3种NOS同工酶,分别为神经原型NOS(meuronal NOS,nNOS）、诱导型NOS(inducible NOS,iNOS）和内皮细胞型NOS（endothelial NOS,eNOS）。3种NOS由位于不同染色体上的基因所编码。人iNOS基因位于第17号染色体长臂(17q11.2～17q12）,全长约37kb,含有26个外显子,iNOS可在多种类型的细胞中通过IL-1、IFN-a、INF-γ等细胞因子和其他介质的刺激作用而诱导表达。iNOS基因5‘-端调控区内存在一个CCTTT串联重复的多态性位点,这一多态性基因座已居北爱尔兰的糖尿病患者中证实与微血管病变有关。另有实验表明,CCTTT串联重复序列的变化对iNOS基因的转录将产生不同影响。目前在东方种族中有关iNOS基因CCTTT串联重复多态性尚未见报道。将303名中国汉族人基因组DNA用于iNOS基因CCTTT串联重复多态性分析,鉴定出了12种等位基因和49种基因型,其中重复17次、18次和19次的等位基因是在人类中首次发现的新等位基因。统计学检验和比较表明,中国汉族人iNOS基因CCTTT串联重复序列的6个等位基因频率与来自英格兰的高加索人差异显著,说明这一多态性位点的等位基因频率分布存在种族差异。在中国正常人群中获得的有关iNOS基因STR多态性的统计资料,对于进一步研究这一多态性基因座与心脑血管疾病的相关性将有重要应用价值。     

Distinct effects on splicing of two monoclonal antibodies directed against the amino-terminal domain of galectin-3

Previous experiments had established that galectin-3 (Gal3) is a factor involved in cell-free splicing of pre-mRNA. Addition of monoclonal antibody NCL-GAL3, whose epitope maps to the NH₂-terminal 14 amino acids of Gal3, to a splicing-competent nuclear extract inhibited the splicing reaction. In contrast, monoclonal antibody anti-Mac-2, whose epitope maps to residues 48-100 containing multiple repeats of a 9-residue motif PGAYPGXXX, had no effect on splicing. Consistent with the notion that this region bearing the PGAYPGXXX repeats is sequestered through interaction with the splicing machinery and is inaccessible to the anti-Mac-2 antibody, a synthetic peptide containing three perfect repeats of the sequence PGAYPGQAP (27-mer) inhibited the splicing reaction, mimicking a dominant-negative mutant. Addition of a peptide corresponding to a scrambled sequence of the same composition (27-mer-S) failed to yield the same effect. Finally, GST-hGal3(1-100), a fusion protein containing glutathione-S-transferase and a portion of the Gal3 polypeptide including the PGAYPGXXX repeats, also exhibited a dominant-negative effect on splicing.     

Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients

Fragile X‐associated Tremor/Ataxia Syndrome (FXTAS) is a neurodegenerative disorder caused by expansion of 55–200 CGG repeats in the 5′‐UTR of the FMR1 gene. FXTAS is characterized by action tremor, gait ataxia and impaired executive cognitive functioning. It has been proposed that FXTAS is caused by titration of RNA‐binding proteins by the expanded CGG repeats. Sam68 is an RNA‐binding protein involved in alternative splicing regulation and its ablation in mouse leads to motor coordination defects. Here, we report that mRNAs containing expanded CGG repeats form large and dynamic intranuclear RNA aggregates that recruit several RNA‐binding proteins sequentially, first Sam68, then hnRNP‐G and MBNL1. Importantly, Sam68 is sequestered by expanded CGG repeats and thereby loses its splicing‐regulatory function. Consequently, Sam68‐responsive splicing is altered in FXTAS patients. Finally, we found that regulation of Sam68 tyrosine phosphorylation modulates its localization within CGG aggregates and that tautomycin prevents both Sam68 and CGG RNA aggregate formation. Overall, these data support an RNA gain‐of‐function mechanism for FXTAS neuropathology, and suggest possible target routes for treatment options.     

Evidence for the regulation of alternative splicing via complementary DNA sequence repeats

MOTIVATION: While the mechanism for regulating alternative splicing is poorly understood, secondary structure has been shown to be integral to this process. Due to their propensity for forming complementary hairpin loops and their elevated mutation rates, tandem repeated sequences have the potential to influence splicing regulation. RESULTS: An analysis of human intronic sequences reveals a strong correlation between alternative splicing and the prevalence of mono- through hexanucleotide tandem repeats that may engage in complementary pairing in introns that flank alternatively spliced exons. While only 44% of the 18 173 genes in the Human Alternative Splicing Database are known to be alternatively spliced, they contain 84% of the 694 237 intronic complementary repeat pairs. Significantly, the normalized frequency and distribution of repeat sequences, independent of their potential for pairing, are indistinguishable between alternatively spliced and non-alternatively spliced genes. Thus, the increased prevalence of repeats with pairing potential in alternatively spliced genes is not merely a consequence of more repeats or repeat composition bias. These results suggest that complementary repeats may play a role in the regulation of alternative splicing. CONTACT: harold.garner@utsouthwestern.edu.     

Structural and functional conservation of the Drosophila doublesex splicing enhancer repeat elements.

We have compared the RNA sequences and secondary structures of the Drosophila melanogaster and Drosophila virilis doublesex (dsx) splicing enhancers. The sequences of the two splicing enhancers are highly divergent except for the presence of nearly identical 13-nt repeat elements (six in D. melanogaster and four in D. virilis) and a stretch of nucleotides at the 5' and 3' ends of the enhancers. In vitro RNA structure probing of the two enhancers revealed that the 13-nt repeats are predominantly single-stranded. Thus, both the primary sequences and single-stranded nature of the repeats are conserved between the two species. The significance of the primary sequence conservation was demonstrated by showing that the two enhancers are functionally interchangeable in Tra-/Tra2-dependent in vitro splicing. In addition, inhibition of splicing enhancer activity by antisense oligonucleotides complementary to the repeats demonstrated the importance of the conserved single-stranded structure of the repeats. In vitro binding studies revealed that Tra2 interacts with each of the D. melanogaster repeat elements, except for repeat 2, with affinities that are indistinguishable, whereas Tra binds nonspecifically to the enhancer. Taken together, these observations indicate that the organization of sequences within the dsx splicing enhancers of D. melanogaster and D. virilis results in a structure in which each of the repeat elements is single-stranded and therefore accessible for specific recognition by the RNA-binding domain of Tra2.