The Formation Mechanism and Functional Implication of Chimeric RNAs / 中国生物化学与分子生物学报

Traditionally, chimeric RNA is thought to be generated by chromosome rearrangement, and its products (RNAs and proteins) were once considered as unique features of cancer. However, with the advancement of next-generation sequencing technologies and the development of bioinformatics software tools, increasing numbers of chimeric RNAs are being identified from various RNA-Seq database. Recently, numerous chimeric RNAs were discovered in human normal tissues and cell lines, with physiological functions. Besides chromosome rearrangement, chimeric RNAs are formed by different molecular mechanisms, including trans-splicing, cis-splicing of adjacent genes. Chimeric RNAs, without chromosomal changes, are regulated at the transcriptional level, and they show specific physiological functions and regulation patterns. Their dysregulation may induce cell differentiation and tumorogenisis. In addition, chimeric RNAs also play roles in normal cell growth and/or migration, cell cycle and apoptosis, induce genomic aberration by influencing chromosome rearrangement, act as potential competitive endogenous RNA, and influence stem cell differentiation. The expression of chimeric RNAs in specific tissues and cell development stages has the potential to be used as diagnostic and therapeutic biomarkers. Histological mapping studies can improve the specificity of treatment for unique cell types, and the chimeric RNA provides a new perspective to achieve this goal. The widespread existence of chimeric RNAs suggests that they may extend the diversity of genomes in human and higher animals.

Advances in protein cyclization / 生物工程学报

Proteins, which exist mainly in linear form in vivo, are easily affected by the change of ambient temperature and pH. The application of proteins (enzymes) in the fields of industrial catalyzing, food manufacturing and medicine are restricted due to their properties. The cyclic structure of natural cyclic peptides confers high thermal stability on itself; such mechanism can be referred to in further enhancement of the thermal stability and transformation of the structure of enzymes. This article reviewed the latest progress in the domestic and international studies on protein cyclization and summarized the traditional methods (such as protein trans-splicing, expressed protein ligation and sortase-catalyzed transpeptidation) in protein cyclization. A novel method based on SpyTag/SpyCather-mediated enzyme cyclization was discussed in more detail.

Análisis de secuencias de moléculas de Taenia solium procesadas post-transcripcionalmente mediante trans splicing / Sequences analysis of molecules of Taenia solium post-transcriptionally processed by trans-splicing

La neurocisticercosis es una enfermedad neurológica causada por la presencia de cisticercos de Taenia solium en el sistema nervioso central. La clonación de genes del parásito es importante para la identificación y estudio de moléculas claves en la biología del parásito, en diagnóstico, protección y en las relaciones parásito-hospedador. En T. solium, ocurre un mecanismo alternativo en el procesamiento de algunos ARNm, denominado trans-splicing, en el cual una pequeña molécula de ARN (Spliced Leader, SL) es añadida al extremo 5´ de una molécula de pre-ARNm, formando diferentes ARNm maduros que contienen un extremo 5´ común. El objetivo de este trabajó fue realizar el análisis de las secuencias de algunas moléculas que utilizan este procesamiento, para conocer mejor este mecanismo en T. solium. Para ello, se realizó un cribado mediante PCR de genotecas de expresión de cisticerco de T. solium utilizando como cebador directo SL y como reverso ZAP-3´UP, oligonucleótido que hibrida con la secuencia del vector. Se obtuvieron diferentes ADN complementarios (ADNc), que fueron clonados en el plásmido pGEM-T-easy, secuenciados y comparados con las bases de datos (GenBank). Un total de 14 moléculas diferentes fueron obtenidas, las cuales muestran similitud principalmente con proteínas de T. solium, Echinococcus sp. e Hymenolepis sp. Se obtuvieron transcriptos completos que codifican una variedad de proteínas que forman parte de la biología propia de organismos vivos, tales como; enzimas, transportadores, proteínas estructurales, entre otras. Aunque no fue posible determinar si existen grupos específicos de ADNc (con funciones comunes), escogidos para llevar a cabo esta modificación post-transcripcional, se pudo observar que el proceso de trans-splicing ocurre en una gran variedad de ARN que codifican diferentes proteínas de importancia biológica para T. solium.

Neurocysticercosis is a neurological disease caused by the presence of Taenia solium cysticerci in the central nervous system. T. solium uses an alternative mechanism for processing some mRNAs, known as trans-splicing, in which a small RNA molecule (Spliced Leader, SL) is added to the 5' end, of one pre-mRNA molecule, leading to the formation of different mature mRNAs that all contain a common 5' end. The aim of this study was to analyze the sequences of some of the molecules that undergo this type of post-transcriptional processing in order to learn more about this mechanism in T. solium. Expression libraries of T. solium cysticerci were screened using PCR with SL as the forward primer and ZAP 3' UP, an oligonucleotide that hybridizes to the vector sequence, as the reverse primer. Different cDNAs were obtained which were cloned in the pGEM-T-easy plasmid, sequenced and then compared with sequences in databases (GenBank). A total of 14 different molecules showing similarities to T. solium, Echinococcus sp. and Hymenolepis sp. proteins were obtained. Complete transcripts encoding a variety of proteins that are part of the biology of living organisms, such as enzymes, transporters and structural proteins, were also identified. Although we could not determine whether specific cDNA groups (with common functions) are selected to carry out this post-transcriptional modification, we were able to observe that the process of trans-splicing occurs in a variety of RNAs that code for several proteins biologically important for T. solium.

A directed approach for the identification of transcripts harbouring the spliced leader sequence and the effect of trans-splicing knockdown in Schistosoma mansoni

Schistosomiasis is a major neglected tropical disease caused by trematodes from the genus Schistosoma. Because schistosomes exhibit a complex life cycle and numerous mechanisms for regulating gene expression, it is believed that spliced leader (SL) trans-splicing could play an important role in the biology of these parasites. The purpose of this study was to investigate the function of trans-splicing in Schistosoma mansoni through analysis of genes that may be regulated by this mechanism and via silencing SL-containing transcripts through RNA interference. Here, we report our analysis of SL transcript-enriched cDNA libraries from different S. mansoni life stages. Our results show that the trans-splicing mechanism is apparently not associated with specific genes, subcellular localisations or life stages. In cross-species comparisons, even though the sets of genes that are subject to SL trans-splicing regulation appear to differ between organisms, several commonly shared orthologues were observed. Knockdown of trans-spliced transcripts in sporocysts resulted in a systemic reduction of the expression levels of all tested trans-spliced transcripts; however, the only phenotypic effect observed was diminished larval size. Further studies involving the findings from this work will provide new insights into the role of trans-splicing in the biology of S. mansoni and other organisms. All Expressed Sequence Tags generated in this study were submitted to dbEST as five different libraries. The accessions for each library and for the individual sequences are as follows: (i) adult worms of mixed sexes (LIBEST_027999: JZ139310 - JZ139779), (ii) female adult worms (LIBEST_028000: JZ139780 - JZ140379), (iii) male adult worms (LIBEST_028001: JZ140380 - JZ141002), (iv) eggs (LIBEST_028002: JZ141003 - JZ141497) and (v) schistosomula (LIBEST_028003: JZ141498 - JZ141974).

Los productos alternativos de LYT1 de Trypanosoma cruzi tienen un patrón de localización diferencial / The alternative products of Trypanosoma cruzi LYT1 have different localization patterns

LYT1 is a molecule with lytic activity under acidic conditions that, as genetically demonstrated, participates in the infection and stage transition of T. cruzi. The differing functions of this protein result from alternative trans-splicing, resulting in proteins that contain either a secretion and nuclear sequence (LYT1s) or the nuclear sequence alone (LYT1n). To determine the localization of different LYT1 products, transgenic parasites expressing LYT1s or LYT1n fused to the enhanced green fluorescence sequence were analyzed. LYT1s-EGFP localized to the flagellum, vacuoles, membrane and regions of the nucleus and kinetoplast; LYT1n-EGFP localized to the nucleus and kinetoplast, and occasionally in vacuoles. These results show that even though different LYT1 products localize to the same sites, they are also found in different intracellular organelles and microenvironments, which could influence their multifunctional behavior.

LYT1 es una molécula con actividad lítica en condiciones ácidas, que según se demostró genéticamente, participa en el proceso de infección y transición de estadio de T. cruzi. Su diferente funcionalidad es resultado de la producción de dos proteínas, obtenidas por trans-empalme alternativo, que contienen una secuencia de secreción y una nuclear (LYT1s) o únicamente la secuencia nuclear (LYT1n). Para evaluar la localización de los diferentes productos de LYT1, se analizaron parásitos transgénicos que expresan la secuencia de LYT1s o LYT1n fusionada con la secuencia de la verde fluorescente. LYT1s-EGFP se localiza en flagelo, vacuolas, membrana y región del núcleo y cinetoplasto; mientras que, LYT1n-EGFP se localiza en la región del núcleo y cinetoplasto, y ocasionalmente en vesículas. Estos resultados muestran que aún cuando los distintos productos de LYT1 comparten algunos sitios de localización, también se encuentran en distintos organelos y microambientes intracelulares que podrían influir en su comportamiento multifuncional.

New insights into trypanosomatid U5 small nuclear ribonucleoproteins

Several protozoan parasites exist in the Trypanosomatidae family, including various agents of human diseases. Multiple lines of evidence suggest that important differences are present between the translational and mRNA processing (trans splicing) systems of trypanosomatids and other eukaryotes. In this context, certain small complexes of RNA and protein, which are named small nuclear ribonucleoproteins (U snRNPs), have an essential role in pre-mRNA processing, mainly during splicing. Even though they are well defined in mammals, snRNPs are still not well characterized in trypanosomatids. This study shows that a U5-15K protein is highly conserved among various trypanosomatid species. Tandem affinity pull-down assays revealed that this protein interacts with a novel U5-102K protein, which suggests the presence of a sub-complex that is potentially involved in the assembly of U4/U6-U5 tri-snRNPs. Functional analyses showed that U5-15K is essential for cell viability and is somehow involved with the trans and cis splicing machinery. Similar tandem affinity experiments with a trypanonosomatid U5-Cwc21 protein led to the purification of four U5 snRNP specific proteins and a Sm core, suggesting U5-Cwc-21 participation in the 35S U5 snRNP particle. Of these proteins, U5-200K was molecularly characterized. U5-200K has conserved domains, such as the DEAD/DEAH box helicase and Sec63 domains and displays a strong interaction with U5 snRNA.

Post-translational ligation and function of dual-vector transferred split CFTR gene / 药学学报

The mutation of cystic fibrosis transmembrane conductance regulator (CFTR) gene leads to an autosomal recessive genetic disorder cystic fibrosis (CF). The gene therapy for CF using adeno-associated virus (AAV) vectors delivering CFTR gene is restricted by the contents limitation of AAV vectors. In this study the split CFTR genes severed at its regulatory domain were delivered by a dual-vector system with an intein- mediated protein trans-splicing as a technique to investigate the post-translational ligation of CFTR half proteins and its function as a chloride ion channel. A pair of eukaryotic expression vectors was constructed by breaking the human CFTR cDNA before Ser712 codon and fusing with Ssp DnaB intein coding sequences. After co-transfection into baby hamster kidney (BHK) cells followed by transient expression, patch clamps were carried out to record the chloride current of whole-cell and the activity of a single channel, and the ligation of two halves of CFTR was observed by Western blotting. The results showed that the intein-fused half genes co-tansfected cells displayed a high whole cell chloride current and activity of a single channel indicating the functional recovery of chloride channel, and an intact CFTR protein band was figured out by CFTR-specific antibodies indicating that intein can efficiently ligate the separately expressed half CFTR proteins. The data demonstrated that protein splicing strategy could be used as a strategy in delivering CFTR gene by two vectors,encouraging our ongoing research program on dual AAV vector system based gene transfer in gene therapy for cystic fibrosis.

RNA Mapping of Mutant Myotonic Dystrophy Protein Kinase 3'-Untranslated Region Transcripts

Myotonic dystrophy type 1 (DM1), which is a dominantly inherited neurodegenerative disorder, results from a CTG trinucleotide repeat expansion in the 3'-untranslated region (3'-UTR) of the myotonic dystrophy protein kinase (DMPK) gene. Retention of mutant DMPK (mDMPK) transcripts in the nuclei of affected cells has been known to be the main cause of pathogenesis of the disease. Thus, reducing the RNA toxicity through elimination of the mutant RNA has been suggested as one therapeutic strategy against DM1. In this study, we suggested RNA replacement with a trans -splicing ribozyme as an alternate genetic therapeutic approach for amelioration of DM1. To this end, we identified the regions of mDMPK 3'-UTR RNA that were accessible to ribozymes by using an RNA mapping strategy based on a trans - splicing ribozyme library. We found that particularly accessible sites were present not only upstream but also downstream of the expanded repeat sequence. Repair or replacement of the mDMPK transcript with the specific ribozyme will be useful for DM1 treatment through reduction of toxic mutant transcripts and simultaneously restore wild-type DMPK or release nucleus-entrapped mDMPK transcripts to the cytoplasm.

In Vivo Target RNA Specificity of Trans-Splicing Phenomena by the Group I Intron

The Tetrahymena group I intron has been shown to employ a trans-splicing reaction and has been modified to specifically target and replace human telomerase reverse transcriptase (hTERT) RNA with a suicide gene transcript, resulting in the induction of selective cytotoxicity in cancer cells that express the target RNA, in animal models as well as in cell cultures. In this study, we evaluated the target RNA specificity of trans -splicing phenomena by the group I intron in mice that were intraperitoneally inoculated with hTERT-expressing human cancer cells to validate the anti-cancer therapeutic applicability of the group I intron. To this end, an adenoviral vector that encoded for the hTERT-targeting group I intron was constructed and systemically injected into the animal. 5'-end RACE-PCR and sequencing analyses of the trans-spliced cDNA clones revealed that all of the analyzed products in the tumor tissue of the virus-infected mice resulted from reactions that were generated only with the targeted hTERT RNA. This study implies the in vivo target specificity of the trans - splicing group I intron and hence suggests that RNA replacement via a trans -splicing reaction by the group I intron is a potent anti-cancer genetic approach.

RNA polymerase I promoter and splice acceptor site recognition affect gene expression in non-pathogenic Leishmania species

Leishmania (Sauroleishmania) tarentolae has biotechnological potential for use as live vaccine against visceral leishmaniasis and as a system for the over expression of eukaryotic proteins that possess accurate post-translational modifications. For both purposes, new systems for protein expression in this non-pathogenic protozoan are necessary. The ribosomal RNA promoter proved to be a stronger transcription driver since its use yielded increased levels of recombinant protein in organisms of both genera Trypanosoma or Leishmania. We have evaluated heterologous expression systems using vectors with two different polypyrimidine tracts in the splice acceptor site by measuring a reporter gene transcribed from L. tarentolae RNA polymerase I promoter. Our data indicate that the efficiency of chloramphenicol acetyl transferase expression changed drastically with homologous or heterologous sequences, depending on the polypyrimidine tract used in the construct and differences in size and/or distance from the AG dinucleotide. In relation to the promoter sequence the reporter expression was higher in heterologous lizard-infecting species than in the homologous L. tarentolae or in the mammalian-infecting L. (Leishmania) amazonensis.

Rapid test for the evaluation of the activity of the prodrug hydroxymethylnitrofurazone in the processing of Trypanosoma cruzi messenger RNAs

No fully effective treatment has been developed since the discovery of Chagas' disease by Carlos Chagas in 1909. Since drug-resistant Trypanosoma cruzi strains are occurring and the current therapy is effectiveness in the acute phase but with various adverse side effects, more studies are needed to characterize the susceptibility of T. cruzi to new drugs. Many natural and/or synthetic substances showing trypanocidal activity have been used, even though they are not likely to be turned into clinically approved drugs. Originally, drug screening was performed using natural products, with only limited knowledge of the molecular mechanism involved in the development of diseases. Trans-splicing, which is unusual RNA processing reaction and occurs in nematodes and trypanosomes, implies the processing of polycistronic transcription units into individual mRNAs; a short transcript spliced leader (SL RNA) is trans-spliced to the acceptor pre-mRNA, giving origin to the mature mRNA. In the present study, permeable cells of T. cruzi epimastigote forms (Y, BOL and NCS strains) were treated to evaluate the interference of two drugs (hydroxymethylnitrofurazone - NFOH-121 and nitrofurazone) in the trans-splicing reaction using silver-stained PAGE analysis. Both drugs induced a significant reduction in RNA processing at concentrations from 5 to 12.5 æM. These data agreed with the biological findings, since the number of parasites decreased, especially with NFOH-121. This proposed methodology allows a rapid and cost-effective screening strategy for detecting drug interference in the trans-splicing mechanism of T. cruzi.

Gene expression responses in vivo by human telomerase reverse transcriptase (hTERT)-targeting trans-splicing ribozyme

A trans-splicing ribozyme which can specifically reprogram human telomerase reverse transcriptase (hTERT) RNA was previously suggested as a useful agent for tumor-targeted gene therapy. In this study, we evaluated in vivo function of the hTERT-targeting trans-splicing ribozymes by employing the molecular analysis of expression level of genes affected by the ribozyme delivery into peritoneal carcinomatosis mice model. To this effect, we constructed adenoviral vector encoding the specific ribozyme. Noticeably, more than four-fold reduction in the level of hTERT RNA was observed in tumor nodules by the systemic infection of the ribozyme-encoding virus. Such hTERT RNA knockdown in vivo induced changes in the global gene expression profile, including the suppression of specific genes associated with anti-apoptosis including bcl2, and genes for angiogenesis and metastasis. In addition, specific trans-splicing reaction with the targeted hTERT RNA took place in the tumors established as peritoneal carcinomatosis in mice by systemic delivery of the ribozyme. In conclusion, this study demonstrates that an hTERT-specific RNA replacement approach using trans-splicing ribozyme represents a potential modality to treat cancer.

An RNA Mapping Strategy to Identify Ribozyme-Accessible Sites on the Catalytic Subunit of Mouse Telomerase

Telomerase reverse transcriptase (TERT) is an enzymatic ribonucleoprotein that prolongs the replicative life span of cells by maintaining protective structures at the ends of eukaryotic chromosomes. Telomerase activity is highly up-regulated in 85-90% of human cancers, and is predominately regulated by hTERT expression. In contrast, most normal somatic tissues in humans express low or undetectable levels of telomerase activity. This expression profile identifies TERT as a potential anticancer target. By using an RNA mapping strategy based on a trans-splicing ribozyme library, we identified the regions of mouse TERT (mTERT) RNA that were accessible to ribozymes. We found that particularly accessible sites were present downstream of the AUG start codon. This mTERTspecific ribozyme will be useful for validation of the RNA replacement as cancer gene therapy approach in mouse model with syngeneic tumors.

Repeating exon 2 mutation caused by trans-splicing dystrophin gene in Duchenne muscular dystrophin (DMD) patient

The dystrophin gene is the largest human gene. Mutations in this gene cause Duchenne muscular dystrophin (DMD) disease. This is complex genomic unit exhibiting many errors splicing during mRNA process. More than 10 alternative splicing products have been identified in the 5' region of the dystrophin gene. In this study, two dystrophin transcripts including one containing exon 2 and exon X duplications, other one containing single exon 2 duplication were identified in peripheral blood lymphocytes of DMD case. Interestingly, genomic Southern blot analysis ruled out the hypothesis of duplication of dystrophin at exon 2. Therefore, these data suggested that exon 2 duplication transcripts were likely generated by trans-splicing event that occurring during the mARN maturation in which RNA segments of two independent transcripts are spliced together to generate a new mRNA species. However, the mechanisms modulating the trans-splicing activity of the dystrophin exon 2 remain to be clarified.

Functional Modification of a Specific RNA with Targeted Trans-Splicing

The self-splicing group I intron from Tetrahymena thermophila has been demonstrated to perform splicing reaction with its substrate RNA in the trans configuration. In this study, we explored the potential use of the trans-splicing group I ribozymes to replace a specific RNA with a new RNA that exerts any new function we want to introduce. We have chosen thymidine phosphorylase (TP) RNA as a target RNA that is known as a valid cancer prognostic factor. Cancer-specific expression of TP RNA was first evaluated with RT-PCR analysis of RNA from patients with gastric cancer. We determined next which regions of the TP RNA are accessible to ribozymes by employing an RNA mapping strategy, and found that the leader sequences upstream of the AUG start codon appeared to be particularly accessible. A specific ribozyme recognizing the most accessible sequence in the TP RNA with firefly luciferase transcript as a 3' exon was then developed. The specific trans-splicing ribozyme transferred an intended 3' exon tag sequence onto the targeted TP transcripts, resulting in a more than two fold induction of the reporter activity in the presence of TP RNA in mammalian cells, compared to the absence of the target RNA. These results suggest that the Tetrahymena ribozyme can be a potent anti-cancer agent to modify TP RNAs in tumors with a new RNA harboring anti-cancer activity.

ChimerDB - Database of Chimeric Sequences in the GenBank

Fusion proteins resulting from chimeric sequences are excellent targets for therapeutic drug development. We developed a database of chimeric sequences by examining the genomic alignment of mRNA and EST sequences in the GenBank. We identified 688 chimeric mRNA and 20,998 chimeric EST sequences. Including EST sequences greatly expands the scope of chimeric sequences even though it inevitably accompanies many artifacts. Chimeric sequences are clustered according to the ECgene ID so that the user can easily find chimeric sequences related to a specific gene. Alignments of chimeric sequences are displayed as custom tracks in the UCSC genome browser. ChimerDB, available at http://genome.ewha.ac.kr/ECgene/ChimerDB/, should be a valuable resource for finding drug targets to treat cancers.