HRP-2, the Caenorhabditis elegans Homolog of Mammalian Heterogeneous Nuclear Ribonucleoproteins Q and R, Is an Alternative Splicing Factor That Binds to UCUAUC Splicing Regulatory Elements

Alternative splicing is regulated by cis sequences in the pre-mRNA that serve as binding sites for trans-acting alternative splicing factors. In a previous study, we used bioinformatics and molecular biology to identify and confirm that the intronic hexamer sequence UCUAUC is a nematode alternative splicing regulatory element. In this study, we used RNA affinity chromatography to identify trans factors that bind to this sequence. HRP-2, the Caenorhabditis elegans homolog of human heterogeneous nuclear ribonucleoproteins Q and R, binds to UCUAUC in the context of unc-52 intronic regulatory sequences as well as to RNAs containing tandem repeats of this sequence. The three Us in the hexamer are the most important determinants of this binding specificity. We demonstrate, using RNA interference, that HRP-2 regulates the alternative splicing of two genes, unc-52 and lin-10, both of which have cassette exons flanked by an intronic UCUAUC motif. We propose that HRP-2 is a protein responsible for regulating alternative splicing through binding interactions with the UCUAUC sequence.Alternative pre-mRNA splicing is a mechanism for generating multiple mRNA isoforms from a single gene. This process can allow a gene to encode for more than one protein isoform. For some genes, it is a mechanism for regulating message stability through production of alternative mRNA isoforms that are substrates for the nonsense-mediated mRNA decay pathway (1). The majority of human genes undergo alternative splicing (2), and the process can be regulated in tissue-specific and developmental stage-specific manners. Current models propose that cis elements on the pre-mRNA, in exons and introns, serve as recognition sites for trans-acting protein factors that bind to the pre-mRNA and regulate assembly of the splicing machinery, thus regulating splice site choice (3).In recent years, a number of groups have employed bioinformatics techniques to identify cis splicing regulatory elements (4). These techniques include using multiple interspecies sequence alignments to identify conserved intronic regions, identification of short sequences in exons that are bounded by weak consensus splice sites, and identification of common intronic sequences flanking similarly regulated alternative exons (5–9). These efforts have added many new sequences to the list of known and potential splicing regulators. The identification of the protein factor partners for these sequences will be important for understanding their function in alternative splicing regulation.Experimental approaches have identified alternative splicing factors that interact with specific cis elements (10), but the number of trans factors discovered still lags behind the number of newly identified cis element partners. Some examples of well-characterized cis element/trans-acting factor interactions include the NOVA K homology domain splicing factor binding to the sequence UCAY (11), the FOX splicing factors binding to the sequence UGCAUG (12–14), and hnRNP³ F/H proteins binding to the sequence GGGG (15, 16). By using cross-linking immunoprecipitation followed by large scale sequencing, entire catalogs of RNAs that the splicing factors NOVA, SF2/ASF, and FOX2 bind to in vivo have been determined (17–19). These approaches have led to models for how the proteins binding to their cis regulatory elements may alter splicing. These models include a role for the relative position of a cis element to an alternative cassette exon in determining alternative exon inclusion or skipping (18, 19).In a previous bioinformatics analysis of evolutionarily conserved intronic sequences flanking alternatively spliced exons, we identified the hexamer sequence UCUAUC as a novel splicing regulatory element (8). UCUAUC is found flanking both sides of alternative exon 16 of the unc-52 gene of Caenorhabditis elegans. Genetic analysis of a class of viable unc-52 mutants led to the discovery that exons 16–18 are alternative cassette exons and that every combination of skipping and inclusion of these three exons occurs (20). This splicing is regulated by the alternative splicing factor MEC-8 (21). Fig. 1A shows a schematic diagram of the alternatively spliced region of unc-52, with the MEC-8-enhanced alternative splicing events indicated. Using an unc-52 splicing reporter trans gene containing alternative exons 15–19, we previously reported that alternative splicing is regulated by the intronic motif UCUAUC in the intron downstream of exon 16 (8). In addition we showed that this element works cooperatively with a UGCAUG hexamer (the consensus FOX-1-binding site) in the upstream intron to regulate alternative splicing (8).Open in a separate windowFIGURE 1.RNA affinity chromatography identifies HRP-2 as binding to UCUAUC elements. A, schematic representation of the alternatively spliced region of unc-52 (adapted from Ref. 21). The alternative splicing events promoted by MEC-8 are indicated by bold lines. The lines next to introns 15 and 16 are the sites of the UCUAUC elements in those introns whose sequences were used in the RNA affinity chromatography. B, table showing sequences of RNAs immobilized to beads in the RNA affinity chromatography experiment. C, Coomassie-stained SDS-PAGE analysis of RNA affinity chromatography. C. elegans embryo extract was incubated with the different immobilized RNA substrates listed on top of the gel. Proteins identified by mass spectrometry are listed to the right of the gel, with arrows pointing to coincident protein bands. D, the left panel shows the silver stain result for the RNA affinity chromatography experiment. Each lane represents a different immobilized substrate, as indicated above. The band corresponding to HRP-2 is indicated by an arrow. The right panel is an immunoblot of the same gel using anti-HRP-2 polyclonal antibody. E, anti-HRP-2 immunoblot of an RNA affinity chromatography experiment for the indicated substrates.In this study, we report the results of a biochemical identification of a protein factor from C. elegans that binds to the UCUAUC intronic splicing regulatory element. We transcribed different short RNA sequences containing the UCUAUC element in its native intronic context, or as part of a repeating unit, and immobilized these onto agarose beads. After passing embryo extracts across these beads, we found that the protein HRP-2, the C. elegans homolog of the mammalian hnRNP Q/R proteins, binds to this sequence with high affinity. By using RNAi to reduce the level of HRP-2 in worms, we observed changes in alternative splicing of unc-52 and lin-10, two genes that contain UCUAUC elements in introns flanking alternative exons. We propose that HRP-2 is an alternative splicing factor that works through the UCUAUC intronic elements to regulate alternative splicing.     

Variations on the SnCl4 and CF3CO2Ag-promoted glycosidation of sugar acetates: a direct, versatile and apparently simple method with either α or β stereocontrol

Glycosidation of sugar peracetates (d-gluco, d-galacto) with SnCl₄ and CF₃CO₂Ag led to either 1,2-cis-, or 1,2-trans-glycosides, depending primarily on the alcohols used. In particular, 1,2-trans-glycosides, expected from acyl-protected glycosyl donors, were formed in high yields with alcohols sharing specific features such as bulkiness, presence of electron-withdrawing groups or polyethoxy motifs. In contrast, simple alcohols afforded 1:1 mixtures of 2,3,4,6-tetra-O-acetyl, and 3,4,6-tri-O-acetyl 1,2-cis-glycosides due to anomerization and/or acid-catalyzed fragmentation of 1,2-orthoester intermediates. After reacetylation or deacetylation, acetylated or fully deprotected 1,2-cis-glycosides (α-d-gluco, α-d-galacto) were obtained in 90% yields by a simple and direct method.     

Fungal catabolic gene regulation: Molecular genetic analysis of theamdS gene ofAspergillus nidulans

Aspergillus nidulans is an excellent experimental organism for the study of gene regulation. Genetic and molecular analyses oftrans-acting andcis-acting mutations have revealed a complex pattern of regulation involving multiple independent controls. Expression of theamdS gene is regulated by thefacB andamdA genes which encode positively acting regulatory proteins mediating a major and a minor form of acetate induction respectively. The product of theamdR gene mediates omega amino acid induction ofamdS. The binding sites for each of these proteins have been localised throughamdS cis-acting mutations which specifically affect the interaction with the regulatory protein. The global controls of nitrogen metabolite repression and carbon catabolite repression regulate the expression of many catabolic genes, includingamdS. Nitrogen control is exerted through the positively actingareA gene product and carbon control is dependent on thecreA gene product. Each of the characterized regulatory genes encodes a DNA-binding protein which recognises particular sequences in theamdS promoter to activate or repress gene expression. In addition, there is evidence for other genetically uncharacterised proteins, including a CCAAT-binding complex, which interact with the 5 region of theamdS gene.     

Genetic analysis of the minimal replicon of the Lactococcus lactis subsp. lactis biovar diacetylactis citrate plasmid

Using a combination of mutagenesis with the transposon and polymerase chain reaction subcloning, the essential elements of the replication region of the Lactococcus lactis subsp. lactis biovar diacetylactis citrate plasmid have been identified. An open reading frame, coding for a protein with homology to Rep proteins from other Lactococcus plasmids, is essential. This protein is trans-acting and could not be replaced by the Rep protein from another Lactococcus plasmid. A second open reading frame immediately downstream from the first could be removed or inactivated with no apparent effect on plasmid replication. A region containing two 10 by direct repeats and three tandem repeats of a 22 by sequence, immediately upstream of the essential open reading frame, is also essential and probably includes the origin of replication. A 181-bp DNA fragment containing this region was sufficient to allow replication in Lactococcus if the trans-acting protein was provided on another replicon. Single-stranded replication intermediates could not be detected, suggesting that the citrate plasmid uses theta replication rather than rolling-circle replication.     

Functional selection and systematic analysis of intronic splicing elements identify active sequence motifs and associated splicing factors

Despite the critical role of pre-mRNA splicing in generating proteomic diversity and regulating gene expression, the sequence composition and function of intronic splicing regulatory elements (ISREs) have not been well elucidated. Here, we employed a high-throughput in vivo Screening PLatform for Intronic Control Elements (SPLICE) to identify 125 unique ISRE sequences from a random nucleotide library in human cells. Bioinformatic analyses reveal consensus motifs that resemble splicing regulatory elements and binding sites for characterized splicing factors and that are enriched in the introns of naturally occurring spliced genes, supporting their biological relevance. In vivo characterization, including an RNAi silencing study, demonstrate that ISRE sequences can exhibit combinatorial regulatory activity and that multiple trans-acting factors are involved in the regulatory effect of a single ISRE. Our work provides an initial examination into the sequence characteristics and function of ISREs, providing an important contribution to the splicing code.     

SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing

RNA provides the framework for the assembly of some of the most intricate macromolecular complexes within the cell, including the spliceosome and the mature ribosome. The assembly of these complexes relies on the coordinated association of RNA with hundreds of trans-acting protein factors. While some of these trans-acting factors are RNA-binding proteins (RBPs), others are adaptor proteins, and others still, function as both. Defects in the assembly of these complexes results in a number of human pathologies including neurodegeneration and cancer. Here, we demonstrate that Silencing Defective 2 (SDE2) is both an RNA binding protein and also a trans-acting adaptor protein that functions to regulate RNA splicing and ribosome biogenesis. SDE2 depletion leads to widespread changes in alternative splicing, defects in ribosome biogenesis and ultimately complete loss of cell viability. Our data highlight SDE2 as a previously uncharacterized essential gene required for the assembly and maturation of the complexes that carry out two of the most fundamental processes in mammalian cells.     

A mutation affecting amdS expression in Aspergillus nidulans contains a triplication of a cis-acting regulatory sequence

Summary In Aspergillus nidulans expression of the acetamidase structural gene, amdS, is under the control of at least four regulatory genes including the trans-acting amdA regulatory gene. A cis-acting mutation (amdI66) consisting of an 18 by duplication in the 5 region of the amdS gene results in very high levels of acetamidase activity but only in strains carrying semi-dominant mutations in the amdA gene. In selecting for increased amdS expression in an amdI66 amdA ^– strain, an A. nidulans strain with a mutation in the 5 region of the amdS gene was isolated. The nucleotide sequence was determined of the region containing the mutation, designated amdI666. The mutant strain carries three tandem copies of the 18 by sequence that is duplicated in the amdI66 mutation. Thus, from a strain carrying a duplication of an apparent regulatory protein binding site with little effect on gene expression, a strain has been derived that carries a triplication of the site with consequent major effects on regulation. The multiple copies of regulatory sites present in many genes may have been generated by a similar mechanism.     

Predominant contribution of cis‐regulatory divergence in the evolution of mouse alternative splicing

Divergence of alternative splicing represents one of the major driving forces to shape phenotypic diversity during evolution. However, the extent to which these divergences could be explained by the evolving cis‐regulatory versus trans‐acting factors remains unresolved. To globally investigate the relative contributions of the two factors for the first time in mammals, we measured splicing difference between C57BL/6J and SPRET/EiJ mouse strains and allele‐specific splicing pattern in their F1 hybrid. Out of 11,818 alternative splicing events expressed in the cultured fibroblast cells, we identified 796 with significant difference between the parental strains. After integrating allele‐specific data from F1 hybrid, we demonstrated that these events could be predominately attributed to cis‐regulatory variants, including those residing at and beyond canonical splicing sites. Contrary to previous observations in Drosophila, such predominant contribution was consistently observed across different types of alternative splicing. Further analysis of liver tissues from the same mouse strains and reanalysis of published datasets on other strains showed similar trends, implying in general the predominant contribution of cis‐regulatory changes in the evolution of mouse alternative splicing.     

Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression

Intron removal from a pre-mRNA by RNA splicing was once thought to be controlled mainly by intron splicing signals. However, viral and other eukaryotic RNA exon sequences have recently been found to regulate RNA splicing, polyadenylation, export, and nonsense-mediated RNA decay in addition to their coding function. Regulation of alternative RNA splicing by exon sequences is largely attributable to the presence of two majorcis-acting elements in the regulated exons, the exonic splicing enhancer (ESE) and the suppressor or silencer (ESS). Two types of ESEs have been verified from more than 50 genes or exons: purine-rich ESEs, which are the more common, and non-purine-rich ESEs. In contrast, the sequences of ESSs identified in approximately 20 genes or exons are highly diverse and show little similarity to each other. Through interactions with cellular splicing factors, an ESE or ESS determines whether or not a regulated splice site, usually an upstream 3 splice site, will be used for RNA splicing. However, how these elements function precisely in selecting a regulated splice site is only partially understood. The balance between positive and negative regulation of splice site selection likely depends on thecis-element's identity and changes in cellular splicing factors under physiological or pathological conditions.     

Regulation of plant genes specifically induced in nitrogen-fixing nodules: role of cis-acting elements and trans-acting factors in leghemoglobin gene expression

Transgenic alfalfa plants harboring a gene fusion between the soybean leghemoglobin (lbc3) promoter region and the chloramphenicol acetyl transferase (cat) gene were used to determine the influence of rhizobial mutants on lb gene expression in nodules. The promoter region of the Sesbania rostrata glb3 (Srglb3) leghemoglobin gene was examined for the presence of conserved motifs homologous to binding site 1 and 2 of the soybean lbc3 promoter region, found to interact with a trans-acting factor present in soybean nodule nuclear extracts (Jensen EO, Marcker KA, Schell J, de Bruijn FJ, EMBO J 7: 1265–1271, 1988). Subfragments of the S. rostrata glb3 (Srglb3) promoter region were examined for binding to trans-acting factors from nodule nuclear extracts. In addition to the binding sites previously identified (Metz BA, Welters P, Hoffmann HJ, Jensen EO, Schell J, de Bruijn FJ, Mol Gen Genet 214: 181–191), several other sites were found to interact with trans-acting factors. In most cases the same trans-acting factor(s) were shown to be involved. One fragment (202) was found to bind specifically to a different factor (protein) which was extremely heat-resistant (100°C). The appearance of this factor was shown to be developmentally regulated since the expected protein-DNA complexes were first observed around 12 days after infection, concomitant with the production of leghemoglobin proteins. Fragments of the Srglb3 5 upstream region were fused to the -glucuronidase reporter gene with its own CAAT and TATA box region or those of the cauliflower mosaic virus 35S and nopaline synthase (nos) promoters. These constructs were used to generate transgenic Lotus corniculatus plants and their expression was measured in different plant tissues. The Srglb3 CAAT and TATA box region was found to be required for nodule-specific expression and several upstream enhancer-type regions were identified.     

Purification and characterization of a novel ribosome-inactivating protein from seeds of Trichosanthes kirilowii Maxim

A novel ribosome-inactivating protein, designated Trichosanthrip, was purified from mature seeds of Trichosanthes kirilowii Maxim by cation-exchange and gel-filtration chromatography. Trichosanthrip migrated as a single band in SDS–PAGE, with an apparent molecular mass of 13 kDa. The molecular mass of Trichosanthrip was 10,964.617 Da as determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Trichosanthrip showed N-glycosidase activity on 28 S rRNA and strongly inhibited cell-free protein synthesis, with an IC₅₀ of 1.6 ng/ml. Liquid chromatography–tandem mass spectrometry showed that Trichosanthrip was a novel protein with similar sequence to other proteins present in members of the Cucurbitaceae.     

Phylogeography of the frog Leptodactylus validus (Amphibia: Anura): Patterns and timing of colonization events in the Lesser Antilles

The frog Leptodactylus validus occurs in northern South America, Trinidad and Tobago, and the southern Lesser Antilles (Grenada and St. Vincent). Mitochondrial DNA sequences were used to perform a nested clade phylogeographic analysis (NCPA), to date colonization events, and to analyze colonization patterns using on a relaxed molecular clock and coalescent simulations. L. validus originated on the mainland and first colonized Trinidad with subsequent independent colonizations of Tobago and the Lesser Antilles from Trinidad. The NCPA suggests a historical vicariant event between populations in Trinidad and Tobago from those in the Lesser Antilles. The colonization of Trinidad occurred 1 million years ago (mya) and the colonization of the Lesser Antillean islands occurred 0.4 mya. The coalescent approach supported the scenario where L. validus dispersed from Trinidad to St. Vincent and from there to Grenada, a dispersal event that could have been mediated by human introduction as recent as 1600 years ago.     

Pronase digestion of brush border membrane-bound Cry1Aa shows that almost the whole activated Cry1Aa molecule penetrates into the membrane

Bacillus thuringiensis insecticidal proteins, Cry toxins, following ingestion by insect larvae, induce insecticidal effect by penetrating the brush border membranes (BBM) of midgut epithelial cells. Purified, activated B. thuringiensis Cry1Aa bound to Bombyx mori BBMV or unbound Cry1Aa were vigorously digested with Pronase. Both digests were compared by Western blotting. Free Cry1Aa was digested to α-helix and/or to amino acids at 1 mg Pronase/mL within 2.4 h at 37 °C. Whereas, BBMV-bound Cry1Aa was very resistant to Pronase digestion and even at 2 mg for 24 h, 7.5 kDa and 30 kDa peptide were detected by α-2,3 antiserum, and α-4,5 and α-6,7 antisera, respectively. Another 30 kDa peptide was also detected by β-6-11 and domain III antisera. These fragments are believed either to be embedded in or to strongly interact with the BBMV. The 7.5 and former 30 kDa peptides are thought to be derived from α-2,3 helix and stretch of α-4 to α-7 helices. Furthermore the latter 30 kDa was thought to include the stretch of β-6 to domain III. Moreover, the embedded Cry1Aa molecule appears to be segregated in some areas of β-1-5 sheets, resulting in the above two 30 kDa peptides. From these digestion patterns, we proposed new membrane insertion model for single Cry1Aa molecule. On the other hand, in digestion of BBMV-bound Cry1Aa, 15 kDa peptide which was recognized only by α-4,5 antiserum was observed. This fragment must be dimeric α-4,5 helices and we discussed the origin of this peptide.     

Transcriptome-wide modulation of splicing by the exon junction complex

Background

The exon junction complex (EJC) is a dynamic multi-protein complex deposited onto nuclear spliced mRNAs upstream of exon-exon junctions. The four core proteins, eIF4A3, Magoh, Y14 and MLN51, are stably bound to mRNAs during their lifecycle, serving as a binding platform for other nuclear and cytoplasmic proteins. Recent evidence has shown that the EJC is involved in the splicing regulation of some specific events in both Drosophila and mammalian cells.

Results

Here, we show that knockdown of EJC core proteins causes widespread alternative splicing changes in mammalian cells. These splicing changes are specific to EJC core proteins, as knockdown of eIF4A3, Y14 and MLN51 shows similar splicing changes, and are different from knockdown of other splicing factors. The splicing changes can be rescued by a siRNA-resistant form of eIF4A3, indicating an involvement of EJC core proteins in regulating alternative splicing. Finally, we find that the splicing changes are linked with RNA polymerase II elongation rates.

Conclusion

Taken together, this study reveals that the coupling between EJC proteins and splicing is broader than previously suspected, and that a possible link exists between mRNP assembly and splice site recognition.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0551-7) contains supplementary material, which is available to authorized users.     

Similar tissue-specific expression of the Adh genes from different Drosophila species is mediated by distinct arrangements of cis-acting sequences

In Drosophila melanogaster transformants, the alcohol dehydrogenase (Adh) genes from D. affinidisjuncta and D. grimshawi show similar levels of expression except in the adult midgut where the D. affinidisjuncta gene is expressed about 10- to 20-fold more strongly. To study the arrangement of cis-acting sequences responsible for this regulatory difference, homologous restriction sites were used to create a series of chimeric genes that switched fragments from the 5 and 3 flanking regions of these two genes. Chimeric genes were introduced into the germ-line of D. melanogaster, and Adh gene expression was analyzed by measuring RNA levels. Various gene fragments in the promoter region and elsewhere influence expression in the adult midgut and in whole larvae and adults. Comparison of these results with earlier studies involving chimeras between the D. affinidisjuncta and D. hawaiiensis genes indicates that expression in the adult midgut is influenced by multiple regulatory sequences and that distinct arrangements of regulatory sequences can result in similar levels of expression both in the adult midgut and in the whole organism.     

Fine structure characterization of amylopectins from grain amaranth starch

The aim of this study was to determine the fine structure of amylopectin from grain amaranth. Amaranthus amylopectin was hydrolyzed with α-amylase, and single clusters and a group of clusters (domain) were isolated by methanol precipitation. The domain and the clusters were treated with phosphorylase a and then β-amylase to remove all external chains, whereby the internal structure was obtained. The ,β-limit dextrins were analyzed on Sepharose CL 6B. The average DP (degree of polymerization) and peak-DP values of fractions of clusters were 57 and 82, respectively; the values of the domain were 137 and 309, respectively. The unit chain length profiles were analyzed by high-performance anion-exchange chromatography with pulsed amperometric detector (HPAEC–PAD). The results showed that the domain fraction contained 2.2 clusters, and single clusters were composed of 13 chains. The ,β-limit dextrins of the clusters were further hydrolyzed with α-amylase to characterize their building block composition. The average DP of the branched blocks was 11 and they contained on average 2.5 chains. Their average chain length, internal chain length, and degree of branching were approximately 4.3, 2.8, and 14, respectively. A cluster consisted of 6 branched blocks, and the internal chain length between the blocks was 6.8.     

Decomposition of four macrophytes in wetland sediments: Organic matter and nutrient decay and associated benthic processes

Decomposition rates of Phragmites australis, Carex riparia, Nuphar luteum and Salvinia natans and benthic processes were measured from December 2003 to December 2004 in a shallow wetland (Paludi di Ostiglia, Northern Italy) by means of litter bags and intact cores incubations. Decay rate was highest for N. luteum (k = 0.0152 d⁻¹), intermediate for S. natans (k = 0.0041 d⁻¹) and similar for P. australis (k = 0.0027 d⁻¹) and C. riparia (k = 0.0028 d⁻¹).Benthic metabolism followed a seasonal pattern with summer peaks of O₂ demand and TCO₂, CH₄ and NH₄⁺ efflux whilst soluble reactive phosphorus (SRP) fluxes were negligible also under hypoxic conditions, indicating that P was mainly retained by sediment. The initial C:P ratio was similar in N. luteum and S. natans (170) and significantly lower than that of P. australis and C. riparia (360). During the detritus decay P was progressively lost by N. luteum and S. natans tissues, whereas, after an initial leaching, it was probably re-used during the microbial decomposition of the more refractory P. australis and C. riparia detritus. Nuphar luteum, P. australis and S. natans had comparable initial C:N mass ratio (15), significantly lower than that of C. riparia (26). The C:N ratio was rather constant for N. luteum (12.9 ± 1.5) and S. natans (14.6 ± 0.9), decreased slightly to below 20 for C. riparia and increased up to 30 for P. australis. Overall, differences among species were likely due to the recalcitrance of decomposing detritus, whilst process rates were controlled by limitation of microbial processes by nutrients and electron acceptor availability.