Splicing of retrotransposon insertions from transcripts of the Drosophila melanogaster vermilion gene in a revertant

Transcriptional interference mediated by retrotransposons within the genome of their host: lessons from alleles of the white gene from Drosophila melanogaster

Systematic sequencing of model genomes has accelerated our knowledge on genome structure and shown that a large proportion of intergenic regions are made up of mobile element families. Among them, retrotransposons that are mobilized via an RNA intermediate and thus do not excise during their replication cycle are certainly essential factors able to imprint novel and heritable transcriptional regulation within the genome of their host. Today, a crucial complement to the systematic sequencing data is thus to elucidate the potential role of these elements in the regulation of nearby genes, and ultimately in the evolution of eukaryotic genomes.

Transposable element insertions respecify alternative exon splicing in three Drosophila myosin heavy chain mutants

Insertions of transposable elements into the myosin heavy chain (Mhc) locus disrupt the regulation of alternative pre-mRNA splicing for multi-alternative exons in the Mhc2, Mhc3, and Mhc4 mutants in Drosophila. Sequence and expression analyses show that each inserted element introduces a strong polyadenylation signal that defines novel terminal exons, which are then differentially recognized by the alternative splicing apparatus. Mhc2 and Mhc4 have insertion elements located within intron 7c and exon 9a, respectively, and each expresses a single truncated transcript that contains an aberrant terminal exon defined by the poly(A) signal of the inserted element and the 3' acceptor of the upstream common exon. In Mhc3, a poly(A) signal inserted into Mhc intron 7d defines terminal exons using either the upstream 3' acceptor of common exon 6 or the 7d acceptor, leading to the expression of 4.1- and 1.7-kb transcripts, respectively. Acceptor selection is regulated in Mhc3 transcripts, where the 3' acceptor of common Mhc exon 6 is preferentially selected in larvae, whereas the alternative exon 7d acceptor is favored in adults. These results reflect the adult-specific use of exon 7d and suggest that the normal exon 7 alternative splicing mechanism continues to influence the selection of exon 7d in Mhc3 transcripts. Overall, transposable element-induced disruptions in alternative processing demonstrate a role for the nonconsensus 3' acceptors in Mhc exons 7 and 9 alternative splicing regulation.

Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA

The eukaryotic small nucleolar RNAs (snoRNAs) are involved in processing of pre-rRNA and modification of rRNA nucleotides. Some snoRNAs are derived from mono- or polycistronic transcription units, whereas others are encoded in introns of protein genes. The present study addresses the role of the RNA lariat-debranching enzyme (Dbr1p) in the synthesis and function of intronic snoRNAs in the yeast Saccharomyces cerevisiae. Intronic snoRNA production was determined to depend on Dbr1p. Accumulation of mature intronic snoRNAs is reduced in a dbr1 mutant; instead, intronic snoRNAs are "trapped" within host intron lariats. Interestingly, the extent of intronic snoRNA accumulation in the form of lariats in dbr1 cells varied among different intronic snoRNAs. Intronic snoRNAs encoded within shorter introns, such as U24 and snR38, accumulate more unprocessed lariat precursors than those encoded within longer introns, e.g., U18 and snR39. This correlation was corroborated by experiments conducted with model intron:U24 snoRNA constructs. These results support a splicing-dependent exonucleolytic pathway for the biosynthesis of intronic snoRNAs. Curiously, U24 in a lariat may be functional in directing methylation of ribosomal RNA.

The Drosophila suppressor of sable protein binds to RNA and associates with a subset of polytene chromosome bands

Mutations of the Drosophila melanogaster suppressor of sable [su(s)] gene, which encodes a 150-kDa nuclear protein [Su(s)], increase the accumulation of specific transcripts in a manner that is not well understood but that appears to involve pre-mRNA processing. Here, we report biochemical analysis of purified, recombinant Su(s) [rSu(s)] expressed in baculovirus and in Escherichia coli as maltose binding protein (MBP) fusions and immunocytochemical analysis of endogenous Su(s). This work has shown that purified, baculovirus-expressed rSu(s) binds to RNA in vitro with a high affinity and limited specificity. Systematic evolution of ligands by exponential enrichment was used to identify preferred RNA targets of rSu(s), and a large proportion of RNAs isolated contain a full or partial match to the consensus sequence UCAGUAGUCU, which was confirmed to be a high-affinity rSu(s) binding site. An MBP-Su(s) fusion protein containing the N-terminal third of Su(s) binds RNAs containing this sequence with a higher specificity than full-length, baculovirus-expressed rSu(s). The consensus sequence resembles both a cryptic 5' splice site and a sequence that is found near the 5' end of some Drosophila transcripts. Immunolocalization studies showed that endogenous Su(s) is distributed in a reticulated pattern in Drosophila embryo and salivary gland nuclei. In salivary gland cells, Su(s) is found both in the nucleoplasm and in association with a subset of polytene chromosome bands. Considering these and previous results, we propose two models to explain how su(s) mutations affect nuclear pre-mRNA processing.

Splicing removes the Caenorhabditis elegans transposon Tc1 from most mutant pre-mRNAs

The transposable element Tc1 is responsible for most spontaneous mutations that occur in many Caenorhabditis elegans strains. We analyzed the abundance and sequence of mRNAs expressed from five different Tc1 insertions within either hlh-1 (a MyoD homolog) or unc-54 (a myosin heavy chain gene). Each of the mutants expresses substantial quantities of mature mRNA in which most or all of Tc1 has been removed by splicing. Such mRNAs contain small insertions of Tc1 sequences and/or deletions of target gene sequences at the resulting spliced junctions. Most of these mutant mRNAs do not contain premature stop codons, and many are translated in frame to produce proteins that are functional in vivo. The number and variety of splice sites used to remove Tc1 from these mutant pre-mRNAs are remarkable. Two-thirds of the Tc1-containing introns removed from hlh-1 and unc-54 lack either the 5'-GU or AG-3' dinucleotides typically found at the termini of eukaryotic introns. We conclude that splicing to remove Tc1 from mutant pre-mRNAs allows many Tc1 insertions to be phenotypically silent. Such mRNA processing may help Tc1 escape negative selection.

Imprecise excision of the Caenorhabditis elegans transposon Tc1 creates functional 5' splice sites

Imprecise excision of the Caenorhabditis elegans transposon Tc1 from a specific site of insertion within the unc-54 myosin heavy chain gene generates either wild-type or partial phenotypic revertants. Wild-type revertants and one class of partial revertants contain insertions of four nucleotides in the unc-54 third exon (Tc1 "footprints"). Such revertants express large amounts of functional unc-54 myosin despite having what would appear to be frameshifting insertions in the unc-54 third exon. We demonstrate that these Tc1 footprints act as efficient 5' splice sites for removal of the unc-54 third intron. Splicing of these new 5' splice sites to the normal third intron splice acceptor removes the Tc1 footprint from the mature mRNA and restores the normal translational reading frame. Partial revertant unc-54(r661), which contains a single nucleotide substitution relative to the wild-type gene, is spliced similarly, except that the use of its new 5' splice site creates a frameshift in the mature mRNA rather than removing one. In all of these revertants, two alternative 5' splice sites are available to remove intron 3. We determined the relative efficiency with which each alternative 5' splice site is used by stabilizing frameshifted mRNAs with smg(-) genetic backgrounds. In all cases, the upstream member of the two alternative sites is used preferentially (> 75% utilization). This may reflect an inherent preference of the splicing machinery for the upstream member of two closely spaced 5' splice sites. Creation of new 5' splice sites may be a general characteristic of Tc1 insertion and excision events.

Imprecise excision of the Caenorhabditis elegans transposon Tc1 creates functional 5' splice sites

Imprecise excision of the Caenorhabditis elegans transposon Tc1 from a specific site of insertion within the unc-54 myosin heavy chain gene generates either wild-type or partial phenotypic revertants. Wild-type revertants and one class of partial revertants contain insertions of four nucleotides in the unc-54 third exon (Tc1 "footprints"). Such revertants express large amounts of functional unc-54 myosin despite having what would appear to be frameshifting insertions in the unc-54 third exon. We demonstrate that these Tc1 footprints act as efficient 5' splice sites for removal of the unc-54 third intron. Splicing of these new 5' splice sites to the normal third intron splice acceptor removes the Tc1 footprint from the mature mRNA and restores the normal translational reading frame. Partial revertant unc-54(r661), which contains a single nucleotide substitution relative to the wild-type gene, is spliced similarly, except that the use of its new 5' splice site creates a frameshift in the mature mRNA rather than removing one. In all of these revertants, two alternative 5' splice sites are available to remove intron 3. We determined the relative efficiency with which each alternative 5' splice site is used by stabilizing frameshifted mRNAs with smg(-) genetic backgrounds. In all cases, the upstream member of the two alternative sites is used preferentially (> 75% utilization). This may reflect an inherent preference of the splicing machinery for the upstream member of two closely spaced 5' splice sites. Creation of new 5' splice sites may be a general characteristic of Tc1 insertion and excision events.

Evidence for a role of the Drosophila melanogaster suppressor of sable gene in the pre-mRNA splicing pathway

Recessive mutations of the Drosophila melanogaster suppressor of sable [su(s)] gene result in elevated accumulation of RNA from vermilion (v) mutant alleles that have an insertion of the 7.5-kb retrotransposon 412 in the first exon of the v gene. During transcription of such a v mutant gene, the 412 sequences are incorporated into the primary transcripts and are subsequently removed by splicing at cryptic sites within 412 sequences. In a su(s)+ background, the level of these unusually spliced transcripts is exceedingly low, and su(s) mutations increase their accumulation. We previously proposed that v RNA levels are elevated in su(s) mutants because of increased recognition of the cryptic splice sites, and the aim of this study was to test this hypothesis. We generated a v mutant derivative with a smaller 412 insertion, introduced alterations into the 412-associated splice sites, and examined the effect of su(s) mutations on expression of these derivatives after germ line transformation. To increase overall expression levels, the v promoter was replaced with the stronger Metallothionein (Mtn) gene promoter. We found that transformants bearing a v derivative with 480 bp of 412 sequences accumulate both transcripts, with 412 sequences spliced out and transcripts that retain 412 sequences. Mutations of su(s) increase the levels of both transcript classes without affecting the relative amounts of the two forms. Strikingly, replacement of the cryptic 5' splice sites with a 5' consensus produces the same effect as, and eliminates the response to, a su(s) mutation. In addition, we demonstrated that mutations of su(s) lead to increased accumulation of v transcripts even when the previously identified cryptic 412 5' and 3' splice sites were destroyed and that other cryptic splice sites reside within Mtn and 412 sequences. These results indicate that the v mutant transcripts are stabilized by assembly of the 412 sequences into splicing complexes and support the hypothesis that splicing complexes more readily assemble on cryptic splice sites in su(s) mutants.

Evidence for a role of the Drosophila melanogaster suppressor of sable gene in the pre-mRNA splicing pathway

Recessive mutations of the Drosophila melanogaster suppressor of sable [su(s)] gene result in elevated accumulation of RNA from vermilion (v) mutant alleles that have an insertion of the 7.5-kb retrotransposon 412 in the first exon of the v gene. During transcription of such a v mutant gene, the 412 sequences are incorporated into the primary transcripts and are subsequently removed by splicing at cryptic sites within 412 sequences. In a su(s)+ background, the level of these unusually spliced transcripts is exceedingly low, and su(s) mutations increase their accumulation. We previously proposed that v RNA levels are elevated in su(s) mutants because of increased recognition of the cryptic splice sites, and the aim of this study was to test this hypothesis. We generated a v mutant derivative with a smaller 412 insertion, introduced alterations into the 412-associated splice sites, and examined the effect of su(s) mutations on expression of these derivatives after germ line transformation. To increase overall expression levels, the v promoter was replaced with the stronger Metallothionein (Mtn) gene promoter. We found that transformants bearing a v derivative with 480 bp of 412 sequences accumulate both transcripts, with 412 sequences spliced out and transcripts that retain 412 sequences. Mutations of su(s) increase the levels of both transcript classes without affecting the relative amounts of the two forms. Strikingly, replacement of the cryptic 5' splice sites with a 5' consensus produces the same effect as, and eliminates the response to, a su(s) mutation. In addition, we demonstrated that mutations of su(s) lead to increased accumulation of v transcripts even when the previously identified cryptic 412 5' and 3' splice sites were destroyed and that other cryptic splice sites reside within Mtn and 412 sequences. These results indicate that the v mutant transcripts are stabilized by assembly of the 412 sequences into splicing complexes and support the hypothesis that splicing complexes more readily assemble on cryptic splice sites in su(s) mutants.

Additional sequence complexity in the muscle gene, unc-22, and its encoded protein, twitchin, of Caenorhabditis elegans

Null mutations of the Caenorhabditis elegans unc-22 gene cause a pronounced body surface twitch associated with impaired movement and disruption of muscle structure. Partial sequence analysis of unc-22 has previously revealed that its encoded polypeptide, named twitchin, consists of a single protein kinase domain and multiple copies of both an immunoglobulin-like domain and a fibronectin type III-like domain. This paper reports additional DNA sequence information that has revealed the transcription start of unc-22, the N terminus of twitchin, and an explanation for the weak phenotype of a transposon insertion allele. These new data indicate that the unc-22 gene is 18 kb larger than previously reported and has a transcription unit of 38,308 bp. These data add 791 amino acids to the twitchin N terminus for a complete polypeptide size of 6,839 amino acids and a predicted molecular weight of 753,494. This new polypeptide sequence includes four additional copies of the above-mentioned immunoglobulin-like domains and also includes a glycine-rich sequence that might form a flexible hinge. The additional coding sequence reveals that the insertion of the Tc1 transposon, in the unc-22 allele, st139, should disrupt twitchin structure because it is located in an exon. However, cDNA sequencing has revealed that several cryptic splice donors and acceptors adjacent to the Tc1 insertion site are used to splice the transposon out of unc-22(st139) mRNA. One of these splicing events produces a near wild-type mRNA that deletes only six amino acids from twitchin, and this might explain the unusually mild phenotype associated with this mutation.

Site-selected insertion of the transposon Tc1 into a Caenorhabditis elegans myosin light chain gene

We used the polymerase chain reaction to detect insertions of the transposon Tc1 into mlc-2, one of two Caenorhabditis elegans regulatory myosin light chain genes. Our goals were to develop a general method to identify mutations in any sequenced gene and to establish the phenotype of mlc-2 loss-of-function mutants. The sensitivity of the polymerase chain reaction allowed us to identify nematode populations containing rare Tc1 insertions into mcl-2. mlc-2::Tc1 mutants were subsequently isolated from these populations by a sib selection procedure. We isolated three mutants with Tc1 insertions within the mlc-2 third exon and a fourth strain with Tc1 inserted in nearby noncoding DNA. To demonstrate the generality of our procedure, we isolated two additional mutants with Tc1 insertions within hlh-1, the C. elegans MyoD homolog. All of these mutants are essentially wild type when homozygous. Despite the fact that certain of these mutants have Tc1 inserted within exons of the target gene, these mutations may not be true null alleles. All three of the mlc-2 mutants contain mlc-2 mRNA in which all or part of Tc1 is spliced from the pre-mRNA, leaving small in-frame insertions or deletions in the mature message. There is a remarkable plasticity in the sites used to splice Tc1 from these mlc-2 pre-mRNAs; certain splice sites used in the mutants are very different from typical eukaryotic splice sites.

The splicing of transposable elements and its role in intron evolution

Recent studies have demonstrated that transposable elements in maize and Drosophila are spliced from pre-mRNA. These transposable element introns represent the first examples of recent addition of introns into nuclear genes. The eight reported examples of transposable element splicing include members of the maize Ac/Ds and Spm/dSpm and the Drosophila P and 412 element families. The details of the splicing of these transposable elements and their relevance to models of intron origin are discussed.