Trans splicing involves a novel form of small nuclear ribonucleoprotein particles

Bruzik, James P.; Doren, K Van; Hirsh, David; Steitz, Joan A.

doi:10.1038/335559a0

Cited by 196 publications

(185 citation statements)

References 33 publications

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“…Most of the SL RNAs described previously can be folded into a conserved secondary structure that contains three stem-loops and a single-stranded binding site for the Sm protein (8). Exceptions to this structure include the SL RNA from the flatworm Schistosoma mansoni, in which the second stem-loop is absent (29), and the Ciona SL RNA, which lacks the second and third stem-loops (1).…”

Section: Discussionmentioning

confidence: 99%

“…However, SL additions in unicellular eukaryotes and metazoans do share several features. Many SL RNAs have a highly conserved structure that includes three stem-loops, and all of the SL RNAs have a binding site for the Sm protein (8). In a number of uni-and multicellular species, copies of the SL RNA genes are found to be repeated within the 5S rDNA cluster (9).…”

mentioning

confidence: 99%

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Trans-spliced leader addition to mRNAs in a cnidarian

Stover

Steele

2001

Proc. Natl. Acad. Sci. U.S.A.

108

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Trans-spliced leader addition to mRNAs in a cnidarian

Stover

Steele

2001

Proc. Natl. Acad. Sci. U.S.A.

108

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“…Pre-mRNA splicing in nematodes includes both conventional cis-splicing as well as trans-splicing (for reviews, see Blumenthal & Steward, 1997;Nilsen, 1997)+ In the trans-splicing reaction, the 59 exon is donated from a separate transcript, the spliced leader RNA (SL RNA), which contains hallmarks of the small nuclear RNAs (snRNAs) involved in standard splicing reactions (Bruzik et al+, 1988;Thomas et al+, 1988;Nilsen et al+, 1989)+ Required cofactors for trans-splicing include the U2, U5, and U4/U6 small nuclear ribonucleoprotein particles (snRNPs; Hannon et al+, 1991;Maroney et al+, 1996) as well as serine/arginine-rich splicing factors (SR proteins; Sanford & Bruzik, 1999b)+ Although extensive similarities between the required cofactors for cis-and trans-splicing have been documented, there is a clear difference in the necessity for U1 snRNP at the 59 splice site (Hannon et al+, 1991)+ Thus, the transsplicing reaction naturally occurring in nematodes has been deemed independent of the need for the 59 end of U1 that normally base pairs with the 59 splice site+ A large body of work has elucidated many of the cis-acting elements involved in pre-mRNA splicing in higher eukaryotes (for review, see Reed & Palandjian, 1997)+ These include the 39 splice site AG dinucleotide whose necessity is coupled to the length of the preceding polypyrimidine tract (Reed, 1989)+ Because trans-splicing substrates lack the potential for spliceosomal interactions across an intron, they have been suggested to be exquisitely AG-dependent at the 39 splice site (Wu et al+, 1999)+ Additionally, the effects of 39 exonic sequences on splicing of an upstream intron were documented over a decade ago (Somasekhar & Mertz, 1985;Reed & Maniatis, 1986)+ More recently, discrete elements termed exonic splicing enhancers (ESEs) have been identified that promote upstream splicing in both alternatively spliced (for review, see Wang & Manley, 1997) as well as constitutive premRNAs (Schaal & Maniatis, 1999a)+ Many of these ESEs have been shown to interact with SR proteins+ The two major domains of SR proteins, an N-terminal RNA recognition motif(s) (RRM) and a C-terminal region rich in RS dipeptides, allow for RNA binding and protein-protein interactions, respectively (for review, see Graveley, 2000)+ In addition to the predominantly purinerich ESEs, several examples of other general classes of splicing enhancers have been identified+ These include the A/C-rich splicing enhancers (Coulter et al+, 1997), intronic splicing enhancers (for examples, see , and splicing enhancers that modulate 59 splice site usage (Humphrey et al+, 199...…”

Section: Introductionmentioning

confidence: 99%

Functional selection of splicing enhancers that stimulate trans-splicing in vitro

Boukis

Bruzik

2001

RNA

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The role of exonic sequences in naturally occurring trans-splicing has not been explored in detail. Here, we have identified trans-splicing enhancers through the use of an iterative selection scheme. Several classes of enhancer sequences were identified that led to dramatic increases in trans-splicing efficiency. Two sequence families were investigated in detail. These include motifs containing the element G / C GAC G / C and also 59 splice site-like sequences. Distinct elements were tested for their ability to function as splicing enhancers and in competition experiments. In addition, discrete trans-acting factors were identified. This work demonstrates that splicing enhancers are able to effect a large increase in trans-splicing efficiency and that the process of exon definition is able to positively enhance trans-splicing even though the reaction itself is independent of the need for the 59 end of U1 snRNA. Due to the presence of internal introns in messages that are trans-spliced, the natural arrangement of 59 splice sites downstream of trans-splicing acceptors may lead to a general promotion of this unusual reaction.

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“…The SL1 sequence in a stem-loop structure may render transcription of SL1 sequence and thus explain rationally the transsplicing event of this particular sequence. The spacer region also contains a consensus nucleotide sequence, 5'-AAUUUUGG-3', identical to the binding site for Sm, an antigen associated with small nuclear ribonucleoprotein particles in C. elegans [4,15].…”

Section: O N O F L I T O M O S O I D E S C a R I N I I A N D Achantmentioning

confidence: 99%

Characteristics of Nucleotide Sequences Flanking the trans-Spliced Leader SL1 Exon in Dirofilaria immitis, Brugia malayi, and Brugia pahangi.

Harasawa

Maeda

Nogami

et al. 1997

The Journal of Veterinary Medical Science

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ABSTRACT. Nucleotide sequences surrounding the trans-spliced leader SL1 exon in the 5S rRNA gene spacer regions of Dirofilaria immitis, Brugia malayi, and B. pahangi were determined after PCR amplification, aligned with the genus Onchocerca for comparison, and used for the prediction of secondary structures. The nucleotide sequence of this region in B. pahangi was first shown in the present study. Hypothetical secondary structures of the spacer region suggested that the SL1 transcript is capable to form a stable stem-loop structure which may render transposition of the SL1 sequence to mRNA molecules. A homologous sequence to Sm-binding site was assigned on a bulge loop. No significant difference was observed in adult worms of D. immitis irrespective of sex or location. No difference was apparent between the two species in genus Brugia. -KEY WORDS: Brugia, Dirofilaria, trans-splicing. J. Vet. Med. Sci. 59(12): 1149-1152, 1997 Of the four adult worms of D. immitis, two (male and female, each) were from Japan, which are referred to as "Japanese adult worms", and two (male and female, each) were from the U.S.A. which are referred to as "American adult worms", hereafter. Japanese adult worms in the heart were collected from naturally infected dogs at necropsy [11]. American adult worms were collected from naturally infected dogs. To determine the prevalence of D. immitis infection in dogs, these dogs were killed by euthanasic procedure and immediately provided from a dog pound of Wake County, Raleigh, North Carolina, U.S.A. Two Brugia species, B. malayi and B. pahangi, have been maintained in the second author's laboratory. Exact source of the B. malayi strain has been described elsewhere [9]. All adult worms were identified by morphological features. DNA of D. immitis was isolated from a single adult worm, and DNA of Brugia was extracted from frozen specimens of adult worms by the hydroxyapatite batch elution technique [3]. Parasite DNAs were subjected to PCR to amplify the 5S rRNA gene and its 3' flanking spacer region by using a pair of primers based on genomic sequences of high homology between Dirofilaria and Onchocerca [17]. The PCR primers F1 (5'-GTC TAC GAC CAT ACC ACG TT-3') and R1 (5'-CAG GAC GTT CCA AAA TTT-3') were custom-made by Takara Shuzo Co., Ltd. (Kyoto). The PCR amplification was carried out with 50-µl reaction mixtures containing 5 µl of DNA solution, 5 µl of 10X buffer, 1.25 U of Taq DNA polymerase (Perkin-Elmer Corp., Norwalk, Conn.), dNTPs to a final concentration of 0.2 mM each, 0.25 µl of each pair of primers F1 and R1 (40 pmol/µl each), and water to a final volume of 50 µl. The cycle was repeated 30 times with denaturation at 94°C for 30 sec, annealing at 56°C for 120 sec, and extension at 72°C for 120 sec. The PCR products were extracted from gels after electrophoresis, and subjected to direct sequencing three times on each strand A spliced leader sequence at the 5' end of a mRNA was first demonstrated in African trypanosomes [2]. This trypanosome leader sequence is derived from an RNA tra...

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Trans splicing involves a novel form of small nuclear ribonucleoprotein particles

Cited by 196 publications

References 33 publications

Trans-spliced leader addition to mRNAs in a cnidarian

Trans-spliced leader addition to mRNAs in a cnidarian

Functional selection of splicing enhancers that stimulate trans-splicing in vitro

Characteristics of Nucleotide Sequences Flanking the trans-Spliced Leader SL1 Exon in Dirofilaria immitis, Brugia malayi, and Brugia pahangi.

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