Intron Splicing and Intron-mediated Enhanced Expression in Monocots

Sinibaldi, Ralph M.; Mettler, Irvin J.

doi:10.1016/s0079-6603(08)60577-2

Cited by 60 publications

(60 citation statements)

References 51 publications

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“…Table I of Brendel et al, (1998), or Table IV of Sinibaldi & Mettler, (1992)), indicating that the choice of 50 base windows for calculating the compositional contrast does not introduce special biases as a result of the particular window size. The predicted splice site strength P displays a wide range, exceptionally weak sites scoring close to zero.…”

Section: Distribution Of Splice Site Scoresmentioning

confidence: 97%

Prediction of splice sites in plant pre-mRNA from sequence properties

Brendel

Kleffe

Carle-Urioste

et al. 1998

Journal of Molecular Biology

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Heterologous introns are often inaccurately or inef®ciently processed in higher plants. The precise features that distinguish the process of premRNA splicing in plants from splicing in yeast and mammals are unclear. One contributing factor is the prominent base compositional contrast between U-rich plant introns and¯anking G C-rich exons. Inclusion of this contrast factor in recently developed statistical methods for splice site prediction from sequence inspection signi®cantly improved prediction accuracy. We applied the prediction tools to re-analyze experimental data on splice site selection and splicing ef®ciency for native and more than 170 mutated plant introns. In almost all cases, the experimentally determined preferred sites correspond to the highest scoring sites predicted by the model. In native genes, about 90% of splice sites are the locally highest scoring sites within the bounds of the¯anking exon and intron. We propose that, in most cases, local context (about 50 bases upstream and downstream from a potential intron end) is suf®cient to account for intrinsic splice site strength, and that competition for transacting factors determines splice site selection in vivo. We suggest that computer-aided splice site prediction can be a powerful tool for experimental design and interpretation.

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Section: Distribution Of Splice Site Scoresmentioning

confidence: 97%

Prediction of splice sites in plant pre-mRNA from sequence properties

Brendel

Kleffe

Carle-Urioste

et al. 1998

Journal of Molecular Biology

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confidence: 94%

“…Not all plant introns enhance gene expression. Three dicot introns do not enhance gene expression in transgenic plants (Chee et al, 1986;Kuhlemeier et al, 1988;Vancanneyt et al, 1990) and two maize introns are nonenhancing in transient assays: Adh1 intron 9 (Mascarenhas et al, 1990) and Hsp81 intron 1 (Sinibaldi et al, 1992).Intron-mediated enhancement of gene expression has been studied in plants for about 15 years, and although the underlying mechanisms have not been identified, several features are known. Positioning of the intron in the natural orientation within the 5Ј portion of the transcription unit is typically required for enhancement (Callis et al, 1987;Mascarenhas et al, 1990;Maas et al, 1991;Clancy et al, 1994;Snowden et al, 1996;Bourdon et al, 2001;Chaubet-Gigot et al, 2001), establishing that introns do not function as traditional transcriptional enhancers.…”

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confidence: 99%

“…Positioning of the intron in the natural orientation within the 5Ј portion of the transcription unit is typically required for enhancement (Callis et al, 1987;Mascarenhas et al, 1990;Maas et al, 1991;Clancy et al, 1994;Snowden et al, 1996;Bourdon et al, 2001;Chaubet-Gigot et al, 2001), establishing that introns do not function as traditional transcriptional enhancers. Length (Sinibaldi and Mettler, 1992) and composition of flanking sequences influence the degree of stimulation (Luehrsen and Walbot, 1991;Maas et al, 1991;Clancy et al, 1994). The degree of enhancement is usually greater for relatively weak promoters (Callis et al, 1987;Vasil et el., 1987;Mascarenhas et al, 1990;.…”

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confidence: 99%

“…The degree of enhancement is usually greater for relatively weak promoters (Callis et al, 1987;Vasil et el., 1987;Mascarenhas et al, 1990;. The magnitude of stimulation also depends on the coding sequences (Sinibaldi and Mettler, 1992;Rethmeier et al, 1997Rethmeier et al, , 1998, the tissue of expression, and physiological conditions (Tanaka et al, 1990;Sinibaldi and Mettler, 1992;Gallie and Young, 1994;Park, 1995a, 1995b;ChaubetGigot et al, 2001;Plesse et al, 2001).…”

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Splicing of the Maize Sh1 First Intron Is Essential for Enhancement of Gene Expression, and a T-Rich Motif Increases Expression without Affecting Splicing

2002

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Certain plant and animal introns increase expression of protein-coding sequences when placed in the 5Ј region of the transcription unit. The mechanisms of intron-mediated enhancement have not been defined, but are generally accepted to be post-or cotranscriptional in character. One of the most effective plant introns in stimulating gene expression is the 1,028-bp first intron of the Sh1 gene that encodes maize (Zea mays) sucrose synthase. To address the mechanisms of intron-mediated enhancement, we used reporter gene fusions to identify features of the Sh1 first intron required for enhancement in cultured maize cells. A 145-bp derivative conferred approximately the same 20-to 50-fold stimulation typical for the full-length intron in this transient expression system. A 35-bp motif contained within the intron is required for maximum levels of enhancement but not for efficient transcript splicing. The important feature of this redundant 35-bp motif is T-richness rather than the specific sequence. When transcript splicing was abolished by mutations at the intron borders, enhancement was reduced to about 2-fold. The requirement of splicing for enhancement was not because of upstream translation initiation codons contained in unspliced transcripts. On the basis of our current findings, we conclude that splicing of the Sh1 intron is integral to enhancement, and we hypothesize that transcript modifications triggered by the T-rich motif and splicing may link the mRNA with the trafficking system of the cell.Most plant genes contain intervening sequences (introns) that are transcribed into pre-mRNA and later removed by splicing. Introns separate gene segments (exons) that hold protein-coding information or are non-coding but retained in the mature transcript. The observation that some introns stimulate gene expression was first made in animal systems and extended to plants when Callis et al. (1987) demonstrated that the maize (Zea mays) Adh1 first intron increased expression of several genes. Other maize introns that have been shown to increase expression include the Bz1 intron (Callis et al., 1987), Hsp82 first intron (Silva et al., 1988), Sh1 first intron (Vasil et al., 1989), Adh1 introns 2 and 6 (Mascarenhas et al., 1990), actin third intron (Luehrsen and Walbot, 1991), GapA1 first intron (Donath et al., 1995), Ubi1 first intron (Vain et al., 1996), and the RpoT fourth intron (Bourdon et al., 2001).Plant introns that stimulate expression have been documented in petunia (Petunia hybrida; Dean et al., 1989;Vain et al., 1996) Leon et al., 1991;Fu et al., 1995aFu et al., , 1995b, Arabidopsis (Rose and Last, 1997; ChaubetGigot et al., 2001), soybean (Glycine max; Kato et al., 1998), and tobacco (Nicotiana tabacum; Plesse et al., 2001). The approximately 2-to 10-fold range of intron-mediated enhancement usually seen in dicots is much less than increases observed in monocots, which can be more than 100-fold (for review, see Simpson and Filipowicz, 1996). Not all plant introns enhance gene expression. Three dicot introns do no...

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Characterization of two Maize HSP90 heat shock protein genes: Expression during heat shock, embryogenesis, and pollen development

Marrs¹,

Casey²,

Capitant³

et al. 1993

Dev. Genet.

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We have isolated two genes from Zea mays encoding proteins of 82 and 81 kD that are highly homologous to the Drosophila 83-kD heat shock protein gene and have analyzed the structure and pattern of expression of these two genes during heat shock and development. Southern blot analysis and hybrid select translations indicate that the highly homologous hsp82 and hsp81 genes are members of a small multigene family composed of at least two and perhaps three or more gene family members. The deduced amino acid sequence of these proteins based on the nucleotide sequence of the coding regions shows 64-88% amino acid homology to other hsp90 family genes from human, yeast, Drosophila, and Arabidopsis. The promoter regions of both the hsp82 and hsp81 genes contain several heat shock elements (HSEs), which are putative binding sites for heat shock transcription factor (HSF) commonly found in the promoters of other heat shock genes. Gene-specific oligonucleotide probes were synthesized and used to examine the mRNA expression patterns of the hsp81 and hsp82 genes during heat shock, embryogenesis, and pollen development. The hsp81 gene is only mildly heat inducible in leaf tissue, but is strongly expressed in the absence of heat shock during the pre-meiotic and meiotic prophase stages of pollen development and in embryos, as well as in heat-shocked embryos and tassels. The hsp82 gene shows strong heat inducibility at heat-shock temperatures (37-42 degrees C) and in heat shocked embryos and tassels but is only weakly expressed in the absence of heat shock. Promoter-GUS reporter gene fusions made and analyzed by transient expression assays in Black Mexican Sweet (BMS) Maize protoplasts also indicate that the hsp82 and hsp81 are regulated differentially. The hsp82 promoter confers strong heat-inducible expression of the GUS reporter gene in heat-treated cells (60- to 80-fold over control levels), whereas the hsp81 promoter is only weakly heat inducible (5- to 10-fold over control levels).

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Intron Splicing and Intron-mediated Enhanced Expression in Monocots

Cited by 60 publications

References 51 publications

Prediction of splice sites in plant pre-mRNA from sequence properties

Prediction of splice sites in plant pre-mRNA from sequence properties

Splicing of the Maize Sh1 First Intron Is Essential for Enhancement of Gene Expression, and a T-Rich Motif Increases Expression without Affecting Splicing

Characterization of two Maize HSP90 heat shock protein genes: Expression during heat shock, embryogenesis, and pollen development

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