Characterization of exon skipping mutants of the <i>COP1</i> gene from <i>Arabidopsis</i>

Simpson, Craig G.; McQuade, Clare; Lyon, Jackie; Brown, John W.

doi:10.1046/j.1365-313x.1998.00184.x

Cited by 29 publications

(35 citation statements)

References 38 publications

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“…We postulate that the change in the strategic location of this exon in the context of the Sh2 sequence interferes with its recognition, leading to exon skipping. Exon skipping was demonstrated recently in two mutants of maize and several mutants of Arabidopsis (Brown, 1996;Brown and Simpson, 1998;Simpson et al, 1998;Lal et al, 1999aLal et al, , 1999b.…”

Section: The Sh2-7527 Insertion Contains Putative Pseudogenesmentioning

confidence: 92%

The Maize Genome Contains a Helitron Insertion

et al. 2003

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The maize mutation sh2-7527 was isolated in a conventional maize breeding program in the 1970s. Although the mutant contains foreign sequences within the gene, the mutation is not attributable to an interchromosomal exchange or to a chromosomal inversion. Hence, the mutation was caused by an insertion. Sequences at the two Sh2 borders have not been scrambled or mutated, suggesting that the insertion is not caused by a catastrophic reshuffling of the maize genome. The insertion is large, at least 12 kb, and is highly repetitive in maize. As judged by hybridization, sorghum contains only one or a few copies of the element, whereas no hybridization was seen to the Arabidopsis genome. The insertion acts from a distance to alter the splicing of the sh2 pre-mRNA. Three distinct intron-bearing maize genes were found in the insertion. Of most significance, the insertion bears striking similarity to the recently described DNA helicase-bearing transposable elements termed Helitrons . Like Helitrons , the inserted sequence of sh2-7527 is large, lacks terminal repeats, does not duplicate host sequences, and was inserted between a host dinucleotide AT. Like Helitrons , the maize element contains 5 TC and 3 CTRR termini as well as two short palindromic sequences near the 3 terminus that potentially can form a 20-bp hairpin. Although the maize element lacks sequence information for a DNA helicase, it does contain four exons with similarity to a plant DEAD box RNA helicase. A second Helitron insertion was found in the maize genomic database. These data strongly suggest an active Helitron in the present-day maize genome.

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Section: The Sh2-7527 Insertion Contains Putative Pseudogenesmentioning

confidence: 92%

The Maize Genome Contains a Helitron Insertion

et al. 2003

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“…Thus, whereas UBP1 can enhance splicing efficiency of poorly spliced U2 introns, confirming the findings of Lambermon et al (2000), neither UBP1 nor RBP45 influenced U12 intron splicing directly. Previously, exon bridging interactions between adjacent U2 introns were shown to enhance splicing of plant pre-mRNAs (McCullough et al, 1996;Simpson et al, 1998Simpson et al, , 1999, and flanking U2 introns increased splicing efficiency of the CBP20 U12 intron (Kmieciak et al, 2002). Overexpression of UBP1 or RBP45 did not enhance U12 intron excision in single intron constructs, but may function in intron recognition and recruitment of splicing factors to splice sites via exon bridging interactions.…”

Section: Differential Effects Of U-rich Binding Proteins On U12 and Umentioning

confidence: 92%

Determinants of Plant U12-Dependent Intron Splicing Efficiency

Lewandowska

Simpson²,

Clark³

et al. 2004

Plant Cell

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Factors affecting splicing of plant U12-dependent introns have been examined by extensive mutational analyses in an in vivo tobacco (Nicotiana tabacum) protoplast system using introns from three different Arabidopsis thaliana genes: CBP20, GSH2, and LD. The results provide evidence that splicing efficiency of plant U12 introns depends on a combination of factors, including UA content, exon bridging interactions between the U12 intron and flanking U2-dependent introns, and exon splicing enhancer sequences (ESEs). Unexpectedly, all three plant U12 introns required an adenosine at the upstream purine position in the branchpoint consensus UCCUURAUY. The exon upstream of the LD U12 intron is a major determinant of its higher level of splicing efficiency and potentially contains two ESE regions. These results suggest that in plants, U12 introns represent a level at which expression of their host genes can be regulated. INTRODUCTIONPre-mRNA splicing in eukaryotes is a fundamental step in gene expression and represents an important level at which the expression of protein-coding genes can be regulated (Reed, 2000;Smith and Valcá rcel, 2000;Graveley, 2001;Hastings and Krainer, 2001;Cartegni et al., 2002;Black, 2003). In higher eukaryotes, there are two classes of nuclear pre-mRNA introns. The most abundant class consists of U2-dependent introns (U2 introns), whereas the second rarer class (<0.4% of introns) consists of U12-dependent introns (U12 introns). U12 introns have been found in the nuclear genomes of vertebrates, plants, and insects (Hall and Padgett, 1994;Sharp and Burge, 1997;Tarn and Steitz, 1997; Krainer, 1998, 1999;Burge et al., 1998;Levine and Durbin, 2001;Patel and Steitz, 2003). Introns belonging to these two distinct classes are spliced by two different spliceosomes: the major U2-type spliceosome and the less abundant U12-type spliceosome (Hall and Padgett, 1996;Tarn and Steitz 1996a. Although the first U12 introns to be described had AT-AC-terminal dinucleotides, the majority of U12-type introns contain GT-AG, and a small number contain other noncanonical terminal dinucleotides, such as AT-AA, AT-AG, AT-AT, GT-AT, or GT-GG (Jackson, 1991;Hall and Padgett, 1994;Dietrich et al., 1997Dietrich et al., , 2001aSharp and Burge, 1997;Burge et al., 1998;Wu and Krainer, 1999;Levine and Durbin, 2001;Zhu and Brendel, 2003). Moreover, functional analyses have shown that AT-AC-terminal dinucleotides are not a defining feature of U12 introns (Dietrich et al., 1997(Dietrich et al., , 2001a. Instead, U12 introns contain highly conserved sequences in the 59 splice site (exon:G/ATATCCTY) and branchpoint region (TCCTTRAY) (Hall and Padgett, 1994;Sharp and Burge, 1997;Burge et al., 1998), which are both required for prespliceosome complex formation (Frilander and Steitz, 1999). The 39 splice site consensus sequence of U12 introns (YAC/G:exon) is less informative than their 59 splice site and branchpoint sequences. U12 introns also lack a polypyrimidine tract and have a short distance between the branchpoint and 39 splice si...

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“…The Arabidopsis det3-1 mutation is attributable to a T to A mutation 32 bp upstream of a putative 3Ј splice site, which causes a reduction of the transcript to approximately 50% of the wild-type level (Schumacher et al, 1999). The Arabidopsis cop1-1 allele carries a single-nucleotide change (from G to A) 4 bases upstream from the 3Ј splice site of intron 5, which results in exon skipping (Simpson et al, 1998). At2g24440 is expressed in all six cDNA populations and was amplified from cold-treated cDNA.…”

Section: Analysis Of the Full-length Cdna Sequencesmentioning

confidence: 99%

Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,

Xiao¹,

Malik²,

Whitelaw³

et al. 2002

Plant Physiology

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About 25% of the genes in the fully sequenced and annotated Arabidopsis genome have structures that are predicted solely by computer algorithms with no support from either nucleic acid or protein homologs from other species or expressed sequence matches from Arabidopsis. These are referred to as "hypothetical genes." On chromosome 2, sequenced by The Institute for Genomic Research, there are approximately 800 hypothetical genes among a total of approximately 4,100 genes. To test their expression under various growth conditions and in specific tissues, we used six cDNA populations prepared from cold-treated, heat-treated, and pathogen (Xanthomonas campestris pv campestris)-infected plants, callus, roots, and young seedlings. To date, 169 hypothetical genes were tested, and 138 of them are found to be expressed in one or more of the six cDNA populations. By sequencing multiple clones from each 5Ј-and 3Ј-rapid amplification of cDNA ends (RACE) product and assembling the sequences, we generated full-length sequences for 16 of these genes. For 14 genes, there was one full-length assembly that precisely supported the intron-exon boundaries of their gene predictions, adding only 5Ј-and 3Ј-untranslated region sequences. However, for three of these genes, the other assemblies represent additional exons and alternatively spliced or unspliced introns. For the remaining two genes, the cDNA sequences reveal major differences with predicted gene structures. In addition, a total of six genes displayed more than one polyadenylation site. These data will be used to update gene models in The Institute for Genomic Research annotation database ATH1.With the combined efforts of scientists from Europe, Japan, and the United States, the first higher plant genome-sequencing project, whole-genome sequencing of Arabidopsis has been completed. The sequences of chromosome 2 and 4 were first released in 1999 (Lin et al., 1999;Mayer et al., 1999), and the remaining three chromosomes were sequenced by the end of 2000 (Salanoubat et al., 2000;Tabata et al., 2000;Theologis et al., 2000). This provides scientists a wealth of information and knowledge with which to understand plant biology from a genomic perspective. The whole Arabidopsis genome encodes approximately 25,000 genes (The Arabidopsis Genome Initiative, 2000) and the functional analysis of these genes is a major challenge in this post-sequencing era. One approach to this, taken by several groups (Ceres, Stanford Genome Center, Salk Institute, Plant Gene Expression Center [in collaboration with RIKEN Genomic Sciences Center], and Institut National de la Recherche Agronomique/Genoplante) is to produce full-length cDNAs for all of the 25,000ϩ genes in the Arabidopsis genome, because these complete sequences are essential to fully understand their structure and function (Seki et al., 2001a(Seki et al., , 2001b. Recent comparison of full-length cDNAs from Ceres and SSP with previous genomic annotation revealed that the structures of about one-third of the genes could be improved based on c...

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Characterization of exon skipping mutants of the COP1 gene from Arabidopsis

Cited by 29 publications

References 38 publications

The Maize Genome Contains a Helitron Insertion

The Maize Genome Contains a Helitron Insertion

Determinants of Plant U12-Dependent Intron Splicing Efficiency

Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,

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