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First published online March 4, 2008; 10.1105/tpc.107.057190 The Plant Cell 20:543-551 (2008) © 2008 American Society of Plant Biologists OPEN ACCESS ARTICLE
Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression[W],[OA]
a Molecular and Cellular Biology, University of California, Davis, California 95616 1 Address correspondence to abrose{at}ucdavis.edu.
Introns that elevate mRNA accumulation have been found in a wide range of eukaryotes. However, not all introns affect gene expression, and direct testing is currently the only way to identify stimulatory introns. Our genome-wide analysis in Arabidopsis thaliana revealed that promoter-proximal introns as a group are compositionally distinct from distal introns and that the degree to which an individual intron matches the promoter-proximal intron profile is a strong predictor of its ability to increase expression. We found that the sequences responsible for elevating expression are dispersed throughout an enhancing intron, as is a candidate motif that is overrepresented in first introns and whose occurrence in tested introns is proportional to its effect on expression. The signals responsible for intron-mediated enhancement are apparently conserved between Arabidopsis and rice (Oryza sativa) despite the large evolutionary distance separating these plants.
The positive effect of introns on gene expression, which has been termed intron-mediated enhancement (IME) (Mascarenhas et al., 1990
The mechanism of IME is largely unknown. Some efficiently spliced introns boost expression more than 10-fold, while others have little or no effect, arguing against generic mechanisms related to splicing that would apply to all introns equally. Introns enhance gene expression by increasing the steady state amount of mature mRNA in the cell (Callis et al., 1987
The different enhancing ability of introns suggests that some contain more stimulatory signals than do others, yet prior attempts to identify the responsible sequences by deletion analysis have largely failed to identify any specific elements necessary for IME (Clancy et al., 1994 Here, we report an experimental and computational analysis of the intron sequences responsible for elevating expression. In addition to confirming the distributed nature of enhancing sequences, we found that the signals responsible for boosting expression are most abundant in introns near the start of transcription and that the compositional differences between promoter-proximal and later introns can be used to predict the ability of an intron to stimulate expression.
The Distribution of Stimulatory Sequences To determine if IME signals are dispersed and redundant, we created a series of hybrid introns (Figure 1 ) containing fragments of an enhancing intron (UBQ10 intron 1) within a context of an otherwise nonenhancing intron (COR15a intron 2). Each was inserted at the same location in the TRP1:β-glucuronidase (GUS) reporter gene used previously to compare the UBQ10 and COR15a introns (Rose, 2002
Computational Analysis of Introns To better understand the mechanism of IME, we undertook a bioinformatics approach with two related goals: (1) to build a discriminator that would be able to predict the enhancing ability of an untested intron and (2) to identify sequence motifs responsible for IME. We expected that introns near the start of transcription would be particularly enriched in IME signals because most enhancing introns are first introns (Tables 1 and 2 ) and because of the 1 kb positional requirement. Since introns from the middle or 3' end of genes have not been observed to greatly affect expression, we expected these distal introns to have few IME signals. To determine if compositional properties in promoter-proximal and distal introns were correlated with IME, we built a word-based discriminator called the IMEter. The IMEter reports a log-odds score based on the frequencies of all possible words (nucleotide sequences of a given length): a positive score indicates the input sequence is similar to proximal introns, and a negative score indicates similarity to distal introns.
The IMEter was trained on a set of introns whose positions are known relative to their transcription start sites. We collected all introns in the Arabidopsis genome whose parent gene was represented by full-length cDNAs and formed an IMEter training set with half of these genes. Variable parameters for the training protocol include word size and the threshold positions of proximal and distal introns. For example, a particular parameter set may define a word size of 4, proximal introns as those appearing <200 bp from the transcription start, and distal introns as those appearing >800 bp from the start site. To evaluate a particular parameter set, we ran the IMEter on six experimentally tested introns (Rose, 2002 The high correlation between IMEter score and experimentally observed enhancement suggests that the IMEter can be used to predict the ability of introns to stimulate expression. To test this, we chose six previously uncharacterized Arabidopsis introns that have a range of IMEter scores but are similar in GC composition and length and are all found within 500 bp of the start of single-intron genes. The expression levels mediated by all six introns in single-copy TRP1:GUS fusions correlate with their IMEter scores (Figure 2A, open symbols), giving an R2 value of 0.89 for the entire set of experimentally tested introns.
Arabidopsis Introns
To analyze genome-wide properties of IMEter scores, we ran the IMEter on the testing set, which comprised the half of the Arabidopsis genome not used for training. On average, IMEter scores for introns are slightly negative. Approximately 2% of introns have scores >50, and <1% have scores of 80 or more. Average IMEter scores decline steadily with distance from the start of the gene, becoming negative at
Motifs Associated with Enhancement
Rice Introns Some dicot introns can elevate expression in a monocot (Vain et al., 2004 Although we do not have quantitative expression values for rice introns, and therefore cannot use regression to correlate IMEter scores with expression levels, we trained the IMEter in rice and analyzed the 13 rice introns and three maize introns whose enhancing ability has been reported in the literature (Table 2). Thirteen of the enhancing introns had positive IMEter scores, nine of which were well over 100, while an intron known to have no effect on expression gave a negative score. An examination of all rice introns shows that only 2% of introns have scores of 100 or more (see Supplemental Figure 3A online). As in Arabidopsis, we find that promoter-proximal introns in rice have higher IMEter scores than distal introns (see Supplemental Figure 3B online). Since the IMEter apparently identifies enhancing introns in rice, we looked for motifs in the 100 highest scoring introns with NestedMICA just as we had done for Arabidopsis (see Supplemental Figure 4 online). The most common motif we found is very similar to the core of the Arabidopsis motif (Figure 3C).
Here, we show that signals concentrated in and dispersed throughout promoter-proximal introns are responsible for IME and identify a motif that comprises part of the IME signal. The IMEter algorithm we developed provides a measure of the abundance of promoter-proximal signals in any intron, which strongly predicts the ability of that intron to stimulate gene expression. Although the correlation between the enhancing ability of introns and their IMEter scores is very high, it is not absolute. One potential explanation for discrepancies between IMEter scores and our quantitative expression data is that the distribution of enhancing sequences within an intron could influence its ability to elevate expression. For example, stimulatory sequences near the 5' end of an intron might have the greatest impact on enhancement, while those closer to the 3' end could influence overall IMEter score but have much less effect on expression. Thus, the two hybrid introns with UBQ10 sequences at the 5' end had comparable effects on mRNA accumulation (Figure 1), even though the one with more COR15a sequence had a lower IMEter score. The contribution made to the total IMEter score by each part of an intron can be visualized by scanning the sequence in a sliding window (see Figure 3B), providing a high-resolution method to locate the regions that may be involved in the mechanism of enhancement. The IMEter will be refined to improve accuracy as more is learned about the sequences that boost expression.
The variables that preclude quantitative comparisons of the introns in Tables 1 and 2 are the least for different introns reported in the same publication, allowing a limited evaluation of the IMEter with these introns. In the only work to compare different introns at one location in the same reporter gene, the first intron from the rice tua1 gene was found to stimulate expression to a much higher degree than does the second or third intron from that gene (Jeon et al., 2000
Monocot and dicot introns differ in several ways. For example, the GC content of introns is 32% in Arabidopsis and 39% in rice, and the average length of introns in rice is more than twice that in Arabidopsis. In addition, monocots are better able to splice introns from other species or introns containing stem-loop structures than are dicots (Keith and Chua, 1986
Why should enhancing signals be most common in proximal introns? Transcripts that originate from spurious promoters in the body of a gene are potentially dangerous because they could encode partial proteins with dominant-negative effects, and those from intergenic regions could result in antisense transcripts that could silence genes. A close association of promoters with signals that increase processivity would help to ensure that the majority of stable RNAs from a particular locus correspond to complete mRNAs. The C-terminal domain of the largest subunit of RNA polymerase II is a likely candidate for regulation by introns because the C-terminal domain is known to bind to splicing factors and also to regulate the activity of the transcription machinery (Meinhart et al., 2005 It is unclear why some genes contain enhancing introns and some do not. Although highly expressed genes tend to have more enhancing signals than do poorly expressed ones, many abundantly expressed genes have introns with low IMEter scores. Perhaps there are several mechanisms to ensure complete transcription, and the IMEter is detecting only one kind. Alternatively, IME-like signals may be present in the 5' UTR or coding sequences of these genes, bypassing the need for enhancing introns. Experiments to test these possibilities are underway. The success of many biotechnology ventures depends on optimizing the expression of a transgene from another species. To elevate expression, the transgene should be engineered to contain an intron from the host species to avoid cross-species problems in intron recognition and splicing. The IMEter will be beneficial for finding host introns with a desired degree of enhancement or for identifying IME motifs whose abundance in an intron can be modified. These motifs will also form the basis for the biochemical isolation of factors involved in the mechanism of IME.
Hybrid Introns To introduce BamHI sites into the UBQ10 and COR15a introns, the regions of the intron 5' and 3' to the target site were amplified in separate PCR reactions using primers (see Supplemental Figure 5 online) containing the desired change. The PCR products were cloned and subsequently ligated together using the BamHI site, and the entire intron was verified by sequencing. The BglII or BclI sites were introduced by the same strategy into introns in which the BamHI site had been created. Hybrids between the modified UBQ10 and COR15a introns were made by conventional cloning using BamHI, BclI, and BglII, all of which generate the same cohesive end.
Expression Analysis
Genome Data
The Oryza sativa genome and annotation (release 5) were also downloaded from TIGR. The processing procedure was similar to that used for Arabidopsis with one additional step. We found that some of the introns had abnormally high GC compositions and were possibly erroneous. Therefore, genes containing introns with >50% GC were removed. The final set consisted of 11,857 genes and 61,753 introns that were divided into training and test sets as listed in Supplemental Data Set 1 online. The Caenorhabditis elegans and Drosophila melanogaster genes were obtained from a previous collection (Korf, 2004
The IMEter Algorithm
Accession Numbers
Supplemental Data
This research was supported by USDA Grant 2006-35301-17072 to A.B.R. and by National Institutes of Health Grant K22-HG-0064 to I.K. We thank Kim Blahnik and Artem Zykovich for early contributions and Keith Bradnam and Lesilee Rose for comments on the manuscript.
The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Alan B. Rose (abrose{at}ucdavis.edu).
[W] Online version contains Web-only data.
[OA] Open access articles can be viewed online without a subscription. www.plantcell.org/cgi/doi/10.1105/tpc.107.057190 Received November 27, 2007; Revision received February 1, 2008. accepted February 16, 2008.
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