Introns are key regulatory elements of rice tubulin expression

Fiume, Elisa; Christou, Paul; Gianı̀, Silvia; Breviario, Diego

doi:10.1007/s00425-003-1150-0

Cited by 74 publications

(52 citation statements)

References 47 publications

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“…In recent years, intronic regulatory elements (IREs; Yutzey et al 1989) have been identified which function as enhancers, repressors and promoters of gene transcription (Busch et al 1999;Deyholos and Sieburth 2000;Kapranov et al 2001;Fiume et al 2004). In many cases, IREs reside within the first intron (Wang et al 2002;Gazzani et al 2003;Michaels et al 2003;Fiume et al 2004). …”

Section: Intronic Regulatory Elementsmentioning

confidence: 99%

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

et al. 2005

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The broad adaptability of wheat and barley is in part attributable to their flexible growth habit, in that spring forms have recurrently evolved from the ancestral winter growth habit. In diploid wheat and barley growth habit is determined by allelic variation at the VRN-1 and/or VRN-2 loci, whereas in the polyploid wheat species it is determined primarily by allelic variation at VRN-1. Dominant Vrn-A1 alleles for spring growth habit are frequently associated with mutations in the promoter region in diploid wheat and in the A genome of common wheat. However, several dominant Vrn-A1, Vrn-B1, Vrn-D1 (common wheat) and Vrn-H1 (barley) alleles show no polymorphisms in the promoter region relative to their respective recessive alleles. In this study, we sequenced the complete VRN-1 gene from these accessions and found that all of them have large deletions within the first intron, which overlap in a 4-kb region. Furthermore, a 2.8-kb segment within the 4-kb region showed high sequence conservation among the different recessive alleles. PCR markers for these deletions showed that similar deletions were present in all the accessions with known Vrn-B1 and Vrn-D1 alleles, and in 51 hexaploid spring wheat accessions previously shown to have no polymorphisms in the VRN-A1 promoter region. Twenty-four tetraploid wheat accessions had a similar deletion in VRN-A1 intron 1. We hypothesize that the 2.8-kb conserved region includes regulatory elements important for the vernalization requirement. Epistatic interactions between VRN-H2 and the VRN-H1 allele with the intron 1 deletion suggest that the deleted region may include a recognition site for the flowering repression mediated by the product of the VRN-H2 gene of barley.

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Section: Intronic Regulatory Elementsmentioning

confidence: 99%

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

et al. 2005

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“…We can only speculate about the functional significance of this region, but it is, for instance, possible that intron 3 contains cis-regulatory elements involved in regulating the expression of phyB2. Such regulatory elements have been identified in introns of other plant genes (e.g., Fiume et al 2004).…”

Section: Discussionmentioning

confidence: 99%

Clinal Variation in phyB2, a Candidate Gene for Day-Length-Induced Growth Cessation and Bud Set, Across a Latitudinal Gradient in European Aspen (Populus tremula)

Ingvarsson¹,

García²,

Hall³

et al. 2006

Genetics

168

162

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The initiation of growth cessation and dormancy represents a critical ecological and evolutionary tradeoff between survival and growth in most forest trees. The most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset of these trees in a growth chamber experiment. Buds set showed significant clinal variation with latitude, explaining 90% of the population variation in bud set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of an adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions with excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation can be useful for identifying sites putatively involved in local adaptation.

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“…However, not all introns can enhance gene expression and not all genes are influenced by introns in their pattern of expression (Rethmeier et al 1997). In rice, a regulatory function for introns has been demonstrated for members of the tubulin gene family (Fiume et al 2004). The mechanism of IME is not yet understood, but an involvement of the splicing machinery is probable (Rose and Beliakoff 2000;Clancy and Hannah 2002).…”

Section: Intron Role In Expression Enhancementmentioning

confidence: 99%

Functional analysis of DNA sequences controlling the expression of the rice OsCDPK2 gene

Morello

Bardini

Cricrì

et al. 2005

Planta

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Plant calcium-dependent protein kinases (CDPKs) are involved in calcium-mediated signal transduction pathways. Their expression is finely tuned in different tissues and in response to specific signals, but the mechanism of such a regulation is still largely unknown. OsCDPK2 gene expression is modulated in vivo during rice (Oryza sativa L.) flower development and is downregulated by white light in leaves. In order to identify OsCDPK2 regulatory sequences, we amplified and cloned both the 5' and 3'-flanking regions of the gene. Sequence analysis revealed that the leader sequence is interrupted by an intron, whose regulatory role was investigated. Different ss-gucuronidase (GUS) expression vectors, carrying combinations of the putative OsCDPK2 regulatory regions, were generated and GUS expression was analyzed both in transient assays and in transgenic rice plants. The whole 5'-flanking sequence was able to drive GUS expression in rice calli and leaves transiently transformed with the biolistic technique. Analysis of the GUS expression pattern in transgenic plants revealed strong activity in root tips, leaf veins and mesophyll cells, in flower reproductive organs and in mature pollen grains. Expression was also shown to be subject to an intron-mediated enhancement (IME) mechanism, since the deletion of the leader intron sequence from chimeric OsCDPK2::GUS plasmids almost completely abolished GUS activity. Furthermore, in transiently transformed leaves, GUS expression driven by the OsCDPK2 promoter-leader region was constitutively observed regardless of light or dark exposure. Light-regulated expression was restored by inserting the OsCDPK2 3' untranslated region (3'UTR) downstream of the chimeric OsCDPK2::GUS transcription unit, suggesting that light down-regulation is mediated by a mechanism driven by the 3'UTR.

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Introns are key regulatory elements of rice tubulin expression

Cited by 74 publications

References 47 publications

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat

Clinal Variation in phyB2, a Candidate Gene for Day-Length-Induced Growth Cessation and Bud Set, Across a Latitudinal Gradient in European Aspen (Populus tremula)

Functional analysis of DNA sequences controlling the expression of the rice OsCDPK2 gene

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