Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression  

Abstract

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.

Mapping the low palmitate fap1 mutation and validation of its effects in soybean oil and agronomic traits in three soybean populations

“…The gene expression assay demonstrated that this motif enhanced gene expression of the GmKASIIIA locus, as had been observed before in Arabidopsis (Rose et al 2008). The increases in GmFATB1b, GmFATB2a, and GmFATB2b transcripts observed in Satelite (fap nc and GmKASIIIA mutations) showed that when the transcription of the most highly transcribed GmFATB1a homolog is compromised (Wilson et al 2001b;Cardinal et al 2007), the soybean plant up regulates the transcription of the other three GmFATB genes to try to maintain a ''normal'' fatty acid biosynthesis.…”

“…In contrast, examination of sequencing results for Glyma09g41380 revealed a single unique polymorphism in C1726 (G174A, relative to the start codon) shown in Fig. 1, which was predicted to disrupt the donor splice site recognition between exon one and intron one (Hebsgaard et al 1996;Long and Deutsch 1999 In addition, the G to A change in C1726 creates the GATCTG motif that has been associated with enhanced gene expression when present in the first intron in Arabidopsis (Rose et al 2008).…”

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

“…Several factors can affect gene expression, including gene GC content of the gene (Kudla et al, 2006), intron size (Ren et al, 2006), intron motifs (Rose et al, 2008), methylated transposon distribution (Hollister and Gaut, 2009), and chromosomal rearrangements (Marques-Bonet et al, 2004). Most notable for our study is the negative correlation between transcript level and density of recent transposon insertions that may be methylated (Hollister and Gaut, 2009).…”

“…However, transposon insertions into introns could still be deleterious as not every intron is without function. Introns can encode microRNAs (Ying and Lin, 2009), contain RNA splicing regulatory motifs (Ponthier et al, 2006), or promote intronmediated enhancement (Mascarenhas et al, 1990;Rose et al, 2008). Introns made larger by transposon insertions could affect pre-mRNA splicing and impact plant fitness, as intron size is critical for the splicing efficiency of pre-mRNA (Klinz and Gallwitz, 1985).…”

Role of RNA splicing in mediating lineage-specific expression of the von Willebrand factor gene in the endothelium

“…Introns have been shown to influence gene expression at multiple steps along this pathway. For example, splicing has been reported to enhance mRNA transcription, 26,[34][35][36][37] promote the 39 end processing/polyadenylation, 38,39 and reduce mRNA decay. 40 Our finding that luciferase and LacZ mRNA levels were unchanged in the absence of an intron argues against a role for any one of these mechanisms.…”