Induced splice site mutation generates alternative intron splicing in starch synthase II (<i>SSII</i>) gene in rice

<p>The evolution of starch synthase (SS) has been extensively analysed in the model plant rice, but there have been few detailed studies directed towards exploring the intron splicing variant effect on the divergence of the <i>SS</i> gene. We report here an example that the alternative splicing of a GC-AG intron induced a new splicing isoform of <i>SSII-1</i> expressed in <i>Oryza sativa japonica</i> cultivar Zhonghua-15. In addition, a GT-AG intron flanking the alternative splicing GC-AG intron was simultaneously spliced at an incorrect position, inducing another intron fragment gained in mature <i>SSII-1</i> RNA. Moreover, when a GT-AG intron from <i>SSII-3</i> was artificially mutated into the GC-AG intron, a 28 bp fragment from the intron added to the mature RNA could be observed in transgenic rice. In this study, the alternative intron splicing of the GC-AG intron might offer more variants for genetic divergence of the starch synthase gene family in rice.</p

Additional file 1: of Sensitive Nonenzymatic Electrochemical Glucose Detection Based on Hollow Porous NiO

Supplementary figures and tables. (DOC 6924 kb

Association between <i>BRM</i> promoter haplotypes and risk of HCC^a.

a<p>Haplotype frequencies in cases and controls were compared using logistic regression.</p

Western blot analysis of BRM expression in HCC tissue and adjacent non-tumor tissues.

<p>(A) BRM expression for different BRM-1321 genotypes. (B) BRM expression for different haplotypes. Haplotype #1: −1321 del/del-741 ins/ins, Haplotype #2: −1321 del/del-741 del/del, Haplotype #3: −1321 ins/ins-741 ins/ins.</p

BRM expression in HCC tumor tissues <i>vs.</i> non-tumor tissues and its correlations between BRM-1321 indel polymorphism as well as corresponding haplotypes.

<p>(<b>A</b>) Relative BRM expression in HCC tumor tissues <i>vs.</i> non-tumor tissues (n = 72); (<b>B</b>) Relative BRM expression in three genotypic groups of BRM-1321 (−1321 ins/ins, n = 10, −1321 ins/del, n = 32, −1321 del/del, n = 30); (<b>C</b>) Relative BRM expression in different haplotype groups (haplotype: −1321 ins/ins-741 ins/ins, n = 6, haplotype: −1321 del/del-741 del/del, n = 11, haplotype: −1321 del/del-741 ins/ins, n = 4); (<b>D</b>) Relative BRM expression in hepatoma cell lines with different haplotypes. Data represented as mean ± SEM. *indicates <i>P</i><0.01, **indicates <i>P</i><0.001 compared within the same group (HCC tissue or non HCC tissue).</p

Stratification analysis based on HBV infection status.

a<p>adjusted by age, sex, smoking status and drinking status.</p

Stratification analysis based on drinking status in two populations.

a<p>adjusted by age, sex, smoking status and HBV infection status. Drinkers included light drinkers and heavy drinkers.</p

Example sequencing and genotyping output for the two BRM Indel polymorphisms.

<p>The upper and middle panels showed the sequence of deletion and insertion allele, respectively. The underlined base-pairs indicate the inserted sequences. The lower panel displays an example of the genotyping assay results. For rs34480940 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055169#pone-0055169-g001" target="_blank">Figure 1A</a>), lane 5 and 9, del/del genotype; lane 2, 4 and 6, ins/del genotype; lane 1, negative control; remaining lanes, ins/ins genotype. For rs3832613 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055169#pone-0055169-g001" target="_blank">Figure 1B</a>), lane 3 and 9, ins/ins genotype; lane 3 and 9, del/del genotype; lane 5, negative control; remaining lanes, ins/del genotype.</p

Demographic characteristics among HCC cases and controls.

a<p>Two-sided two-sample <i>t</i>-test between cases and controls.</p>b<p>χ² test for differences between cases and controls.</p

Stratification analysis based on smoking status in two populations.

a<p>adjusted by age, sex, drinking status and HBV infection status. Smokers included former smokers and current smokers.</p