Korir Paul K, Roberts Lisa, Ramesar Raj, Seoighe Cathal
School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, University Road, Galway, Republic of Ireland.
BMC Res Notes. 2014 Jun 27;7:401. doi: 10.1186/1756-0500-7-401.
Substantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci - sQTLs). Genetic variants that affect mRNA splicing in trans are harder to identify because their effects can be more subtle and diffuse, and the variants are not co-located with their targets. We carried out a transcriptome-wide analysis of the effects of a mutation in a ubiquitous splicing factor that causes retinitis pigmentosa (RP) on mRNA splicing, using exon microarrays.
Exon microarray data was generated from whole blood samples obtained from four individuals with a mutation in the splicing factor PRPF8 and four sibling controls. Although the mutation has no known phenotype in blood, there was evidence of widespread differences in splicing between cases and controls (affecting approximately 20% of exons). Most probesets with significantly different inclusion (defined as the expression intensity of the exon divided by the expression of the corresponding transcript) between cases and controls had higher inclusion in cases and corresponded to exons that were shorter than average, AT rich, located towards the 5' end of the gene and flanked by long introns. Introns flanking affected probesets were particularly depleted for the shortest category of introns, associated with splicing via intron definition.
Our results show that a mutation in a splicing factor, with a phenotype that is restricted to retinal tissue, acts as a trans-sQTL cluster in whole blood samples. Characteristics of the affected exons suggest that they are spliced co-transcriptionally and via exon definition. However, due to the small sample size available for this study, further studies are required to confirm the widespread impact of this PRPF8 mutation on mRNA splicing outside the retina.
在识别控制mRNA剪接的序列元件以及这些元件中改变mRNA剪接的遗传变异（称为剪接数量性状位点 - sQTLs）方面已经取得了重大进展。影响mRNA反式剪接的遗传变异更难识别，因为它们的影响可能更微妙和分散，并且这些变异与其靶标不在同一位置。我们使用外显子微阵列对一种导致视网膜色素变性（RP）的普遍存在的剪接因子突变对mRNA剪接的影响进行了全转录组分析。
外显子微阵列数据来自从四名患有剪接因子PRPF8突变的个体和四名同胞对照获得的全血样本。尽管该突变在血液中没有已知的表型，但有证据表明病例组和对照组之间在剪接方面存在广泛差异（影响约20%的外显子）。病例组和对照组之间包含率有显著差异（定义为外显子的表达强度除以相应转录本的表达）的大多数探针集在病例组中的包含率更高，并对应于比平均长度短、富含AT、位于基因５'端且两侧为长内含子的外显子。受影响探针集两侧的内含子在最短的内含子类别中尤其缺乏，这与通过内含子定义进行剪接有关。
我们的结果表明，一种剪接因子的突变，其表型仅限于视网膜组织，在全血样本中作为一个反式sQTL簇起作用。受影响外显子的特征表明它们是共转录剪接且通过外显子定义进行剪接的。然而，由于本研究可用的样本量较小，需要进一步研究来证实这种PRPF8突变对视网膜外mRNA剪接的广泛影响。
