Silencer elements as possible inhibitors of pseudoexon splicing

Abstract

Human pre-mRNAs contain a definite number of exons and several pseudoexons which are located within intronic regions. We applied a computational approach to address the question of how pseudoexons are neglected in favor of exons and to possibly identify sequence elements preventing pseudoexon splicing. A search for possible splicing silencers was carried out on a pseudoexon selection that resembled exons in terms of splice site strength and exon splicing enhancer (ESE) representation; three motifs were retrieved through hexamer composition comparisons. One of these functions as a powerful silencer in transfection-based splicing assays and matches a previously identified silencer sequence with hnRNP H binding ability. The other two motifs are novel and failed to induce skipping of a constitutive exon, indicating that they might act as weak repressors or in synergy with other unidentified elements. All three motifs are enriched in pseudoexons compared with intronic regions and display higher frequencies in intronless gene-coding sequences compared with exons. We consider that a subpopulation of pseudoexons might rely on negative regulators for splicing repression; this hypothesis, if experimentally verified, might improve our understanding of exonic splicing regulatory sequences and provide the identification of a novel mutation target for human genetic diseases.

Diverse roles of hnRNP L in mammalian mRNA processing: A combined microarray and RNAi analysis

“…8C). Specific examples of endogenous genes in this category are ARGBP2 and LIFR, where we found multiple exons to be down-regulated by hnRNP L. There are several similar cases of alternative exon activation in the literature, often caused by intronic mutations that create or strengthen splice signals or that inactivate silencer elements (Sun and Chasin 2000;Pagani et al 2002;Tuffery-Giraud et al 2003;Sironi et al 2004). Finally, the CD45 example of Lynch and coworkers also falls into this category.…”

Computational definition of sequence motifs governing constitutive exon splicing

“…The high proportion of human genomic sequences that can act to inhibit splicing when inserted into an exon suggests that ESSs may also play a role in splice site selection (Fairbrother and Chasin 2000). Sironi et al (2004) searched for potential ESSs among hexamers that are underrepresented in exons compared with pseudo exons and exon flanks; one of three such hexamers tested had silencing activity.…”

Finding a possible biomarker to tackle Parkinson’s disease by splice analysis and random point mutations to counter the expression of genes involved in Parkinson’s disease

“…While silencer motifs are sequences that bind to enhancer motifs and prevent up regulation of genes. Enhancer motifs have been shown to bind negative regulators belonging to the heterogeneous nuclear ribonucleoprotein (hnRNP) family (Sironi et al, 2004).…”