Variation in alternative splicing across human tissues - PubMed (original) (raw)

Comparative Study

Variation in alternative splicing across human tissues

Gene Yeo et al. Genome Biol. 2004.

Abstract

Background: Alternative pre-mRNA splicing (AS) is widely used by higher eukaryotes to generate different protein isoforms in specific cell or tissue types. To compare AS events across human tissues, we analyzed the splicing patterns of genomically aligned expressed sequence tags (ESTs) derived from libraries of cDNAs from different tissues.

Results: Controlling for differences in EST coverage among tissues, we found that the brain and testis had the highest levels of exon skipping. The most pronounced differences between tissues were seen for the frequencies of alternative 3' splice site and alternative 5' splice site usage, which were about 50 to 100% higher in the liver than in any other human tissue studied. Quantifying differences in splice junction usage, the brain, pancreas, liver and the peripheral nervous system had the most distinctive patterns of AS. Analysis of available microarray expression data showed that the liver had the most divergent pattern of expression of serine-arginine protein and heterogeneous ribonucleoprotein genes compared to the other human tissues studied, possibly contributing to the unusually high frequency of alternative splice site usage seen in liver. Sequence motifs enriched in alternative exons in genes expressed in the brain, testis and liver suggest specific splicing factors that may be important in AS regulation in these tissues.

Conclusions: This study distinguishes the human brain, testis and liver as having unusually high levels of AS, highlights differences in the types of AS occurring commonly in different tissues, and identifies candidate cis-regulatory elements and trans-acting factors likely to have important roles in tissue-specific AS in human cells.

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Figures

Figure 1

Figure 1

Levels of alternative splicing in 16 human tissues with moderate or high EST sequence coverage. Horizontal bars show the average fraction of alternatively spliced (AS) genes of each splicing type (and estimated standard deviation) for random samplings of 20 ESTs per gene from each gene with ≥ 20 aligned EST sequences derived from a given human tissue. The different splicing types are schematically illustrated in each subplot. (a) Fraction of AS genes containing skipped exons, alternative 3' splice site exons (A3Es) or 5' splice site exons (A5Es), (b) fraction of AS genes containing skipped exons, (c) fraction of AS genes containing A3Es, (d) fraction of AS genes containing A5Es.

Figure 2

Figure 2

Examples of tissue-specific AS events in human genes with evidence of splice conservation in orthologous mouse genes. (a) Human fragile X mental retardation syndrome-related (FXR1) gene splicing detected in brain-derived EST sequences. FXR1 exhibited two alternative mRNA isoforms differing by skipping/inclusion of exons E15 and E16. Exclusion of E16 creates a shift in the reading-frame, which is predicted to result in an altered and shorter carboxy terminus. The exon-skipping event is conserved in the mouse ortholog of the human FXR1 gene, and both isoforms were detected in mouse brain-derived ESTs. (b) Human betaine-homocysteine _S_-methyltransferase (BHMT) gene splicing detected in liver-derived ESTs. BHMT exhibited two alternative isoforms differing by alternative 5' splice site usage in exon E4. Sequence comparisons indicate that the exon and splice site sequences involved in both alternative 5' splice site exon events are conserved in the mouse ortholog of the human BHMT gene. (c) Human cytochrome P450 2C8 (CYP2C8) gene splicing. CYP2C8 exhibited two alternative mRNA isoforms differing in the 3' splice site usage for exon E4 (detected in ESTs derived from several tissues), where the exclusion of a 71-base sequence creates a premature termination codon in exon E4b. Exons and splice sites involved in the AS event are conserved in the mouse ortholog of CYP2C8.

Figure 3

Figure 3

Correlation of mRNA expression levels of 20 known splicing factors (see Materials and methods) across 26 human tissues (lower diagonal: data from Affymetrix HU-133A DNA microarray experiment [45]; upper diagonal: data from Affymetrix HU-95A DNA microarray experiment [43]). Small squares are colored to represent the extent of the correlation between the mRNA expression patterns of the 20 splicing factor genes in each pair of tissues (see scale at top of figure).

Figure 4

Figure 4

Computation of splice junction difference ratio (SJD). The SJD value for a pair of transcripts is computed as the number of splice junctions in each transcript that are not represented in the other transcript, divided by the total number of splice junctions in the two transcripts, in both cases considering only those splice junctions that occur in portions of the two transcripts that overlap (see Materials and methods for details). SJD value calculations for different combinations of the transcripts shown in the upper part of the figure are also shown.

Figure 5

Figure 5

Comparison of alternative mRNA isoforms across 25 human tissues. (a) Color-coded representation of SJD values between pairs of tissues (see Figure 4 and Materials and methods for definition of SJD). (b) Hierarchical clustering of SJD values using average-linkage clustering. Groups of tissues in clusters with short branch lengths (for example, thyroid/ovary, B-cell/bone) have highly similar patterns of AS. (c) Mean SJD values (versus other 24 tissues) for each tissue.

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