Rapid, transcript-specific changes in splicing in response to environmental stress - PubMed (original) (raw)

Rapid, transcript-specific changes in splicing in response to environmental stress

Jeffrey A Pleiss et al. Mol Cell. 2007.

Abstract

While the core splicing machinery is highly conserved between budding yeast and mammals, the absence of alternative splicing in Saccharomyces cerevisiae raises the fundamental question of why introns have been retained in approximately 5% of the 6000 genes. Because ribosomal protein-encoding genes (RPGs) are highly overrepresented in the set of intron-containing genes, we tested the hypothesis that splicing of these transcripts would be regulated under conditions in which translation is impaired. Using a microarray-based strategy, we find that, within minutes after the induction of amino acid starvation, the splicing of the majority of RPGs is specifically inhibited. In response to an unrelated stress, exposure to toxic levels of ethanol, splicing of a different group of transcripts is inhibited, while the splicing of a third set is actually improved. We propose that regulation of splicing, like transcription, can afford rapid and specific changes in gene expression in response to the environment.

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Figures

Figure 1

Figure 1. Splicing-Specific Microarrays

Probes targeting intron-containing genes are designed to detect the precursor species (P), the mature species (M), or the total transcript (T).

Figure 2

Figure 2. Regulation of Pre-mRNA Splicing in Response to Amino Acid Starvation

Time-resolved splicing profiles resulting from comparisons of (A) wild-type cells either treated with 50 mM 3AT or mock treated for 2, 4, 6, 10, 15, and 20 min; (B) prp8-1 and wild-type cells shifted from 25°C to 37°C for 5, 10, 15, 20, 25, and 30 min; and (C) wild-type cells compared to cells deleted for either RRP6, RAI1, RTT103, SKI2, UPF1, or XRN1. Also included is a comparison of two wild-type strains. The transcripts are ordered identically in all images.

Figure 3

Figure 3. Quantitative RT-PCR Validates the Rapid, Transcript-Specific Downregulation of Splicing in Response to Amino Acid Starvation

The behaviors of RPL21a, RPL17b, HIS4, U3 snRNA, and TEF4 were examined using primers specific to intron regions (red squares) or exon regions (blue diamonds). Error bars are the result of triplicate measurements from a single biological sample.

Figure 4

Figure 4. The Splicing Response to Amino Acid Starvation Does Not Require the Activity of Gcn2

Time-resolved splicing profiles resulting from (A) wild-type cells treated with 50 mM 3AT compared to mock-treated, (B) cells deleted for GCN2 treated with 50 mM 3AT compared to mock-treated, or (C) wild-type cells treated with 50 mM 3AT compared to cells deleted for GCN2 treated with 50 mM 3AT. Included in the final set is a comparison of the wild-type strain with the _GCN2_-deleted strain in the absence of 3AT.

Figure 5

Figure 5. Regulation of Pre-mRNA Splicing in Response to Ethanol Toxicity

(A) Time-resolved splicing profiles resulting from comparisons of wild-type cells either treated with 10% ethanol or mock treated for 5, 10, 15, 20, 25, and 30 min. (B) Genes whose splicing is downregulated (top panel, also highlighted with a red bar in [A]) or upregulated (bottom panel, also highlighted with a green bar in [A]). (C) Behavior of genes highlighted in (B) in response to amino acid starvation.

Figure 6

Figure 6. Comparison of Splicing Responses to Amino Acid Starvation and Ethanol Toxicity

The order of genes is identical to that shown in Figure 2.

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