Figure 6. The increase in TREX occupancy is important for the expression of long transcripts.

(A) Meta gene occupancy profiles of RNAPII (Rpb3), Hpr1, TAP-Tho2 and Tho2-TAP. Whereas TAP-Tho2 shows the 5′-3′ increase typical for THO/TREX components, Tho2-TAP is recruited to genes, but does not increase towards the 3′ end of the gene. The Y-intercept of Tho2-TAP was adjusted with −0.05 in order to superimpose Tho2-TAP and TAP-Tho2 at the transcription site for better visualization. (B) Occupancy of Tho2-TAP does not increase with gene length as other TREX components. Peak occupancy of Hpr1, TAP-Tho2 and Tho2-TAP in comparison to the bona fide transcription elongation factor Spt5. (C–E) TREX is recruited to the PMA1 gene, but its occupancy does not increase in the THO2-TAP mutant. Occupancy of Tho2 (C), Sub2 (D) and Rpb1 (E) at the PMA1 gene in the TAP-THO2 and the THO2-TAP strain. Results of 3 independent experiments are shown (mean +/− SD; **: p<0.01; *: p<0.05). To assess the occupancy of Hpr1 and Sub2 in the presence of the TAP-Tag on Tho2, they were tagged with the Avi-tag. (F) Expression of long transcripts is downregulated in the THO2-TAP strain whereas highly transcribed and GC-rich transcripts are not affected. Microarray analysis reveals that transcripts upregulated in the THO2-TAP strain are shorter than the average of all transcripts, whereas downregulated transcripts are longer. The line indicates the average length or GC-content of all genes while the bars represent the average gene length, RNAPII occupancy or GC-content of up- or down-regulated genes, respectively. The error bars show the SEM and the p-value was calculated using the Wilcoxon rank sum test.