Genes identified by poly(A)+ transcriptome sequencing as overexpressed in trf5-?98-117

Purpose: To study the effects of disrupting the Trf5-Mtr4 interaction Methods: Analyzed TRF5 and trf5-?98-117 strains by transcriptome sequencing of poly(A)+ RNA Results: The set of most significantly affected genes included 71 that were overexpressed in trf5-?98-117 and only 5 that were down-regulated.The set of 71 overexpressed genes was predominated by known TRAMP substrates Conclusions: Disruption of the Trf5-Mtr4 interaction results in a snoRNA processing defect Overall design: Duplicate RNA samples of trf4?, trf5? yeast strains expressing either TRF5 or trf5-?98-117 were enriched for poly(A)+ transcripts and converted to a sequencing library. Transcriptome sequencing was performed on a HiSeq 2500. Each sequenced library yielded between 10 and 14 million 50nt reads that were mapped to the annotated yeast genes using Bowtie. Significantly up- or down-regulated genes in the trf5-?98-117 mutant were identified via edgeR.

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Losh JS, King AK, Bakelar J, Taylor L, Loomis J, Rosenzweig JA, Johnson SJ, van Hoof A