Figure 4. Y14 associates with expressed genes independent of introns in S2 cells.

(A) Genome-wide average Y14 ChIP-seq enrichment 3000 bases around transcription start sites (TSS) of ChIP (blue trace) versus input DNA (green). (B) Y14 ChIP-seq enrichment (after background subtraction) 2000 bases around transcription start sites (TSS) of expressed (blue trace) or unexpressed (green trace) genes in S2 cells (see Material and methods). (C) Average Y14 enrichment of expressed genes with a different number of introns: 0 to >=5, indicated by traces of different colour (see legend on right of the plot). (D) Average Y14 enrichment across genes as in C but including both expressed and unexpressed genes. (E) Representative chromosome region showing Y14 ChIP-seq enrichment profile (blue), versus that of input DNA (grey). Genes are labeled following Flybase nomenclature.

DOI: http://dx.doi.org/10.7554/eLife.19881.012

Figure 4—figure supplement 1. Y14 association with transcribed genes does not correlate with mRNA levels.

Average Y14 enrichment of genes either not expressed (cyan colored line; RPKM = 0) or expressed at different levels (RPKM ranging from 1 to more than 100; indicated by traces of different color).

DOI: http://dx.doi.org/10.7554/eLife.19881.013

Figure 4—figure supplement 2. EJC proteins do not co-purify with RNA Pol II.

Immunoprecipitation (IP) with RNA Pol II Ser2 antibody following either RNase or mock treatment. Proteins were assayed by Western blotting for EJC proteins eIF4AIII, Y14 and MAGO, along with elongation factor Spt6 and Hrb87F (hnRNPA1). Goat IgG was used in a parallel IP as background control.

DOI: http://dx.doi.org/10.7554/eLife.19881.014