Supplementary Figure legends
Figure S1 Gene expression and ChIP-seq data for the MDSR group of genes.
(A) Differential transcriptional response of MDSR genes to serum stimulation in
mycf/f;CreER cells, either without (orange bars) or with OHT to induce c-myc deletion
(grey bars). The plotted values represent the fold-induction of each mRNA by serum,
as determined from our microarray data. Only the maximal induction point during our
time-course is reported for each gene. (B, C) Myc-binding within the TSS ±1kb
interval for each MDSR gene in cells starved (red bars) or stimulated with serum for 8
hours (blue bars). The values represent Myc peaks in our ChIP-seq dataset, reported
as OCR (B) or OCR-RMA (C). The dashed line in (C) indicates the OCR-RMA
threshold of 15 (see text).
Figure S2 Identification of regulatory patterns following Myc deletion and serum
stimulation. The heatmaps show different classes of genes: (A) Up in rat, (B) Mycdependent repression, (C) Super-induced without Myc and (D) Known Myc-repressed
genes (see text for definitions). The groups in (A, D) were determined based on
previous literature and with the Myc database; those in (B, C) represent regulatory
patterns in our microarray data, as those in Fig. 2. The genes in each group were
clustered hierarchically on the basis of their microarray-based expression profiles.
Changes in mRNA levels were expressed as fold-induction relative to time 0 in each
culture, and color-coded as indicated.
Figure S3 Quantitative RT-PCR validation of MISR and NRS genes. Cells were
serum starved either untreated (black bars) or treated with OHT (grey bars) and then
stimulated with serum for the indicated time. Average +/- sd of two independent
experiments is shown for each gene.
Figure S4 Quantitative RT-PCR validation of mRNAs expression. The figure shows
the induction by serum (4 and 8h) in mycf/f;CreER cells, either without (blue bars) or
with OHT pre-treatment to induce c-myc deletion (red bars). All data are normalized
to the untreated control sample. The average +/- s.d. of three independent experiments
is shown for each gene. (A) mRNAs included in the “Myc-dependent repression”
group of Fig. S2B. The graphs are displayed in three sub-groups according to the
outcome of the validation: Repressed and Myc-dependent, Repressed but not Mycdependent, Not repressed. (B) Gadd45a and Cdkn2b mRNAs (see text).
Figure S5 Quantitative RT-PCR validation of mRNAs expression. The mRNAs
shown are all from the group “super-induced without Myc” of Fig. S2B. The
experiment was performed exactly as in Fig. S4. The graphs are displayed in two subgroups according to the outcome of the validation, as indicated.
Figure S6 Correlation of Myc-binding measured by qChIP and ChIP-seq at 76
different loci in starved cells (top graph) or in cells stimulated with serum for 8 hours
(bottom graph).
Figure S7 Distribution of Myc peaks in the genome. (B) Absolute number of peaks in
serum-stimulated cells, distributed over the window between -100 Kb and +100kb
from TSSs. Each bin represents 1 Kb. (B) Distribution of intergenic Myc peaks
relative to CAGE tags. Each intergenic Myc site has been annotated to the nearest
Perna et al. 2010 p. 1
CAGE tag, along with a 10 times bigger dataset of randomly sampled intergenic
regions showing the same length distribution. The two populations were then plotted
as distributions relative to the nearest CAGE tag. The Myc intergenic sites display a
sharper peak around zero.
Figure S8 Myc-binding efficiency at promoters positively correlates with pre-existing
mRNA levels. The box plots show the distribution of median mRNA levels in serumstarved cells, as determined from the microarray data, analysed for groups of genes
bound by Myc with increasing efficiency following serum stimulation (defined by
OCR-RMA values, as shown). Only Myc binding within the TSS ±1 kb window was
considered.
Perna et al. 2010 p. 2