Appendix S1. Technical aspects of the microarray hybridization and exploitation of transcript
profiling data.
For all the elements represented on the microarray, the oligomers constituting the tiling
exhibited an heterogeneous hybridization signal intensity (Figure 1a-d). The Nipponbare genome
harbors two copies of Tos17, only one of them (located on chromosome 7) being transcriptionally
active. Therefore, the heterogeneity of the hybridization signal could not be accounted for by the
superposition of transcription signals of several copies of the same element. We thus conclude that
the variation of the signal intensity is inherent to the hybridization procedure. This is further
supported by the transcript profiling of the actin gene : a clear heterogeneity of the hybridization
signal is observed among the probes that constitute the tiling of this gene, although it is found as a
single copy in the rice genome and its expression is constitutive (Figure 1b).
Moreover, for several elements, only few oligomers showed a significant differential
expression in contrast with the remaining probes of the tiling (Figure 1c). This raised the question
of the representativeness of the signal of these few probes regarding the overall expression profile
of the element. We therefore had to determine a threshold of detection of differential expression in
our screen of the entire set of LTR-retrotransposon families. In order to be retained as differentially
expressed in callus, 30 % of the oligomers tiling the entire sequence should have an expression
above the background (based on the normalization of the biological replicates) and among these, 30
% should be either under- or over-expressed (Figure 1). With these criteria, 15 and 13 families were
found to be either under- or over-expressed, respectively (Table 2). However, for all 28 families, the
differential expression was not observed for all tiles of the entire sequence, unlike for Tos17 (for
which 135 probes out of 138 showed a significant over-expression). For example, although Lullaby
was declared over-expressed following our criteria, Figure 1c clearly shows that this concerns only
two distinct regions of the element. We therefore had to conduct additional experiments in order to
validate these microarray hybridization results. This was done with semi-quantitative RT-PCR using
primers designed in the regions exhibiting an over-expression. All these experiments confirmed the
array hybridization results and lead us to conclude that the variation of the hybridization signals is
most probably due to the hybridization procedure. In any case, they confirmed our choice of the
detection threshold parameters described above.