Genes involved in the synthesis and

Genes involved in the synthesis and response
to hormones (gibberellin, auxin) were also over-represented in the
transcriptome of early buds [21–23]. The overall conclusions of
these time course experiments were that the gene expression programme
under the floral organ identity genes changes over time
and that early stages include a large proportion of regulatory genes
(Fig. 1). The larger number of genes with metabolic and transport
functions expressed at later stages of development could reflect
a change in the types of functions controlled by organ identity
genes, or it could reflect the accumulation of indirect effects on
gene expression. To distinguish between these possibilities, it was
necessary to identify the direct targets of organ identity genes.
Although rapid response to a regulatory gene (as in the temperature
shift experiments described above for DEF) is suggestive,
proof of direct interaction requires chromatin immunoprecipitation
(ChIP). Gomez-Mena et al.[21] used ChIP to confirm that the AG
protein binds directly to some of its early target genes. This included
AG itself, AP3 and SEP3, showing that an auto-regulatory loop maintains
expression of the organ identity proteins that are predicted
to function as a multiprotein complex. More recently, a number
of important insights came from using ChIP-chip and ChIP-seq to
obtain a global view of the direct targets of SEP3 in the wild type
and in the ag mutant [25]. SEP3 bound in vivo to a large number of