Agriculture Reference
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state. Chromatin characteristics, that is, euchromatin versus hetero-
chromatin, had already been associated with generally active versus
inactive portions of chromosomes (Heitz 1928; Muller 1941; Allfrey
et al. 1974; Lippman and Martienssen 2004; Louie et al. 1974; Swift
1974). However, chromatin was also found to be involved with DNA
compaction and gradually became more associated with cell volume
needs and unpacking to allow general accessibility of the transcription
machinery to the DNA (Malik and Henikoff 2003; Grewal and Jia 2007).
Technology advances eventually allowed
finer dissection of
the chromatin and resident DNA structure and function. Eventually, the
powerful tools of recombinant DNA technology began to lead investiga-
tions away from chromatin and toward the role of transcription factor
(TF) interactions with DNA and their control of gene expression. By the
1980s, chromatin had to take a backseat to the fast moving
ner and
eld of
transcription activation or repression by DNA binding proteins. RNA
polymerase activity was
first demonstrated by Weis and Gladstone
(1959). Three different eukaryotic RNA polymerases were separated
and named RNA polymerase I, II, and III by Roeder and Rutter
(1969). The crucial role of the RNA polymerase II
-
transcription factor
-
(Pol
TF) complex and its interaction with
cis
-regulatory DNA
sequences eventually were established as the prime controller of gene
expression (Malik and Roeder 2005; Hochheimer and Tijian 2010). The
observation of the dramatic effects of mutation of components of this Pol
II
II
TF gene expression control system in metazoans, beginning with the
earliest known factors, for example, GURKIN, ENGRAILED, and DOR-
SAL in
Drosophila
(Akam 1987), eventually revealed the critical role of
master control elements, such as the HOX genes in differential gene
expression, and subsequent manifestation of phenotype. It became
widely accepted that the relative activation of this gene expression
system has overwhelming, almost exclusive, in
-
uence on phenotype
evolution and biological diversity, especially of more recently evolved
higher
flowering plants. This view has continued until recently, almost
unabated, despite the evidence that TFs are only a part of the control
system (Zhang et al. 2007a).
Besides the elegant demonstrations of the hierarchical layers of TF-
mediated gene expression control in model systems such as
Drosophila
,
where GAP, PAIR RULE, SEGMENT polarity, and HOMEOTIC HIER-
ARCHICAL classes of genes were discovered, there always seemed to be
a missing layer of control (Akam 1987). Several observations were
dif
cult to explain based only on changes in TF-directed expression
of genes in these transcription cascades. Crucial among these is the
maintenance, through serial mitotic events, of any initiating signal and
