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This story starts more than 50 years ago,
when Barbara McClintock noted similarities
between gene silencing mediated by heterochromatin,
shown here by variegated pigmentation in the eye of drosophila,
and gene silencing mediated by transposable elements,
shown in part c by variegated patterns of pigmentation in corn kernels.
In fact when she discovered transposable elements she didn't call them transposable.
She called them controlling elements.
Because she recognized their ability to control genes.
And she proposed that transposable elements were
little pieces of heterochromatin that were
scattered along the chromosome and regulated genes that so were important for development.
Transposons mediate gene silencing
when they integrate within genes' regulatory regions.
For example, the hcf106 gene in maize confers
pigmentation, chlorophyll pigmentation to the leaves.
When a Mutator transposable Element is inserted into the upstream region,
this brings the gene under its epigenetic control.
In this example, when mutator is unmethylated,
when a DNA corresponding to the transposon is
unmethylated, there is no gene expression from the hcf106 gene.
But when it's methylated,
a promoter at the end of the mutator element,
regulates the hcf106 gene,
restoring the dark green pigment.
This is shown on the left,
in two leaves from a plant containing the hcf106 gene,
in which mutator elements are methylated in the dark green
stripe, and unmethylated in the light green stripes shown in plus and minus.
So in this case then,
transposons regulate genes, in a rather direct way.
With the advent of genome sequencing,