Abstract
Encoded within DNA sequence
is the cis-regulatory logic responsible for controlling gene expression
in metazoans. The precise and predictive decryption of this code is on
going endeavor at the heart of modern genomics. Even though state of the
art technologies in genomics have been generated tremendous amount of
data, how the interplay of multiple transcriptional mechanisms give rise
to the complex expression changes has remain elusive. This dissertation
presents a theoretical model that reconstitutes even-skipped
transcriptional control in silico by implementing molecular regulatory
mechanisms that are essential for the even-skipped gene expression, then
applies the model to even-skipped enhancer fusions in order to elucidate
the underlying rules governing the transcriptional control of the
Drosophila genome. Rearrangements of about 2.5 kb of regulatory DNA
located 5' of the transcription start site of the Drosophila
even-skipped locus generate large scale changes in the expression of
even-skipped stripes 2, 3 and 7. The most radical effects are generated
by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2
and 3 with and without small 'spacer' segments less than 360
bp in length. The model reproduced gene expression of the arrangements
with high fidelity and was able to predict expression patterns driven by
a variety of segments of the genomic DNA totaling 50 kb for gap and
pair-rule genes, even-skipped enhancers not included in the training
set, stripe 2, 3 and 7 enhancers from various Drosophilidae and Sepsidae
species. These results suggest that the molecular mechanisms implemented
in the model are essential not only for Drosophila melanogaster
even-skipped but also for many genes of early Drosophila and Sepsid
embryo development. In addition, the model predicted gene expression of
long segments of even-skipped regulatory DNA which contain multiple
enhancers. This result opens the door to quantitative and predictive
models of entire loci, the physiological units of the genome. The model
demonstrated that two mechanisms, short-range quenching and
coactivation, are key mechanisms conferring the independent action of
enhancers in the large even-skipped regulatory DNA. I establish that
elevated expression driven by a fusion of MSE2 and MSE3 is a consequence
of the recruitment of a portion of MSE3 to become a functional component
of MSE2, demonstrating that cis-regulatory 'elements' are
not elementary objects. Finally, I demonstrate that the conservation of
stripe 2 expression driven by six Drosophila and Sepsid stripe 2
enhancers requires novel molecular interactions, not seen in the
Drosophila melanogaster S2E, presenting a clear example of compensatory
adaptation with a precise mathematical description of the essential
molecular mechanisms.
Description
189 pg.
