Indiana University-Purdue University Indianapolis (IUPUI) / SETMAR is a chimeric protein that originates from the fusion of a SET domain to the
mariner Hsmar1 transposase. This fusion event occurred approximately 50 million years
ago, after the split of an anthropoid primate ancestor from the prosimians. Thus,
SETMAR is only expressed in anthropoid primates, such as humans, apes, and New
World monkeys. Evolutionary sequence analyses have revealed that the DNA-binding
domain, one of the two functional domains in the Hsmar1 transposase, has been
subjected to a strong purifying selection. Consistent with these analyses, SETMAR
retains robust binding specificity to its ancestral terminal inverted repeat (TIR) DNA. In
the human genome, this TIR sequence is dispersed in over 1500 perfect or nearly perfect sites. Given that many DNA-binding domains of transcriptional regulators are derived
from transposases, we hypothesized that SETMAR may play a role in gene regulation. In
this thesis, we determined the crystal structures of the DNA-binding domain bound to
both its ancestral TIR DNA and a variant TIR DNA sequence at 2.37 and 3.07 Å,
respectively. Overall, the DNA-binding domain contains two helix-turn-helix (HTH) motifs
linked by two AT-hook motifs and dimerizes through its HTH1 motif. In both complexes,
minor groove interactions with the AT-hook motifs are similar, and major groove interactions with HTH1 involve a single residue. However, four residues from HTH2
participate in nucleobase-specific interactions with the TIR and only two with the variant
DNA sequence. Despite these differences in nucleobase-specific interactions, the
DNA-binding affinities of SETMAR to TIR or variant TIR differ by less than two-fold. From
cell-based studies, we found that SETMAR represses firefly luciferase gene expression
while the DNA-binding deficient mutant does not. A chromatin immunoprecipitation
assay further confirms that SETMAR binds the TIR sequence in cells. Collectively, our
studies suggest that SETMAR functions in gene regulation.
| Identifer | oai:union.ndltd.org:IUPUI/oai:scholarworks.iupui.edu:1805/10895 |
| Date | 30 June 2016 |
| Creators | Chen, Qiujia |
| Contributors | Georgiadis, Millie M., Hurley, Thomas D., Wek, Ronald C., Turchi, John J., Kelley, Mark R. |
| Source Sets | Indiana University-Purdue University Indianapolis |
| Language | en_US |
| Detected Language | English |
| Type | Dissertation |
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