Originally Published In
Carle CM, Zaher HS, Chalker DL (2016) A Parallel G Quadruplex-Binding Protein Regulates the Boundaries of DNA Elimination Events of Tetrahymena thermophila. PLoS Genet 12(3): e1005842. doi:10.1371/journal.pgen.1005842
Guanine (G)-rich DNA readily forms four-stranded quadruplexes in vitro, but evidence for their participation in genome regulation is limited. We have identified a quadruplex-binding protein, Lia3, that controls the boundaries of germline-limited, internal eliminated sequences (IESs) of Tetrahymena thermophila. Differentiation of this ciliate’s somatic genome requires excision of thousands of IESs, targeted for removal by small-RNA-directed heterochromatin formation. In cells lacking LIA3 (ΔLIA3), the excision of IESs bounded by specific G-rich polypurine tracts was impaired and imprecise, whereas the removal of IESs without such controlling sequences was unaffected. We found that oligonucleotides containing these polypurine tracts formed parallel G-quadruplex structures that are specifically bound by Lia3. The discovery that Lia3 binds G-quadruplex DNA and controls the accuracy of DNA elimination at loci with specific G-tracts uncovers an unrecognized potential of quadruplex structures to regulate chromosome organization.
Non-canonical DNA structures, including four-stranded Guanine quadruplexes (G4 DNA), have been observed readily in vitro, but their regulatory importance within cells has been particularly challenging to demonstrate conclusively. We have discovered a G4 DNA binding protein, Lia3, that specifically regulates programmed DNA elimination events in Tetrahymena thermophila. This ciliate deletes nearly one-third of its germline genome from each developing somatic nucleus. These genomic deletion events must be accurate as the thousands of DNA regions excised are located near genes and/or their promoters, thus aberrant excision may alter gene expression. When we knocked out the gene encoding Lia3, we found that the boundaries of the excised regions were heterogeneous for a subset of loci that are flanked by G-rich (5’-AAAAAGGGGG-3’) boundary controlling sequences. When we tested whether Lia3 bound this sequence, we discovered that the sequence itself formed G4 DNA and that Lia3 bound only when the sequence adopted this conformation. Our findings that Lia3 binds G4 DNA and that deletion of the gene encoding Lia3 perturbs the boundaries of the excised loci which are flanked by this quadruplex-forming DNA provides compelling evidence that this non-canonical DNA structure has a critical role during development of these cells.
Carle, Christine M.; Zaher, Hani S.; and Chalker, Douglas L., "A Parallel G Quadruplex-Binding Protein Regulates the Boundaries of DNA Elimination Events of Tetrahymena thermophila" (2016). Biology Faculty Publications & Presentations. 112.