Conspectus
The story
of the non-duplex DNA form known as the G-quadruplex
(G4) has traversed a winding path. From initial skepticism followed
by debate to a surge in interest, the G4 story intertwines many threads.
Starting with computational predictions of a gene regulatory role,
which now include epigenetic functions, our group was involved in
many of these advances along with many other laboratories. Following
a brief background, set in the latter half of the last century when
the concept of the G4 as a structure took ground, here we account
the developments. This is through a lens that though focused on our
groups’ research presents work from many other groups that
played significant roles. Together these provide a broad perspective
to the G4 story. Initially we were intrigued on seeing potential G4
(pG4)-forming sequences, then known to be found primarily at the telomeres
and immunoglobin switch regions, occurring throughout the genome and
being particularly prevalent in promoters of bacteria. We further
observed that pG4s were not only prevalent but also conserved through
evolution in promoters of human, chimpanzee, mouse and rat genomes.
This was between 2005 and 2007. Encouraged by these partly and partly
in response to the view held by many that genome-wide presence of
G4s were genomic “accidents”, the focus shifted to seeking
experimental evidence.
In the next year, 2008, two independent
findings showed promise.
First, on treating human cancer cells with G4-binding ligands, we
observed widespread change in gene expression. Second, our search
for the missing G4-specific transcription factor, without which, importantly,
G4s in promoters posed only half the story, yielded results. We determined
how NM23-H2 (also known as NME2 or NDPK-B) interacts with G4s and
how interaction of NM23-H2 with a G4 in the promoter of the oncogene c-myc was important for regulation of c-myc transcription. NM23-H2, and subsequently many other similar factors
discovered by multiple groups, is possibly giving shape to what might
be the “G4-transcriptome”. Later, a close look at NM23-H2–G4
interaction in regulation of the human reverse transcriptase gene
(hTERT) revealed the role of G4s in local epigenetic
modifications. Meanwhile work from others showed how G4s impact histone
modifications following replication. Together these show the intrinsic
role of DNA sequence, through formation of DNA structure, in epigenetics.
More recent work, however, was waiting to reveal aspects that tend
to bring forth a completely new understanding of G4s. We observed
that the telomere-repeat-binding-factor-2 (TRF2), known canonically
to be telomere-associated, binds extensively outside telomeres throughout
the genome. Moreover, a large fraction of the non-telomeric TRF2 sites
comprise G4s. Second, the extent of non-telomeric TRF2 binding at
promoters was dependent on telomere length. Thereby TRF2-induced epigenetic
gene regulation was telomere-dependent. Together these implicate underlying
connections that show signs of addressing an intriguing una...
