DNA i-motif levels are overwhelmingly depleted in living human cells: insights from in-cell NMR

Abstract

I-Motifs (iM) are non-canonical DNA structures potentially forming in accessible, single-stranded, cytosine-rich genomic regions, with regulatory roles. Chromatin, protein interactions, and intracellular properties seem to govern iM formation at sites with i-motif formation propensity (iMFPS) in human cells, yet their specific contributions remain unclear. Using in-cell NMR with oligonucleotide iMFPS models, we monitored iM-associated structural equilibria in asynchronous and cell cycle-synchronized HeLa cells at 37°C. Our findings show that iMFPS displaying pHT<7 under reference in vitro conditions occur predominantly in unfolded states in cells, while those with pHT>7 occur as a mix of folded and unfolded states depending on the cell cycle phase. Comparing these results with previous data obtained using an iM-specific antibody (iMab) revealed that cell cycle-dependent iM formation has a dual origin and iM formation concerns only a small fraction (possibly 1%) of genomic sites with iM formation propensity. We propose a comprehensive model aligning observations from iMab and in-cell NMR and enabling the identification of iMFPS capable of adopting iM structures under physiological conditions in living human cells. Our results suggest that many iMFPS may have biological roles linked to their unfolded states.

iMab Antibody Binds Single-Stranded Cytosine-Rich Sequences and Unfolds DNA i-Motifs

“…In line with this hypothesis, a recent in-cell NMR study by Trantirek and coll. demonstrated that iM-forming sequences with pH T < 7 are predominantly unfolded in cells, suggesting that only a minor fraction of iM-forming sequences could form iM structures in physiological conditions (39).…”

“…Interestingly, the high number of iMab peaks observed by Richer and coll. in sequences with pHT < 7 are predominantly unfolded in cells, suggesting that only a minor fraction of iM-forming sequences could form iM structures in physiological conditions (39).…”