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In this study, Mamontova et al. investigated the mechanism that links lncRNA NEAT1 to the DNA damage response (DDR) and describe a protective role against DNA damage that sustains genomic stability. DNA damage controls NEAT1 expression and structure through METTL3-driven m6A methylation, resulting in NEAT1's accumulation at promoter-associated DNA double-strand breaks and its regulation of CHD4-mediated histone acetylation.

Various genomic DNA sequences including a MYCpromoter sequence are amenable to the formation of a G-quadruplex featuring a snap-back loop with the incorporation of a 3′-terminal guanine into the quadruplex core. To evaluate relative stabilities and ligand binding in more detail, optical, microcalorimetric, and NMR structural studies were performed on both a minimal mutant sequence Pu22Tthat exclusively folds into a snap-back loop quadruplex and a parallel MYCquadruplex proposed to be the most relevant fold of the MYCpromoter in a cellular environment. Similar thermal stabilities for Pu22Tand MYCsuggest the coexistence of both quadruplexes when derived from a sequence able to fold into both topologies. Isothermal titration calorimetry indicates a mostly identical enthalpy-driven strong binding of an indoloquinoline ligand but with a reduced number of high-affinity binding sites in Pu22Tin line with a novel modified FRET competitive melting assay. Corroborated by fluorescence titrations using 2-aminopurine as a fluorescent probe, NMR chemical shift footprints show binding of the ligand at the Pu22T5′-outer tetrad with the formation of a binding pocket. On the other hand, steric restrictions due to the snap-back loop severely restrict ligand stacking on the 3′-outer tetrad of Pu22T.