Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations

Abstract

DNA cytosine methylation in mammals modulates gene expression and chromatin accessibility. It also impacts mutation rates, via spontaneous oxidative deamination of 5-methylcytosine (5mC) to thymine. In most cases the resulting T:G mismatches are repaired, following T excision by one of the thymine DNA glycosylases, TDG or MBD4. We found that C-to-T mutations are enriched in the binding sites of CCAAT/enhancer binding proteins (CEBP). Within a CEBP site, the presence of a T:G mismatch increased CEBPβ binding affinity by a factor of >60 relative to the normal C:G base pair. This enhanced binding to a mismatch inhibits its repair by both TDG and MBD4 in vitro. Furthermore, repair of the deamination product of unmethylated cytosine, which yields a U:G DNA mismatch that is normally repaired via uracil DNA glycosylase, is also inhibited by CEBPβ binding. Passage of a replication fork over either a T:G or U:G mismatch, before repair can occur, results in a C-to-T mutation in one of the daughter duplexes. Our study thus provides a plausible mechanism for accumulation of C-to-T human somatic mutations.

Backbone Conformational Equilibrium in Mismatched DNA Correlates with Enzyme Activity

“…Copyright 2006 American Chemical Society and CC BY 4.0, respectively. d Adapted with permission from ref . Copyright 1995 Oxford University Press. e Adapted with permission from ref . Copyright 2012 Oxford University Press. f There is no error provided, and the value is given as the lower limit, but we used it directly in our analysis.…”

“…has also been studied extensively 22,23 and other types of proteins such as CEBPβ have varying degrees of activity and binding strength on DNA containing T:G mismatches. 30,31 To attempt to quantify a relationship to enzyme properties, we have determined the equilibrium conformational populations of the DNA backbone using 31 P solution NMR. The specific conformation of the DNA phosphodiester backbone is described by a series of dihedral angles, 32,33 where the angles ε and ζ for the primary conformations are traditionally defined (Figure 1) as trans/g-in BI (ε -ζ ∼ −90°) and g-/trans in BII (ε -ζ ∼ +90°).…”

“…The enzyme activity on various base-paired substrates (e.g., T:G, U:G, C:G, T:A, etc.) has also been studied extensively , and other types of proteins such as CEBPβ have varying degrees of activity and binding strength on DNA containing T:G mismatches. , …”

Physiological mechanisms of stress-induced evolution

“…Importantly, DNA methylation functions beyond an epigenetic mark as well, in a much more permanent manner. Namely, it increases rates of mutation by frequently causing cytosine to thymine transitions (Zhou et al, 2020;Yang et al, 2021;Holliday and Grigg, 1993). This pattern is so apparent that species with widespread DNA methylation exhibit global depletion of CpG dinucleotides, because this is where DNA methylation most often occurs (Gruenbaum et al, 1982).…”

Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases

“…If the T:G mismatch is inaccessible to MBD4 and is not repaired in time, replication generates a C:G to T:A transition ( Figure 4g ). Two transcription factors, CEBPβ and ETS1, whose binding motifs contain CpG, restrict access by MBD4 to the mismatch and boost C→T mutation rates within their respective binding sites [ 73 – 75 ]. ETS1 binding both increases generation of UV-induced cyclopyrimidine dimers (CPDs), and blocks repair of cytosine-deaminated CPDs [ 75 – 77 ].…”