Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution.
In mammals, the cytosine in CG dinucleotides is typically methylated producing 5-methylcytosine (5mC), a chemically less stable form of cytosine that can spontaneously deaminate to thymidine resulting in a T•G mismatched base pair. Unlike other eukaryotes that efficiently repair this mismatched base pair back to C•G, in mammals, 5mCG deamination is mutagenic, sometimes producing TG dinucleotides, explaining the depletion of CG dinucleotides in mammalian genomes. It was suggested that new TG dinucleotides generate genetic diversity that may be critical for evolutionary change. We tested this conjecture by examining the DNA sequence properties of regulatory sequences identified by DNase I hypersensitive sites (DHSs) in human and mouse genomes. We hypothesized that the new TG dinucleotides generate transcription factor binding sites (TFBS) that become tissue-specific DHSs (TS-DHSs). We find that 8-mers containing the CG dinucleotide are enriched in DHSs in both species. However, 8-mers containing a TG and no CG dinucleotide are preferentially enriched in TS-DHSs when compared with 8-mers with neither a TG nor a CG dinucleotide. The most enriched 8-mer with a TG and no CG dinucleotide in tissue-specific regulatory regions in both genomes is the AP-1 motif ( TG: A(C)/GT CA: N), and we find evidence that TG dinucleotides in the AP-1 motif arose from CG dinucleotides. Additional TS-DHS-enriched TFBS containing the TG/CA dinucleotide are the E-Box motif (G CA: GC TG: C), the NF-1 motif (GG CATG: CC), and the GR (glucocorticoid receptor) motif (G-A CATG: T-C). Our results support the suggestion that cytosine methylation is mutagenic in tetrapods producing TG dinucleotides that create TFBS that drive evolution.
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
Ximiao
X
He
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
Desiree
D
Tillo
Department of Genome Sciences, University of Washington.
Jeff
J
Vierstra
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
Khund-Sayeed
KS
Syed
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
Callie
C
Deng
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
G Jordan
GJ
Ray
Department of Genome Sciences, University of Washington.
John
J
Stamatoyannopoulos
Genome Analysis Unit, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
Peter C
PC
FitzGerald
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland vinsonc@mail.nih.gov.
Charles
C
Vinson
D044503:5-Methylcytosine / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D005075:Biological Evolution; D003596:Cytosine / Q000737:chemistry; D019175:DNA Methylation; D015226:Dinucleoside Phosphates / Q000235:genetics*; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D011485:Protein Binding; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics*
D044503:5-Methylcytosine; D003596:Cytosine; D015226:Dinucleoside Phosphates; D014157:Transcription Factors; C015772:CpG dinucleotide
AP-1; CG methylation; TFBS; TG dinucleotide; coelacanth; tissue specific