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Impact of cytosine methylation on DNA binding specificities of human transcription factors.

ABSTRACT: The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.

SUBMITTER: Yin Y

PROVIDER: S-EPMC8009048 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Impact of cytosine methylation on DNA binding specificities of human transcription factors.

Project description:The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. The methylation is heritable across cell divisions, and contributes to the epigenetic memory that maintains the differentiated state of distinct cell types. Active gene regulatory elements are generally undermethylated relative to their flanking regions, and the undermethylation is thought to be important for their activity. Consistently with this model, the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By systematic analysis of 542 human TFs using methylation sensitive SELEX, we find here that a large number of TFs also prefer to bind to CpG methylated sequences. Most of these represent the extended homeodomain family. Structural analysis of HOXB13, CDX1, CDX2 and LHX4 revealed that the specificity of homeodomain proteins towards methylcytosine depends on amino-acids that form direct hydrophobic interactions with the 5-methyl group of methylcytosine. Our results provide a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity, and reveal that many developmentally important homeodomain proteins display strong preference for binding to mCpG containing sequences. Genome-scale analysis reveals that binding of most transcription factors is affected by CpG methylation, and that many developmentally important homeodomain TFs directly recognize the 5-methyl group of methylcytosine.

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