Characterization of Allele-Specific Regulation of Telomerase Reverse Transcriptase in Promoter Mutant Thyroid Cancer Cell Lines.

Telomerase reverse transcriptase () promoter mutations play a role in carcinogenesis and are found in both tumors and cancer cell lines. promoter methylation, transcription factor binding, chromatin remodeling, and alternative splicing are also known to play an integral role in regulation. Using nanopore Cas9 targeted sequencing, we characterized allele-specific methylation in thyroid cancer cell lines heterozygous for the promoter mutation. Furthermore, using chromatin immunoprecipitation followed by Sanger sequencing, we probed allele-specific binding of the transcription factors (GA binding protein transcription factor subunit alpha) and , as well as the chromatin marks H3K4me3 and H3K27me3. Finally, using coding single nucleotide polymorphisms and the long-read sequencing, we examined complementary DNA for monoallelic expression (MAE). We found the mutant promoter allele to be significantly less methylated than wild type, while more methylated in the gene body in heterozygous mutant cell lines. We demonstrated that the transcriptional activators and bind only to the mutant allele. In addition, the activating and repressive chromatin marks H3K4me3 and H3K27me3, respectively, bind mutant and wild-type alleles exclusively. Finally, in heterozygous mutant cell lines, exhibits from the mutant allele only. In summary, by employing new long-read sequencing methods, we were able to definitively demonstrate allele-specific DNA methylation, histone modifications, transcription factor binding, and the resulting monoallelic transcription in cell lines with heterozygous mutations.