Methylation of adenine in the nuclear DNA of Tetrahymena is internucleosomal and independent of histone H1

Abstract

There are about 50 copies of each chromosome in the somatic macronucleus of the ciliated protozoan TETRAHYMENA: Approximately 0.8% of the adenine residues in the macronuclear DNA of Tetrahymena are methylated to N6-methyladenine. The degree of methylation varies between sites from a very low percentage to >90%. In this study a correlation was found between nucleosome positioning and DNA methylation. Eight GATC sites with different levels of methylation were examined. There was a direct correlation between the degree of methylation and proximity to linker DNA at these sites. Although methylation occurs preferentially in linker DNA, the patterns and extent of methylation in a histone H1 knockout strain were virtually indistinguishable from those in wild-type cells.

DNA N6-methyladenine: a new epigenetic mark in eukaryotes?

“…Similar 6mA sites have also been identified in the genome of Tetrahymena thermophila 40 . Nearest-neighbor analyses assisted by 3 H labeling revealed that the methylation in T. thermophila occurs at the sequence 5′-NAT-3′ 41 , which is similar to the N 6 -adenine methylation motif found in C. reinhardtii 17 .…”

“…3a). This could be explained by the methylation machinery favoring linker DNA, potentially due to physical ease of access 40 , or by 6mA regulating nucleosome positioning. Interestingly, methylation in CG repeats in certain algae species occurs at extreme densities, which disfavors nucleosome assembly and thus dictates nucleosome positioning 63 .…”

Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing

“…We previously reported that N 6 -mA occurrence at TSS exhibits a periodic pattern with maxima that are complementary to nucleosome binding sites, suggesting that N 6 -mA potentially is involved in nucleosome positioning in C. reinhardtii, 8 which is also consistent with early observation in Tetrahymena thermophile . 33 In this study, we presented that N 6 -mA can directly interact with RNA pol II and cause transcriptional pausing/stalling. Considering the distribution patterns of N 6 -mA across the genome in different organisms, it is possible that these stalling effects may add a new layer of fine-tuned regulation of Pol II transcription elongation dynamics.…”

N6-Methyladenine: A Conserved and Dynamic DNA Mark

“…In the protists Tetrahymena and Chlamydomonas 6mA is preferentially located in the linker regions between nucleosomes (Karrer, VanNuland 2002; Fu et al 2015; Pratt, Hattman 1983), raising the possibility that 6mA could help to direct nucleosome positioning. Alternatively, enrichment of 6mA in linker regions may reflect increased accessibility, or recruitment of the methyltransferase at regions of open chromatin.…”