Genome-wide analysis of chromatin and transcription in the ciliates Oxytricha trifallax and Tetrahymena thermophila

DNA N6-adenine methylation (6mA) has recently been reported in diverse eukaryotes, spanning unicellular organisms to metazoans. Yet the functional significance of 6mA remains elusive due to its low abundance, difficulty of manipulation within native DNA, and lack of understanding of eukaryotic 6mA writers. Through biochemical fractionation of nuclear extracts, we identify a putative DNA 6mA methyltransferase in ciliates, termed MTA1. It contains an MT-A70 domain but is phylogenetically distinct from all known RNA and DNA methyltransferases. Disruption of MTA1 leads to the genome-wide loss of 6mA in vegetative cells and abolishment of the consensus ApT dimethylated motif in vivo. Genes exhibit subtle changes in chromatin organization or RNA expression upon 6mA loss, depending on their starting methylation level. Mutants fail to complete the sexual cycle, which normally coincides with a peak of MTA1 expression. Thus, MTA1 functions in a developmental stage-specific manner. We then determine the impact of 6mA on chromatin organization in vitro by reconstructing full-length ciliate chromosomes harboring 6mA in native or ectopic positions. Using these synthetic chromosomes, we show that 6mA directly disfavors nucleosomes in a local, quantitative manner in vitro, independent of DNA sequence. Furthermore, the chromatin remodeler ACF can overcome this effect. Our study identifies a novel MT-A70 protein necessary for eukaryotic 6mA methylation and defines the impact of 6mA on chromatin organization using epigenetically defined chromosomes. Datasets: 1) MNase-seq in vivo on chromatin from vegetative Oxytricha cells; 2) MNase-seq in vitro on chromatin reconstituted from Oxytricha histones and native Oxytricha genomic DNA; 3) MNase-seq in vitro on chromatin reconstituted from Xenopus histones and native Oxytricha genomic DNA; 4) MNase-seq in vitro on chromatin reconstituted from Oxytricha histones and PCR-amplified Oxytricha DNA lacking methylation; 5) MNase-seq in vitro on chromatin reconstituted from Xenopus histones and PCR-amplified Oxytricha DNA lacking methylation; 6) Oxytricha DNA N6-methyladenine (6mA) IP-seq using an anti-6mA antibody; 7) Input DNA from Oxytricha 6mA IP-seq experiment; 8) polyA+ RNAseq from vegetative Oxytricha cells; 9) TSS-seq (5'-capped RNAseq) from vegetative Oxytricha cells; 10) SMRT-seq to identify 6mA modifications in wild type Tetrahymena thermophila native genomic DNA; 11) MNase-seq in vivo on chromatin from MTA1 mutant and matched wild type Oxytricha cells; 12) polyA+ RNAseq from MTA1 mutant and matched wild type Oxytricha cells; 13) SMRT-seq to identify 6mA modifications in MTA1 mutant and matched wild type native genomic DNA; 14) Sequencing of naked MNase-digested genomic DNA