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Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation

ABSTRACT: Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation

PROVIDER: PRJNA629340 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11646500_1.fastq.gz	Fastqsanger.gz
	SRR11646500_2.fastq.gz	Fastqsanger.gz
	SRR11646501_1.fastq.gz	Fastqsanger.gz
	SRR11646501_2.fastq.gz	Fastqsanger.gz
	SRR11646502_1.fastq.gz	Fastqsanger.gz

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Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation

Project description:We examined genome-wide patterns of DNA methylation from whole genome DNA methylation maps of five tissues (brain, kidney, lung, skeletal muscle, and pancreas) from one male koala and one female koala (Phascolarctos cinereus), and present the first whole genome, multi-tissue “methylome atlas” with information on tissue- and sex-specific variation of DNA methylation for a marsupial.

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Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation.

Project description:X chromosome inactivation (XCI) mediated by differential DNA methylation between sexes is an iconic example of epigenetic regulation. Although XCI is shared between eutherians and marsupials, the role of DNA methylation in marsupial XCI remains contested. Here, we examine genome-wide signatures of DNA methylation across fives tissues from a male and female koala (Phascolarctos cinereus), and present the first whole-genome, multi-tissue marsupial 'methylome atlas'. Using these novel data, we elucidate divergent versus common features of representative marsupial and eutherian DNA methylation. First, tissue-specific differential DNA methylation in koalas primarily occurs in gene bodies. Second, females show significant global reduction (hypomethylation) of X chromosome DNA methylation compared to males. We show that this pattern is also observed in eutherians. Third, on average, promoter DNA methylation shows little difference between male and female koala X chromosomes, a pattern distinct from that of eutherians. Fourth, the sex-specific DNA methylation landscape upstream of Rsx, the primary lncRNA associated with marsupial XCI, is consistent with the epigenetic regulation of female-specific (and presumably inactive X chromosome-specific) expression. Finally, we use the prominent female X chromosome hypomethylation and classify 98 previously unplaced scaffolds as X-linked, contributing an additional 14.6 Mb (21.5%) to genomic data annotated as the koala X chromosome. Our work demonstrates evolutionarily divergent pathways leading to functionally conserved patterns of XCI in two deep branches of mammals.

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