3 minute lightning oral presentation (and poster) ESA-SRB 2023 in conjunction with ENSA

The PRKACB locus is imprinted in marsupials (#209)

Trent Newman 1 , Teruhito Ishihara 1 2 , Phoebe Rizzoli 1 , Lucinda Xiao 3 , Quentin Gouil 3 , Donna Bond 4 , Tim Hore 4 , Geoff Shaw 1 , Marilyn B Renfree 1
  1. School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
  2. Epigenetics programme, Babraham Institute, Cambridge, United Kingdom
  3. Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
  4. Department of Anatomy, University of Otago, Dunedin, New Zealand

Genomic imprinting has largely been studied in eutherians, particularly humans and mice, but marsupials also have imprinted genes, albeit a smaller number so far. For many imprinted genes, parental identity is marked by a differentially methylated region (DMR) in which the DNA methylation status differs between the two alleles. We detected several candidate DMRs in a publicly-available koala whole genome bisulfite sequencing dataset1, using a custom computational pipeline. One candidate DMR was associated with PRKACB, a gene encoding a catalytic subunit of the cAMP-dependent protein kinase. Nothing is known about the imprinting status of PRKACB in eutherians, even though mutations of this gene can cause multiple developmental abnormalities. Intriguingly, the G-protein Gsα functions upstream of PRKACB in the cAMP signalling pathway and is encoded by the GNAS gene which is imprinted in eutherians2 but not marsupials3. Comparison of the PRKACB start site indicated a longer 4 kb CpG island (CGI) in marsupials relative to the 1 kb CGI in eutherians. In the brushtail possum, direct nanopore DNA sequencing detected allele-specific methylation over the PRKACB CGI. In the tammar wallaby, using bisulfite PCR, the maternal allele was 90% methylated (12 reads) and the paternal allele was 1% methylated (5 reads), across two animal replicates. Transcriptional analysis using nanopore sequencing of a collection of tammar tissues identified two antisense lncRNAs and nine PRKACB transcript isoforms produced from the locus. Allele-specific expression analysis identified paternal expression of an antisense PRKACB lncRNA in tammar pouch young liver and muscle tissue. We conclude that there is DMR-associated imprinting of the PRKACB locus in marsupials. Lineage-specific imprinting of GNAS in eutherians and PRKACB in marsupials could indicate a conserved selection pressure for imprinting of the cAMP signalling pathway in therian mammals.

  1. Singh, D., Sun, D., King, A. G., Alquezar-Planas, D. E., Johnson, R. N., Alvarez-Ponce, D., & Yi, S. V. (2021). Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation. Proceedings of the Royal Society B, 288(1945), 20202244.
  2. Plagge, A., Gordon, E., Dean, W., Boiani, R., Cinti, S., Peters, J., & Kelsey, G. (2004). The imprinted signaling protein XLαs is required for postnatal adaptation to feeding. Nature genetics, 36(8), 818-826.
  3. Suzuki, S., Shaw, G., Kaneko-Ishino, T., Ishino, F., & Renfree, M. B. (2011). The evolution of mammalian genomic imprinting was accompanied by the acquisition of novel CpG islands. Genome Biology and Evolution, 3, 1276-1283.