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Background  Genomic imprinting leads to maternal expression of  IGF2R  in both mouse and opossum. In mouse, the antisense long noncoding (lnc) RNA  Airn,  which is paternally expressed from the differentially methylated region (DMR) in the second intron of  Igf2r,  is required to silence the paternal  Igf2r . In opossum, however, intriguingly, the DMR was reported to be in a different downstream intron (intron 11) and there was no antisense lncRNA detected in previous analyses. Therefore, clarifying the imprinting mechanism of marsupial  IGF2R  is of great relevance for understanding the origin and evolution of genomic imprinting in the  IGF2R  locus. Thus, the antisense lncRNA associated with the marsupial DMR can be considered as the ‘missing link’. In this study, we identified a novel antisense lncRNA,  ALID,  after detailed analysis of the  IGF2R  locus in an Australian marsupial, the tammar wallaby,  Macropus eugenii , and compared it to that of the grey short-tailed opossum,  Monodelphis domestica.Results  Tammar  IGF2R  showed maternal expression and had a maternally methylated CpG island (CGI) in intron 12 as well as a promoter CGI without differential methylation, but none in the second intron. Re-analysis of the  IGF2R  of opossum detected the CGI in intron 12, not intron 11, as previously reported, confirming that the DMR in intron 12 is conserved between these marsupials and so is the putative imprinting control region of marsupial  IGF2R .  ALID  is paternally expressed from the middle of the DMR and is approximately 650 bp long with a single exon structure that is extremely short compared to  Airn . Hence, the lncRNA transcriptional overlap of the  IGF2R  promoter, which is essential for the  Igf2r  silencing in the mouse, is likely absent in tammar. This suggests that fundamental differences in the lncRNA-based silencing mechanisms evolved in eutherian and marsupial  IGF2R  and may reflect the lack of differential methylation in the promoter CGI of marsupial  IGF2R .    Conclusions  Our study thus provides the best candidate factor for establishing paternal silencing of marsupial  IGF2R  without transcriptional overlap, which is distinct from the  Igf2r  silencing mechanism of  Airn,  but which may be analogous to the mode of action for the flanking  Slc22a2  and  Slc22a3  gene silencing in the mouse placenta.    Electronic supplementary material  The online version of this article (10.1186/s13072-018-0227-8) contains supplementary material, which is available to authorized users.

Identification of a novel antisense noncoding RNA, ALID, transcribed from the putative imprinting control region of marsupial IGF2R