Poster Presentation ESA-SRB-ANZBMS 2024 in conjunction with ENSA

Evolution of genomic imprinting of IGF2R in marsupial and eutherian mammals (#445)

Trent Newman 1 , Jenna Pride 1 , Quentin Gouil 2 , Lucinda Xiao 2 , Jocelyn A van den Bergen 3 , Katie L Ayers 3 , Teruhito Ishihara 1 , Geoff Shaw 1 , Marilyn B Renfree 1
  1. School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
  2. Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
  3. Genetics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia

The insulin-like growth factor receptor gene (IGF2R) is an important maternally-expressed developmental regulator in eutherians and marsupials. In mice it is regulated by an ~118 kb antisense Igf2r-RNA (Air) transcribed from a differentially methylated region (DMR) in intron 2 which silences paternal Igf2r expression by transcriptional overlap [1]. In tammar wallabies there is an antisense transcript ALID but it is short (~650 bp) and transcribed from a DMR in intron 12 [2]. We investigated ALID in allele-specific IGF2R expression in this marsupial.

We assessed evolution of the IGF2R intragenic CpG island (CGI) using reference genomes. Histone profiling of tammar placenta was done using CUT&RUN. Promoter activity was tested by luciferase assay. To find longer isoforms of ALID we performed long-read cDNA capture-seq of tammar placenta. To detect DNA interactions in 3D we analysed public marsupial Hi-C data.

An IGF2R intragenic CGI was found in therians but not monotremes. The intragenic CGI was 30 kb from the start site in eutherians and 86 kb in marsupials. The tammar intragenic CGI was enriched for active histone 3 lysine 4 tri-methylation and in the reverse orientation promoted luciferase expression 10-fold. Four sequencing reads covered an antisense transcript starting in the intragenic CGI with a final exon by the IGF2R start site. Hi-C interaction mapping showed the intragenic CGI was a boundary for a local domain of interaction with the IGF2R start site and a broader domain containing the maternally expressed solute carrier family 22 member 3 gene (SLC22A3) [3] ~250 kb away.

We conclude that lineage-specific positioning of the IGF2R intragenic DMR evolved early in therians. IGF2R regulation by antisense transcriptional overlap is a possible mechanism in marsupials. Chromatin loops could allow the intragenic IGF2R DMR to cis-regulate transcription of IGF2R and SLC22A3.

 

  1. Latos, P. A., Pauler, F. M., Koerner, M. V., Şenergin, H. B., Hudson, Q. J., Stocsits, R. R., ... & Barlow, D. P. (2012). Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science, 338(6113), 1469-1472.
  2. Suzuki, S., Shaw, G., & Renfree, M. B. (2018). Identification of a novel antisense noncoding RNA, ALID, transcribed from the putative imprinting control region of marsupial IGF2R. Epigenetics & Chromatin, 11, 1-11.
  3. Ishihara, T., Griffith, O. W., Suzuki, S., & Renfree, M. B. (2022). Placental imprinting of SLC22A3 in the IGF2R imprinted domain is conserved in therian mammals. Epigenetics & Chromatin, 15(1), 32.