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bioRxiv · 10.1101/2025.07.14.664778

Ancient retrotransposon-derived promoters for mammalian genomic imprinting

Kim, J.
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Abstract

In mammalian genomic imprinting, RNA Pol II-driven transcription by upstream alternative promoters is responsible for establishing gametic DNA methylation on downstream Imprinting Control Regions (ICRs). According to surveys on germ cell transcripts, the alternative promoters for paternally expressed PEG3, MEST and PLAGL1 are evolutionarily conserved and transcriptionally active mainly in the oocytes of the mammalian species. These promoters are usually bi-directional, producing transcripts in both directions. Furthermore, these alternative promoters are either part of or closely associated with the ancient retrotransposons that have inserted into the genomes more than 100 million years ago. The oocyte-specific alternative promoter of human SNRPN and the promoter of mammalian AIRN are also believed to have originated from the ancient transposon of similar evolutionary ages. These results are overall consistent with the well-known properties of retrotransposons, de-repression and transcriptional activity in germ cells. This further suggests that ancient retrotransposons may have been co-opted as cis-regulatory elements for establishing DNA methylation for genomic imprinting.

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Kim, J.. 2025-07-18. Ancient retrotransposon-derived promoters for mammalian genomic imprinting. https://doi.org/10.1101/2025.07.14.664778

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