mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth

Lin, D. H.; Elcavage, L. E.; Khalizeva, E.; Bartel, D. P.

doi:10.1101/2025.11.06.686990

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bioRxiv · 10.1101/2025.11.06.686990

mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth

Lin, D. H.·Elcavage, L. E.·Khalizeva, E.·Bartel, D. P.

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Abstract

MicroRNAs direct downregulation of target mRNAs. Sometimes, however, this regulatory paradigm inverts, and a target RNA triggers the degradation of a microRNA. This target-directed microRNA degradation (TDMD) requires ZSWIM8. Zswim8-/- mice exhibit reduced growth and perinatal lethality, accompanied by stabilization of dozens of microRNAs. Nonetheless, studies of TDMD function in mammals have been limited because only two TDMD-triggering RNAs have been identified in mice. Here, we computationally identify and validate five new TDMD-triggering sites in mouse models. One site in Atp6v1g1 and two in Lpar4 direct degradation of miR-335-3p, which shows that in mammals, two sites in the same transcript, and multiple sites in different transcripts, can collaborate to destabilize a microRNA. Moreover, sites in Plagl1 and Lrrc58 direct degradation of miR-322 and miR-503, respectively. Mice lacking the Plagl1 and Lrrc58 sites exhibit reduced growth, demonstrating that target-directed degradation of miR-503 and miR-322 promotes mammalian growth. Both miR-335-3p and Plagl1 are maternally imprinted, implying that they participate in parental conflict, but their corresponding triggers or target microRNA partner are not imprinted. Thus, 3' UTRs directly participate in parental conflict by engaging TDMD to access an additional layer of regulation within a network of imprinted and biallelic genes.

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Lin, D. H., Elcavage, L. E., Khalizeva, E., Bartel, D. P.. 2025-11-06. mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth. https://doi.org/10.1101/2025.11.06.686990

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