Pseudouridine guides germline small RNA transport and epigenetic inheritance

Rowan P Herridge; Jakub Dolata; Valentina Migliori; Cristiane de Santis Alves; Filipe Borges; Andrea J Schorn; Frédéric van Ex; Ann Lin; Mateusz Bajczyk; Jean-Sebastien Parent; Tommaso Leonardi; Alan Hendrick; Tony Kouzarides; Robert A Martienssen

doi:10.1038/s41594-024-01392-6

Pseudouridine guides germline small RNA transport and epigenetic inheritance

Nat Struct Mol Biol. 2024 Sep 6. doi: 10.1038/s41594-024-01392-6. Online ahead of print.

Authors

Rowan P Herridge^#^{1

2}, Jakub Dolata^#^{1

3}, Valentina Migliori^#^{4

5}, Cristiane de Santis Alves^#¹, Filipe Borges^{1

6}, Andrea J Schorn¹, Frédéric van Ex^{1

7}, Ann Lin^{1

8}, Mateusz Bajczyk³, Jean-Sebastien Parent^{1

9}, Tommaso Leonardi^{4

10}, Alan Hendrick¹¹, Tony Kouzarides¹², Robert A Martienssen¹³

Affiliations

¹ Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
² Department of Biochemistry, University of Otago, Dunedin, New Zealand.
³ Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
⁴ Gurdon Institute, University of Cambridge, Cambridge, UK.
⁵ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
⁶ CNRS, INRA Versailles, Versailles, France.
⁷ Inari LLC, Ghent, Belgium.
⁸ Stanford University, Stanford, CA, USA.
⁹ Agriculture Canada, Ottawa, Ontario, Canada.
¹⁰ Center for Genomic Science of IIT@SEMM, Instituto Italiano di Tecnologia (IIT), Milan, Italy.
¹¹ Storm Therapeutics, Ltd., Moneta Building (B280), Babraham Research Campus, Cambridge, UK.
¹² Gurdon Institute, University of Cambridge, Cambridge, UK. t.kouzarides@gurdon.cam.ac.uk.
¹³ Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. martiens@cshl.edu.

^# Contributed equally.

PMID: 39242979
DOI: 10.1038/s41594-024-01392-6

Abstract

Developmental epigenetic modifications in plants and animals are mostly reset during gamete formation but some are inherited from the germline. Small RNAs guide these epigenetic modifications but how inherited small RNAs are distinguished in plants and animals is unknown. Pseudouridine (Ψ) is the most abundant RNA modification but has not been explored in small RNAs. Here, we develop assays to detect Ψ in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs. Germline small RNAs, namely epigenetically activated small interfering RNAs (easiRNAs) in Arabidopsis pollen and Piwi-interacting RNAs in mouse testes, are enriched for Ψ. In pollen, pseudouridylated easiRNAs are transported to sperm cells from the vegetative nucleus, and PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with Ψ and is required for this transport. We further show that Exportin-t is required for the triploid block: small RNA dosage-dependent seed lethality that is epigenetically inherited from pollen. Thus, Ψ has a conserved role in marking inherited small RNAs in the germline.