Chromatin retained MUSHER lncRNA integrates ABA and DOG1 signalling pathways to enhance Arabidopsis seeds dormancy.

Many plant lncRNAs regulate gene expression by binding to chromatin, but how they are retained at the target loci is unclear. We identify a new, chromatin-localized lncRNA - MUSHER, which activates two parallel regulatory pathways to increase Arabidopsis seed dormancy. MUSHER is upregulated in response to high temperatures, contributing to the induction of secondary dormancy. It promotes DOG1 expression by recruitment of the CPSF complex to enhance the proximal cleavage and polyadenylation at the DOG1 transcript. It also increases ABA sensitivity in seeds by activating PIR1 gene transcription. These genes, located on different chromosomes, are both bound by MUSHER, despite lacking sequence homology. The chromatin association of MUSHER enables the integration of the DOG1- and ABA pathways to adjust seed germination timing. Additionally, MUSHER and other lncRNAs interact with U1 snRNP, which is required for their chromatin localisation, revealing a novel function of U1 snRNP in plants. Overall design: 3'RNA-seq: Comparison of Col-0 and msh-1 mutant siliques transcriptomes (13-20 days after pollination - four biological replicas). ChIRP-seq: Chromatin Isolation by RNA Purification using MUSHER probes for Col-0 and msh-1 mutant siliques (13-20 days after pollination - two biological replicas). For Col-0 samples, lacZ probes were used as a negative control. Each sample used for purification with probes has a sequenced input sample. ChIDP-seq: Chromatin Isolation by DNA Purification was employed to identify genomic regions physically interacting with the PIR1 locus using PIR1 probes and Col-0 siliques (13-20 days after pollination - two biological replicas). Samples used for purification with the PIR1 probe have a sequenced input samples.