PhD Student: Procedure no. DSMBBC/2027/01: Chromatin-Associated lncRNAs in Regulating Transcription and Dormancy in Seeds

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Testo originale dell'annuncio (in inglese)

Seed dormancy is a vital adaptive trait allowing seeds to ignore transiently favourable conditions, thereby optimising survival and plant fitness. Its tight regulation involves a complex interplay between genetic, hormonal, and environmental factors. Key among these are the DELAY OF GERMINATION 1 (DOG1) gene and the abscisic acid (ABA) pathway. Our recent discoveries, published in Nature Communications, highlight non-coding RNAs as pivotal regulatory elements, yet their specific mechanisms of integration remain incompletely explored and, in fact, raised many interesting questions. We demonstrated that MUSHER, expressed downstream of DOG1 , enhances DOG1 expression by facilitating termination at the proximal poly (A) site via CPSF recruitment. Contrastingly, MUSHER binds the PIR1 promoter (an E3 ubiquitin ligase positively regulating the ABA signalling pathway), thereby mediating chromatin activation and Pol II recruitment, impacting the ABA response. One promising avenue of research will be to understand how MUSHER coordinates seed dormancy by directly regulating DOG1 and PIR1 in response to diverse environmental cues. This will include physiological, genetic, and molecular analyses combining CRISPR mutagenesis, transcriptomics, chromatin immunoprecipitation, and spatial genomics to resolve the functional consequences of MUSHER’s interactions. Another focus will be to clarify the nuclear retention mechanisms of MUSHER and related long non-coding RNAs (lncRNAs). Our preliminary findings implicate that both factors contribute to anchoring MUSHER to chromatin, thereby enabling its regulatory activity. Through ChIP-seq and RNA-protein interaction assays, this work will define the requirements for chromatin association and their impact on lncRNA-mediated gene regulation. Overall, these studies will provide the mechanistic insight into lncRNA-chromatin retention in plants, clarify the molecular logic of seed dormancy integration, and uncover the extent of lncRNA contribution to adaptive seed behaviour. The question to address during your PhD project may be: How do modifications at the 3' end of non-coding transcripts direct their localisation, and what effect do they have on seed function? Together, we will do our best to better understand the mechanisms underlying lncRNA-chromatin interactions.