Functional Consequences of Splicing of the Antisense Transcript COOLAIR on FLC Transcription

Summary

Antisense transcription is widespread in many genomes; however, how much is functional is hotly debated. We are investigating functionality of a set of long noncoding antisense transcripts, collectively called COOLAIR, produced at Arabidopsis FLOWERING LOCUS C ( FLC). COOLAIR initiates just downstream of the major sense transcript poly(A) site and terminates either early or extends into the FLC promoter region. We now show that splicing of COOLAIR is functionally important. This was revealed through analysis of a hypomorphic mutation in the core spliceosome component PRP8. The prp8 mutation perturbs a cotranscriptional feedback mechanism linking COOLAIR processing to FLC gene body histone demethylation and reduced FLC transcription. The importance of COOLAIR splicing in this repression mechanism was confirmed by disrupting COOLAIR production and mutating the COOLAIR proximal splice acceptor site. Our findings suggest that altered splicing of a long noncoding transcript can quantitatively modulate gene expression through cotranscriptional coupling mechanisms.

Graphical Abstract

Highlights

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  Alternative splicing of noncoding antisense transcripts affects flowering

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  Arabidopsis FLC gene transcription modulated by lncRNA isoforms

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  Positive feedback links chromatin state and antisense transcript splicing

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  Quantitative gene regulation by coupling antisense splicing to chromatin states

Abstract

Marquardt et al. demonstrate that noncoding transcripts antisense to the Arabidopsis floral repressor gene FLC are alternatively spliced. Interfering with this alternative splicing alters FLC transcription quantitatively and affects the timing of flowering. Thus, this work reveals a function for a long noncoding antisense transcript in Arabidopsis.