LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis

Author:

Jin Yu1ORCID,Ivanov Maxim1ORCID,Dittrich Anna Nelson2,Nelson Andrew DL2ORCID,Marquardt Sebastian1ORCID

Affiliation:

1. Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre University of Copenhagen Frederiksberg Denmark

2. Boyce Thompson Institute Cornell University Ithaca NY USA

Abstract

AbstractHow the noncoding genome affects cellular functions is a key biological question. A particular challenge is to distinguish the effects of noncoding DNA elements from long noncoding RNAs (lncRNAs) that coincide at the same loci. Here, we identified the flowering‐associated intergenic lncRNA (FLAIL) in Arabidopsis through early flowering flail mutants. Expression of FLAIL RNA from a different chromosomal location in combination with strand‐specific RNA knockdown characterized FLAIL as a trans‐acting RNA molecule. FLAIL directly binds to differentially expressed target genes that control flowering via RNA–DNA interactions through conserved sequence motifs. FLAIL interacts with protein and RNA components of the spliceosome to affect target mRNA expression through co‐transcriptional alternative splicing (AS) and linked chromatin regulation. In the absence of FLAIL, splicing defects at the direct FLAIL target flowering gene LACCASE 8 (LAC8) correlated with reduced mRNA expression. Double mutant analyses support a model where FLAIL‐mediated splicing of LAC8 promotes its mRNA expression and represses flowering. Our study suggests lncRNAs as accessory components of the spliceosome that regulate AS and gene expression to impact organismal development.

Funder

Carlsbergfondet

European Research Council

National Science Foundation

Novo Nordisk Fonden

Publisher

Springer Science and Business Media LLC

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,Molecular Biology,General Neuroscience

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