LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis
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LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis. / Jin, Yu; Ivanov, Maxim; Dittrich, Anna Nelson; Nelson, Andrew D.L.; Marquardt, Sebastian.
In: EMBO Journal, Vol. 42, No. 11, e110921, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis
AU - Jin, Yu
AU - Ivanov, Maxim
AU - Dittrich, Anna Nelson
AU - Nelson, Andrew D.L.
AU - Marquardt, Sebastian
N1 - Publisher Copyright: © 2023 The Authors. Published under the terms of the CC BY NC ND 4.0 license.
PY - 2023
Y1 - 2023
N2 - How 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.
AB - How 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.
KW - alternative splicing
KW - chromatin
KW - flowering regulation
KW - gene expression
KW - lncRNA
U2 - 10.15252/embj.2022110921
DO - 10.15252/embj.2022110921
M3 - Journal article
C2 - 37051749
AN - SCOPUS:85152545810
VL - 42
JO - E M B O Journal
JF - E M B O Journal
SN - 0261-4189
IS - 11
M1 - e110921
ER -
ID: 346454261