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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE140140 | GEO | 2019/11/09

REPOSITORIES: GEO

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Exogenously overexpressed intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis.

Project description:Involvement of long non-coding RNAs (lncRNAs) in the regulation of gene expression in cis has been well studied in eukaryotes but relatively little is known whether and how lncRNAs affect gene expression in tans. In Arabidopsis thaliana, COLDAIR, a previously reported lncRNA, is produced from the first intron of FLOWERING LOCUS C (FLC), which encodes a repressor of flowering time. Our results indicated that the exogenously overexpressed COLDAIR enhances the expression of FLC in trans, resulting in a late-flowering phenotype. In 35S-COLDAIR lines, the enhanced expression of FLC is correlated with the down-regulation of the repressive histone mark H3K27me3 and with the up-regulation of the active histone mark H3K4me3 at the FLC chromatin. Furthermore, we demonstrated that overexpression of intronic lncRNAs from several other H3K27me3-enriched MADS-box genes also activates the expression of their host genes. This study suggests that the involvement of overexpressed intronic lncRNAs in gene activation may be conserved in H3K27me3-enriched genes in eukaryotes.

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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (smallRNA-seq)

Project description:Intronic RNAs are spliced from precursor-messenger RNAs and are usually subjected to degradation in eukaryotes. COLDAIR, a previously reported intronic long noncoding RNA (lncRNA), is produced from the first intron of a MADS-box gene, Flowering Locus C (FLC), which encodes a repressor of flowering time. Here we show that overexpression of a foreign COLDAIR sequence causes enhanced expression of FLC in trans, resulting in a late-flowering phenotype. In COLDAIR-overexpression lines, enhanced expression of FLC is correlated with up-regulation of the active histone mark H3K4me3 and down-regulation of the repressive histone mark H3K27me3. We demonstrate that overexpression of COLDAIR makes the corresponding FLC intronic region accessible to the histone H3K4 methyltransferase ATX1 but exclusive to the histone H3K27 methyltransferase CLF. Furthermore, we demonstrate that overexpression of intronic lncRNAs from many other MADS-box genes also activate the expression of their host genes in trans, suggesting that intronic lncRNAs act as enhancer RNAs in many MADS-box genes. Considering that MADS-box genes are highly conserved in multicellular eukaryotes, we suggest that involvement of intronic lncRNAs from MADS-box genes in gene activation may represent an evolutionarily conserved mechanism.

2019-11-09 | GSE140138 | GEO

Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (RNA-seq)

2019-11-09 | GSE140137 | GEO

Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (ChIP-seq)

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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (stranded-RNA-seq)

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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis

Project description:Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis

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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (smallRNA-seq)

Project description:Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (smallRNA-seq)

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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (RNA-seq)

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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (ChIP-seq)

Project description:Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (ChIP-seq)

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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (stranded-RNA-seq)

Project description:Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (stranded-RNA-seq)

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