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

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

PROVIDER: PRJNA588412 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10423078_1.fastq.gz	Fastqsanger.gz
	SRR10423078_2.fastq.gz	Fastqsanger.gz
	SRR10423079_1.fastq.gz	Fastqsanger.gz
	SRR10423079_2.fastq.gz	Fastqsanger.gz

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Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (stranded-RNA-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 | GSE140139 | GEO

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 (RNA-seq)

Project description: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 (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 (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 (smallRNA-seq)

2019-11-09 | GSE140138 | GEO

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

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Identification of protein-coding and intronic noncoding RNAs down-regulated in clear cell renal carcinoma

Project description:The clear cell subtype of renal cell carcinoma (RCC) is the most lethal and prevalent cancer of the urinary system. To investigate the molecular changes associated with malignant transformation in clear cell RCC, the gene expression profiles of matched samples of tumor and adjacent non-neoplastic tissue were obtained from 6 patients. A custom-built cDNA microarray platform was used, comprising 2,292 probes that map to exons of genes and 822 probes for noncoding RNAs mapping to intronic regions. Intronic transcription was detected in all normal and neoplastic renal tissues. A subset of 55 transcripts was significantly down-regulated in clear cell RCC relative to the matched non-tumor tissue as determined by a combination of two statistical tests and leave-one-out patient cross-validation. Among the down-regulated transcripts, 49 mapped to untranslated or coding exons and 6 were intronic relative to known exons of protein-coding genes. Lower levels of expression of SIN3B, TRIP3, SYNJ2BP and NDE1 (p < 0.02), and of intronic transcripts derived from SND1 and ACTN4 loci (p < 0.05), were confirmed in clear cell RCC by Real-time RT-PCR. A subset of 25 transcripts was deregulated in additional 6 non-clear cell RCC samples, pointing to common transcriptional alterations in RCC irrespective of the histological subtype or differentiation state of the tumor. Our results indicate a novel set of tumor suppressor gene candidates, including noncoding intronic RNAs, which may play a significant role in malignant transformations of normal renal cells. Fluorescently labeled cDNA targets derived from tumor and non-tumor tissue from each patient were combined and hybridized to spotted cDNA microarrays. For each patient, a replicate hybridization with dye-swap of labeled targets was performed. For each tissue (tumor and adjacent non-tumor tissue), there are 4 replicate mesurements for each probe.

2010-06-25 | E-GEOD-7367 | biostudies-arrayexpress

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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