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Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

ABSTRACT: Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions play important roles in key biological processes.Analysis of published transcriptom datasets suggested some lincRNAs may be regulated by SERRATE,CBP20 and CBP80 in Arabidopsis. To further investigate the regulation, we use Arabidopsis lincRNA arrays v1 to detect lincRNA expression in se-2 and cbp20/80 double mutants.We found the expression levels of 940 lincRNAs (20%) out of the 4,634 lincRNAs with probes in array were significantly alerted in all mutants (P-value of eBays ANOVA < 0.05 & fold change of signal intensity > 2). This group included 525 up-regulated and 415 down-regulated lincRNAs.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE35963 | GEO | 2012/09/29

SECONDARY ACCESSION(S): PRJNA152059

REPOSITORIES: GEO

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Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

Project description:Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions play important roles in key biological processes.Analysis of published transcriptom datasets suggested some lincRNAs may be regulated by SERRATE,CBP20 and CBP80 in Arabidopsis. To further investigate the regulation, we use Arabidopsis lincRNA arrays v1 to detect lincRNA expression in se-2 and cbp20/80 double mutants.We found the expression levels of 940 lincRNAs (20%) out of the 4,634 lincRNAs with probes in array were significantly alerted in all mutants (P-value of eBays ANOVA < 0.05 & fold change of signal intensity > 2). This group included 525 up-regulated and 415 down-regulated lincRNAs. Seedlings(Col-0), Seedlings(se-2), Seedlings(cbp20,80 double mutant) x 3 biological replicates

2012-09-29 | E-GEOD-35963 | biostudies-arrayexpress

Transcriptome of SE, CBP20 and CBP80 mutants

Project description:This dataset includes the transcriptomes of plants bearing mutations in genes enconding for three related Arabidopsis proteins: SERRATE (SE), CAP-BINDING PROTEIN 20 (CBP20) and CAP-BINDING PROTEIN 80 (CBP80). The transcriptomes were obtained by mRNA sequencing. Comparison of the RNA accumulation patterns will enable the idenfication of common patterns and uncover possible common functions of SE, CBP20 and CBP80 in regulating gene expression.

2018-01-01 | GSE99367 | GEO

Dual roles of the nuclear cap binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis

Project description:The processing of Arabidopsis thaliana microRNAs (miRNAs) from longer primary transcripts (pri-miRNAs) requires the activity of several proteins, including DICER-LIKE1 (DCL1), the double stranded RNA binding protein HYPONASTIC LEAVES1 (HYL1), and the zinc finger protein SERRATE (SE). It has been noted before that the morphological appearance of weak se mutants is reminiscent of plants with mutations in ABH1/CBP80 and CBP20, which encode the two subunits of the nuclear cap-binding complex. We report that, like SE, the cap-binding complex is necessary for proper processing of pri-miRNAs. Inactivation of either ABH1/CBP80 or CBP20 results in decreased levels of mature miRNAs accompanied by increased levels of pri-miRNAs. Whole genome tiling array analyses reveal that se, abh1/cbp80 and cbp20 mutants also share similar pre-mRNA splicing defects, leading to the accumulation of many partially spliced transcripts. This is unlikely to be an indirect consequence of improper miRNA processing or other mRNA turnover pathways, since introns retained in se, abh1/cbp80 and cbp20 mutants are not affected by mutations in other genes required for miRNA processing or for non-sense-mediated mRNA decay. Taken together, our results uncover dual roles in splicing and miRNA processing that distinguish SE and the cap-binding complex from specialized miRNA processing factors such as DCL1 and HYL1. Keywords: Tiling array analysis of RNA populations from wild type, se, abh1 and cbp20 mutants

2008-05-01 | GSE11043 | GEO

Arabidopsis thaliana

Project description:Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

| PRJNA152059 | ENA

Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

Project description:Long intergenic noncoding RNAs (lincRNA) transcribed from intergenic regions of eukaryotic genomes play important roles in key biological processes; yet, plant lincRNAs remain poorly characterized. Here we profiled lincRNA expression in inflorescences, leaves and roots using ATH lincRNA v1 array. we found 92% lincRNAs could be detected in at least 2 ATH lincRNA v1 arrays and majority of the lincRNAs were expressed at levels higher than those of pri-miRNAs but lower than those of mRNAs.Using a cut-off of 2-fold change, we identified 149 lincRNAs preferentially expressed in inflorescences, 232 in leaves and 164 in roots.

2011-08-06 | GSE30394 | GEO

Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

2011-08-05 | E-GEOD-30394 | biostudies-arrayexpress

Ethylene induced phosphorylation of CBP20 is involved in root growth [RNA-seq]

Project description:We report that CBP20 phosphorylation can regulate root growth in ethylene. We examined the gene expression in roots and shoots of wild type (Col) and cbp20 mutant (in Col background). Ethylene is one of the most essential hormones for plant developmental processes and stress responses. EIN2 is a key factor in ethylene signaling pathway and its function is regulated by phosphorylation. However, the phosphorylation regulation in the ethylene signaling pathway is largely unknown. Here we report the phosphorylation of CBP20 is regulated by ethylene, and the phosphorylation is involved in root elongation. The constitutive phosphorylation format of CBP20 rescues the cbp20 root ethylene hyposensitive phenotype, while the constitutive de-phosphorylation format of CBP20 is unable to rescue the root phenotype of cbp20 in response to ethylene. Genome wide study on ethylene regulated gene expression and microRNA expression in the roots and shoots of both Col and cbp20, together with the result of genetics validation suggest that ethylene induced phosphorylation of CBP20 is involved in root growth and one pathway is through the regulation of microRNAs and their target genes in roots.

2016-10-31 | GSE83573 | GEO

Ethylene induced phosphorylation of CBP20 is involved in root growth [small RNA-seq]

Project description:We report that CBP20 phosphorylation can regulate root growth in ethylene. We examined the small RNA expression in roots and shoots of wild type (Col) and cbp20 mutant (in Col background). Ethylene is one of the most essential hormones for plant developmental processes and stress responses. EIN2 is a key factor in ethylene signaling pathway and its function is regulated by phosphorylation. However, the phosphorylation regulation in the ethylene signaling pathway is largely unknown. Here we report the phosphorylation of CBP20 is regulated by ethylene, and the phosphorylation is involved in root elongation. The constitutive phosphorylation format of CBP20 rescues the cbp20 root ethylene hyposensitive phenotype, while the constitutive de-phosphorylation format of CBP20 is unable to rescue the root phenotype of cbp20 in response to ethylene. Genome wide study on ethylene regulated gene expression and microRNA expression in the roots and shoots of both Col and cbp20, together with the result of genetics validation suggest that ethylene induced phosphorylation of CBP20 is involved in root growth and one pathway is through the regulation of microRNAs and their target genes in roots.

2016-10-31 | GSE83574 | GEO

Next generation sequencing on knockdown of AC093323.3 in lung cancer cells

Project description:In this study we predict functionally important long intergenic non-coding RNAs (lincRNAs) with a role in core essential processes in human. One of the candidate lincRNA, AC093323.3, was experimentally verified to affect cell viability. We performed RNASeq on knockdown of AC093323.3 to further investigate the functional role of this lincRNA.

2019-05-26 | GSE115659 | GEO

Identification of Arabidopsis Long Intergenic Noncoding RNA regulated by RNA-dependent RNA polymerase 2 (RDR2)

Project description:RNA-dependent RNA polymerase 2 (RDR2) is a crucial regulator of RNA-directed DNA methylation (RdDM). Recentily RDR2 was reported to regulate expression of long intergenic noncoding RNAs. Here we used ATH lincRNA v1 expression arrays to compare lincRNA expression in inflorescence tissues of rdr2-1 and WT. Among the 4,634 lincRNAs detected we found that more than 34% of them were differentially expressed, including 676 lincRNAs that were up-regulated and 890 down-regulated in rdr2-1.

2011-08-06 | GSE30395 | GEO

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