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TranscriptomicsRegulatory impact of RNA secondary structure across the Arabidopsis thaliana transcriptome
The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, processing, and functionality. However, the global influence of this feature on plant gene expression is still for the most part unclear. Here, we use a high-throughput, sequencing-based, structure-mappi...
ORGANISM(S): Arabidopsis thaliana 
2012-11-15 | E-GEOD-40209 | biostudies-arrayexpress
GenomicsRNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes
Transcriptional gene silencing controls transposons and other repetitive elements through RNA-directed DNA methylation (RdDM) and heterochromatin formation. A key component of the Arabidopsis RdDM pathway is ARGONAUTE4 (AGO4), which associates with sizs to mediate DNA methylation. Here, we show that...
ORGANISM(S): Arabidopsis thaliana 
2012-10-17 | E-GEOD-35381 | biostudies-arrayexpress
TranscriptomicsGlobal analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
Post-transcriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure, and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus has yet to be compiled for any or...
ORGANISM(S): Arabidopsis thaliana 
2014-12-16 | E-GEOD-58974 | biostudies-arrayexpress
TranscriptomicsChemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans
Post-transcriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as transfer RNAs (tRNAs), growing evidence indicates that messenger RNAs...
ORGANISM(S): Homo sapiens 
2015-10-31 | E-GEOD-66224 | biostudies-arrayexpress
TranscriptomicsDCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis (RNA-seq)
MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) negatively regulate their targets by 1) repressing translation, 2) endonucleolytic RNA cleavage, or 3) DNA methylation resulting in transcriptional silencing. P-body/decapping components are likely required for translational repression, but are ...
ORGANISM(S): Arabidopsis thaliana 
2013-08-16 | E-GEOD-28509 | biostudies-arrayexpress
TranscriptomicsDCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis (smRNA-seq)
MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) negatively regulate their targets by 1) repressing translation, 2) endonucleolytic RNA cleavage, or 3) DNA methylation resulting in transcriptional silencing. P-body/decapping components are likely required for translational repression, but are ...
ORGANISM(S): Arabidopsis thaliana 
2013-08-16 | E-GEOD-28512 | biostudies-arrayexpress
TranscriptomicsHighly integrated epigenome maps in Arabidopsis - methylcytosine immunoprecipitation
Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: methylcytosine ChIP-chip on tiling array Identification of cytosine DNA methylation by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays for wildtype Columbia-0.
ORGANISM(S): Arabidopsis thaliana 
2008-04-20 | E-GEOD-10969 | biostudies-arrayexpress
GenomicsHighly integrated single base resolution maps of the epigenome in Arabidopsis
Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosin...
ORGANISM(S): Arabidopsis thaliana 
2008-04-20 | E-GEOD-10877 | biostudies-arrayexpress
GenomicsHighly integrated epigenome maps in Arabidopsis - whole genome shotgun bisulfite sequencing
Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Gene...
ORGANISM(S): Arabidopsis thaliana 
2008-04-21 | E-GEOD-10966 | biostudies-arrayexpress
TranscriptomicsHighly integrated epigenome maps in Arabidopsis - small RNA sequencing
Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput small RNA sequencing Small RNA sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
ORGANISM(S): Arabidopsis thaliana 
2008-04-20 | E-GEOD-10967 | biostudies-arrayexpress
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