Genome-scale deconvolution of RNA structure ensembles
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PROVIDER: PRJNA663861 | ENA |
REPOSITORIES: ENA
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Project description:The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale. RNA sample was treated with one of two structure-specific enzymes (RNase V1 or RNase S1). Four independent V1 experiments and three independent S1 experiments were carried out. Processed data file linked below. Data processing involves merging (or rather log-ratio-ing) the 7 lanes of SOLiD sequencing data against each other. Also linked below are the genome and transcriptome FASTA files used for mapping, and the annotation file having the format: gene_ID, chromosome, start, end, feature. Start and end are 1-based; feature is "Transcript" for the entire transcript (including introns), "Intron", "Exon", "5UTR" or "3UTR". Genome-wide measurement of RNA secondary structure in yeast, Kertesz et al., Nature Volume:467, Pages:103-107, Date published:(02 September 2010) http://www.nature.com/nature/journal/v467/n7311/abs/nature09322.html
2010-08-24 | E-GEOD-22393 | biostudies-arrayexpress
Project description:The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.
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Project description:The stable formation of remote fear memories is thought to require neuronal gene induction in cortical ensembles that are activated during learning. However, the set of genes expressed specifically in these activated ensembles is not known; knowledge of such transcriptional profiles may offer insights into the molecular program underlying stable memory formation. Here we use RNA-Seq to identify genes whose expression is enriched in activated cortical ensembles labeled during associative fear learning. We first establish that mouse temporal association cortex (TeA) is required for remote recall of auditory fear memories. We then perform RNA-Seq in TeA neurons that are labeled by the activity reporter Arc-dVenus during learning. We identify 944 genes with enriched expression in Arc-dVenus+ neurons. These genes include markers of L2/3, L5b, and L6 excitatory neurons but not glial or inhibitory markers, confirming Arc-dVenus to be an excitatory neuron-specific, layer non-specific activity reporter. Cross comparisons to other transcriptional profiles show that 125 of the enriched genes are also activity-regulated in vitro or induced by visual stimulus in the visual cortex, suggesting that they may be induced generally in the cortex in an experience-dependent fashion. Prominent among the enriched genes are those encoding potassium channels that down-regulate neuronal activity, suggesting the possibility that part of the molecular program induced by fear conditioning may initiate homeostatic plasticity.
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Project description:Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. patens undergoes large scale shifts in RNA secondary structure and RBP-RNA interactions as well as identify sites of RBP-RNA interaction and describe enriched motifs, among which are two purine rich sequences. We further elucidate the collection of proteins that bind to these sequences, among which are P. patens cold shock containing proteins. Together, the data suggest that P. patens undergoes a large-scale change in RNA secondary structure and RBP binding as a response to ABA and also identifies CSPs as well as several other proteins as possible regulators of that response.
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Project description:Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. patens undergoes large scale shifts in RNA secondary structure and RBP-RNA interactions as well as identify sites of RBP-RNA interaction and describe enriched motifs, among which are two purine rich sequences. We further elucidate the collection of proteins that bind to these sequences, among which are P. patens cold shock containing proteins. Together, the data suggest that P. patens undergoes a large-scale change in RNA secondary structure and RBP binding as a response to ABA and also identifies CSPs as well as several other proteins as possible regulators of that response.
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