Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide measurement of RNA folding energies

ABSTRACT: RNA structural transitions are important in the function and regulation of RNAs. Here, we reveal a layer of transcriptome organization in the form of RNA folding energies. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in over 4000 transcripts. Specific signatures of RNA Tm demarcated the polarity of mRNA open reading frames, and highlighted numerous candidate regulatory RNA motifs in 3' untranslated regions. RNA Tm distinguished non-coding versus coding RNAs, identified mRNAs with distinct cellular functions. We identified thousands of putative RNA thermometers, and their presence is predictive of the pattern of RNA decay in vivo during heat shock. The exosome complex recognizes unpaired bases during heat shock to degrade these RNAs, coupling intrinsic structural stabilities to gene regulation. Thus, genome-wide structural dynamics of RNA can parse functional elements of the transcriptome and reveal diverse biological insights. RNA structure probing at 5 different temperatures (23M-BM-0C , 30M-BM-0C , 37M-BM-0C , 55M-BM-0C and 75M-BM-0C) using RNase V1 on polyA-selected log phase S288C yeast RNAs was followed by library construction using a modified SOLiD small RNA cloning kit and deep sequencing on the SOLiD platform. We performed 2 biological replicates for each temperature.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Kun Qu

PROVIDER: E-GEOD-39680 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide measurement of RNA folding energies.

Wan Yue Y Qu Kun K Ouyang Zhengqing Z Kertesz Michael M Li Jun J Tibshirani Robert R Makino Debora L DL Nutter Robert C RC Segal Eran E Chang Howard Y HY

Molecular cell 20120913 2

RNA structural transitions are important in the function and regulation of RNAs. Here, we reveal a layer of transcriptome organization in the form of RNA folding energies. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in over 4000 transcripts. Specific signatures of RNA Tm demarcated the polarity of mRNA open reading frames and highlighted numerous candidate regulatory RNA motifs in 3' untranslated regions. RNA Tm dis ...[more]

PMID: 22981864

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Project description:Transcription factors direct gene expression, and so there is much interest in mapping their genome-wide binding locations. M-BM- Current methods do not allow for the multiplexed analysis of TF binding, and this limits their throughput. We describe a novel method for determining the genomic target genes of multiple transcription factors simultaneously. DNA-binding proteins are endowed with the ability to direct transposon insertions into the genome near to where they bind. The transposon becomes a M-bM-^@M-^\Calling CardM-bM-^@M-^] marking the visit of the DNA-binding protein to that location. A unique sequence M-bM-^@M-^\barcodeM-bM-^@M-^] in the transposon matches it to the DNA-binding protein that directed its insertion. The sequences of the DNA flanking the transposon (which reveal where in the genome the transposon landed) and the barcode within the transposon (which identifies the TF that put it there) are determined by massively-parallel DNA sequencing. To demonstrate the methodM-bM-^@M-^Ys feasibility, we determined the genomic targets of eight transcription factors in a single experiment. The Calling Card method promises to significantly reduce the cost and labor needed to determine the genomic targets of many transcription factors in different environmental conditions and genetic backgrounds. These data contain Ty5 insertion sites mapped by an Illumina GAII analyzer in the S. cerevisiae genome for the background strain without any Sir4 present (1 run), in strains expressing Sir4-tagged copies of three well-characterized TFs: Gal4, Leu3, and Gcn4 (1 run each), and a multiplex of eight Sir4-tagged TFs pooled in a single experiment (2 biological replicates), and insertions from the Thi2-Sir4 fusion expressed from its native locus in two conditions (1 run each). The format of each insertions file is [chromosome number] [position of genomic base] [direction of insertion] [number of reads at that position]. Raw sequencing data comes in two varieties. Paired-end data contains a 5 bp barcode at the beginning of read #2. Single-end data contains a 2 bp barcode on the beggining of read #1.

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Genome-wide measurement of RNA folding energies

Publications

Genome-wide measurement of RNA folding energies.

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