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  Genome-wide Measurement of RNA Folding Energies

Wan, Y., Qu, K., Ouyang, Z., Kertesz, M., Li, J., Tibshirani, R., et al. (2012). Genome-wide Measurement of RNA Folding Energies. MOLECULAR CELL, 48(2), 169-181. doi:10.1016/j.molcel.2012.08.008.

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 Creators:
Wan, Yue1, Author
Qu, Kun1, Author
Ouyang, Zhengqing1, Author
Kertesz, Michael1, Author
Li, Jun2, 3, 4, Author           
Tibshirani, Robert1, Author
Makino, Debora L.5, Author           
Nutter, Robert C.1, Author
Segal, Eran1, Author
Chang, Howard Y.1, Author
Affiliations:
1external, ou_persistent22              
2Max Planck Institute for Medical Research, ou_1125545              
3Department of Molecular Neurobiology, ou_1497704              
4Rolf Sprengel Group, ou_1497741              
5Conti, Elena / Structural Cell Biology, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565144              

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Free keywords: MESSENGER-RNA; NONCODING RNAS; YEAST-CELLS; EXPRESSION; DEGRADATION; EXOSOME; TRANSCRIPTOME; THERMOMETER; STABILITY; CHROMATIN
 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 noncoding versus coding RNAs and 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.

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Language(s): eng - English
 Dates: 2012-10-26
 Publication Status: Published in print
 Pages: 13
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Degree: -

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Title: MOLECULAR CELL
Source Genre: Journal
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Publ. Info: 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA : CELL PRESS
Pages: - Volume / Issue: 48 (2) Sequence Number: - Start / End Page: 169 - 181 Identifier: ISSN: 1097-2765