Pavel P. Kuksa's Publications

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Transcriptome-wide measurement of plant RNA secondary structure

Shawn W Foley, Lee E Vandivier, Pavel P Kuksa, and Brian D Gregory. Transcriptome-wide measurement of plant RNA secondary structure. Current Opinion in Plant Biology, 27:36 – 43, 2015. Cell signalling and gene regulation

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Abstract

\RNAs fold into intricate and precise secondary structures. These structural patterns regulate multiple steps of the \RNA lifecycle, while also conferring catalytic and scaffolding functions to certain transcripts. Therefore, a full understanding of \RNA posttranscriptional regulation requires a comprehensive picture of secondary structure. Here, we review several high throughput sequencing-based methods to globally survey plant \RNA secondary structure. These methods are more accurate than computational prediction, and more scalable than physical techniques such as crystallography. We note hurdles to reliably measuring secondary structure, including RNA-binding proteins, \RNA base modifications, and intramolecular duplexes. Finally, we survey the functional knowledge that has been gleaned from each of these methods, and identify some unanswered questions that remain.

BibTeX

@article{copb2015rnastructrev,
	Abstract = {\{RNAs\} fold into intricate and precise secondary structures. These structural patterns regulate multiple steps of the \{RNA\} lifecycle, while also conferring catalytic and scaffolding functions to certain transcripts. Therefore, a full understanding of \{RNA\} posttranscriptional regulation requires a comprehensive picture of secondary structure. Here, we review several high throughput sequencing-based methods to globally survey plant \{RNA\} secondary structure. These methods are more accurate than computational prediction, and more scalable than physical techniques such as crystallography. We note hurdles to reliably measuring secondary structure, including RNA-binding proteins, \{RNA\} base modifications, and intramolecular duplexes. Finally, we survey the functional knowledge that has been gleaned from each of these methods, and identify some unanswered questions that remain. },
	Author = {Shawn W Foley and Lee E Vandivier and Pavel P Kuksa and Brian D Gregory},
	Bib2Html_Pubtype = {Journal},
	Date-Added = {2015-12-28 18:44:36 +0000},
	Date-Modified = {2020-03-06 13:18:28 -0500},
	Doi = {http://dx.doi.org/10.1016/j.pbi.2015.05.021},
	Issn = {1369-5266},
	Journal = {Current Opinion in Plant Biology},
	Note = {Cell signalling and gene regulation},
	Pages = {36 - 43},
	Title = {Transcriptome-wide measurement of plant {RNA} secondary structure},
	Url = {http://www.sciencedirect.com/science/article/pii/S1369526615000722},
	Volume = {27},
	Year = {2015},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1369526615000722},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.pbi.2015.05.021}}

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