Modeling RNA Secondary Structure with Sequence Comparison &
Experimental Mapping Data
https://www.Cell.com/biophysj/fulltext/S0006-3495(17)30689-6 combines TurboFold sec. structure prediction w/ results of SHAPE assays
Zhen Tan
Gaurav Sharma
David H. Mathews
Open Archive Published:July 20, 2017
DOI:https://doi.org/10.1016/j.bpj.2017.06.039
#RNA Struc. Determinants of Optimal Codons…by MAGESeq
http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4 Probing effect of synonymous changes; towards a better dN/dS
RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4
Genome sequence-independent identification of #RNA editing
siteshttp://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3314.html GIREMI uses LD to separate edit sites from #SNPs
Qing Zhang
& Xinshu Xiao
Nature Methods (2015) doi:10.1038/nmeth.3314Received
The go-between: Life’s unexpected
messengerhttp://www.newscientist.com/article/mg22329860.400-the-gobetween-lifes-unexpected-messenger.html Overview connecting many flavors of #RNA – ie RNAi, siRNA, miRNA & @exRNA
Some bits unclear though – in relation to boundaries betw. siRNA & exRNA
QT:{{”
The RNA in cells is far more mobile than we thought (Image: Renaud Vigourt)
Far from staying put, RNA – the less famous cousin of DNA – can roam far afield, carrying information to other cells in the body and even to other animals
UNDER the soil of the cornfield, the rootworm larvae emerge from their eggs and crawl in search of roots to munch on. But their mother chose the wrong field to lay her eggs in. There’s something special about the maize here – it’s armed with a smart weapon designed to target the rootworms.
As the larvae feed, this weapon is released from the plant and enters their gut cells. There it halts production of a vital protein by blocking one specific gene. In the hours that follow, this “gene silencing” weapon spreads to other cells in the larvae’s bodies. At first there is no …
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New $17M program exploring mysterious extracellular #RNA: defining its action, collecting #bigdata http://scim.ag/18nWSyU MT @lopezjenniferw
http://www.sciencemag.org/content/341/6149/947.full
[News & Analysis] Cell Biology: NIH Effort Gambles on Mysterious Extracellular RNAs
A $17 million research program, announced this month by the U.S. National Institutes of Health, aims to determine whether RNA molecules are deliberately released by cells as hormonelike signals—and whether such extracellular RNAs can be harnessed for diagnosis and treatment of human diseases.
Author: Mitch Leslie
Nice overview of Clipseq/HITS-CLIP
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222227/
QT:”
This advantage relates to the mechanism of UV-mediated crosslinking, which, although incompletely understood, is believed to involve absorption of UV light by nucleic acid bases44 to induce ground state electrons to a singlet higher-energy state that enables the electron to partake in a chemical reaction in which a new covalent bond is formed…
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