216 10 Programming Gene Expression by Engineering Transcript Stability Control and Processing in Bacteria
121 Lucks, J.B., Mortimer, S.A., Trapnell, C., Luo, S. et al. (2011) Multiplexed RNA
structure characterization with selective 2′-hydroxyl acylation analyzed by
primer extension sequencing (SHAPE-Seq). Proc. Natl. Acad. Sci. U.S.A., 108 ,
11063–11068.
122 Kertesz, M., Wan, Y., Mazor, E., Rinn, J.L. et al. (2010) Genome-wide
measurement of RNA secondary structure in yeast. Nature, 467 , 103–107.
123 Mortimer, S.A. and Weeks, K.M. (2007) A fast-acting reagent for accurate
analysis of RNA secondary and tertiary structure by SHAPE chemistry.
J. Am. Chem. Soc., 129 , 4144–4145.
124 Hajdin, C.E., Bellaousov, S., Huggins, W., Leonard, C.W. et al. (2013) Accurate
SHAPE-directed RNA secondary structure modeling, including pseudoknots.
Proc. Natl. Acad. Sci. U.S.A., 110 , 5498–5503.
125 Aviran, S., Trapnell, C., Lucks, J.B., Mortimer, S.A. et al. (2011) Modeling and
automation of sequencing-based characterization of RNA structure. Proc. Natl.
Acad. Sci. U.S.A., 108 , 11069–11074.
126 Overgaard, M., Johansen, J., Møller-Jensen, J., and Valentin-Hansen, P. (2009)
Switching off small RNA regulation with trap-mRNA. Mol. Microbiol., 73 ,
790–800.
127 Figueroa-Bossi, N., Valentini, M., Malleret, L., Fiorini, F. et al. (2009) Caught at
its own game: regulatory small RNA inactivated by an inducible transcript
mimicking its target. Genes Dev., 23 , 2004–2015.
128 Small, I.D. and Peeters, N. (2000) The PPR motif – a TPR-related motif
prevalent in plant organellar proteins. Trends Biochem. Sci, 25 , 46–47.
129 Boch, J., Scholze, H., Schornack, S., Landgraf, A. et al. (2009) Breaking the code
of DNA binding specificity of TAL-type III effectors. Science (New York, N.Y.),
326 , 1509–1512.
130 Barkan, A., Rojas, M., Fujii, S., Yap, A. et al. (2012) A combinatorial amino acid
code for RNA recognition by pentatricopeptide repeat proteins. PLos Genet., 8 ,
e1002910.
131 Pfalz, J., Bayraktar, O.A., Prikryl, J., and Barkan, A. (2009) Site-specific binding
of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts.
EMBO J., 28 , 2042–2052.
132 Prikryl, J., Rojas, M., Schuster, G., and Barkan, A. (2011) Mechanism of RNA
stabilization and translational activation by a pentatricopeptide repeat protein.
Proc. Natl. Acad. Sci. U.S.A., 108 , 415–420.
133 Mohanty, B.K. and Kushner, S.R. (2006) The majority of Escherichia coli
mRNAs undergo post-transcriptional modification in exponentially growing
cells. Nucleic Acids Res., 34 , 5695–5704.
134 Bricker, A.L. and Belasco, J.G. (1999) Importance of a 5′ stem-loop for
longevity of papA mRNA in Escherichia coli. J. Bacteriol., 181 , 3587–3590.