Journal:

Article Title: Molecular Mechanisms of Attenuation of the Sabin Strain of Poliovirus Type 3

doi: 10.1128/JVI.78.20.11097-11107.2004

Figure Lengend Snippet: The PV 5′ UTR. (A) Schematic representation of the predicted secondary structure of the PV 5′ UTR. The shaded box represents the oligopyrimidine tract. (B) Detailed view of domain V and the oligopyrimidine tract for the Leon strain of PV. The mutation involved in attenuation of Sabin3 is boxed. Nucleotides susceptible to RNase ONE cleavage in the Sabin3, but not the Leon, IRES are indicated by triangles (see Fig. ​Fig.2A).2A). Nucleotides protected by PTB or nPTB from V1 cleavage are indicated by circles (see Fig. ​Fig.2B),2B), and nucleotides protected by PTB or nPTB from RNase ONE cleavage are indicated by squares (see Fig. ​Fig.33).

Article Snippet: RNA transcripts were incubated for 10 min at 37°C with greater-than-equal molar amounts of PTB, nPTB, and Nova-1 to form complexes and then probed with RNase ONE (Promega) or RNase V1 (Amersham Pharmacia Biotech) essentially as previously described ( 23 , 42 ).

Techniques: Mutagenesis

Journal:

Article Title: Molecular Mechanisms of Attenuation of the Sabin Strain of Poliovirus Type 3

doi: 10.1128/JVI.78.20.11097-11107.2004

Figure Lengend Snippet: PTB and nPTB bind the Leon and Sabin3 IRESs at a site adjacent to nt 472. Enzymatic footprint of the Leon and Sabin3 IRESs in the region surrounding nt 472 with RNase ONE (A) and RNase V1 (B). In this figure and the subsequent two figures, the table above the gel indicates whether RNA was incubated alone or with proteins and whether RNA-protein complexes were digested with an enzyme. RNA probes were extended with a primer complementary to nt 542 to 559. The region displaying enhanced cleavage by RNase ONE on the Sabin3 strain is indicated by the dashed box (see also triangles in Fig. ​Fig.1B).1B). The location of the PTB- or nPTB-binding site is indicated by the solid box (see also circles in Fig. ​Fig.1B1B).

Article Snippet: RNA transcripts were incubated for 10 min at 37°C with greater-than-equal molar amounts of PTB, nPTB, and Nova-1 to form complexes and then probed with RNase ONE (Promega) or RNase V1 (Amersham Pharmacia Biotech) essentially as previously described ( 23 , 42 ).

Techniques: Incubation, Binding Assay

Journal: Molecular cell

Article Title: The TIA1 RNA-binding-protein family regulates EIF2AK2-mediated stress response and cell cycle progression

doi: 10.1016/j.molcel.2018.01.011

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Software and Algorithms Tophat v2.0.13 ( Trapnell et al., 2012 ) http://ccb.jhu.edu/software/tophat/index.shtml Cuffdiff v2.1.1 ( Trapnell et al., 2012 ) http://cole-trapnell-lab.github.io/cufflinks/ rMATS.3.0.9 Xing Laboratory, UCLA( Shen et al., 2012 ) http://rnaseq-mats.sourceforge.net Cutadapt http://journal.embnet.org/index.php/embnetjournal/article/view/200/458 https://cutadapt.readthedocs.io/en/v1.8.2/installation.html R Studio Version 0.98.1060 Rstudio https://www.rstudio.com/ Prism 7 for Mac OS X Graphpad https://www.graphpad.com ImageJ 1.48v http://imagej.nih.gov/ij PARalyzer ( Corcoran et al., 2011 ; Mukherjee et al., 2014 ) https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ PAR-CLIP suite ( Garzia, Meyer, Morozov, Sajek, & Tuschl, 2017 ) https://rnaworld.rockefeller.edu/PARCLIP_suite/ Open in a separate window KEY RESOURCES TABLE

Techniques: Virus, Recombinant, PCR Cloning, Sequencing, Western Blot, Plasmid Preparation, Generated, Software