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. 2015 Jun;21(6):1159–1172. doi: 10.1261/rna.045559.114

FIGURE 1.

FIGURE 1.

Characteristics of YB-1–associated small RNAs. (A) Length distribution of small RNAs immunoprecipitated with YB-1, hnRNP A/B (control), and rabbit IgG (control), based on Agilent Bioanalyzer (marker peak at 4 nt). (B) Northern blot validation of two abundant small RNAs, Shad1 and Saunc45b. A more abundant ∼100-nt long Shad1 isoform was also detected. (C) RNA EMSA using purified GST-YB-1 protein shows interaction with Shad1. (Lane I) DIG-labeled probe in the absence of YB-1. (Lane II) Labeled probed in the presence of YB-1. (Lane III) Labeled probe, YB-1 and an excess (20×) of unlabeled RNA probes as competitor. All reactions use unlabeled tRNA as a nonspecific competitor. (D) Size distribution of paired-end reads. The red distribution shows all read lengths from the YB-1 RNA immunoprecipitation. The blue distribution shows all read lengths from the YB-1 RNA immunoprecipitation twofold enriched over PC-3 input RNAs. (E) Analysis of distinct YB-1–associated small RNA sequences after removal of input RNAs.