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. 2014 Jul 17;55(2):199–213. doi: 10.1016/j.molcel.2014.05.006

Figure 3.

Figure 3

Hfq Binds Single-Stranded, U-Rich Sequences in sRNAs

(A) Hfq binding relative to sRNA seed sequences. Small RNAs (indicated right) are aligned to the start of their respective seed regions (dashed line). Each heatmap indicates Hfq binding along the sRNA.

(B) A 2U sequence is enriched 5′ of the site of maximal deletions (indicating direct Hfq contact). Positions relative to the site of maximal deletions within 20 Hfq-dependant sRNAs were scored for frequency of a uridine nucleotide. The probability of randomly enriching U at a given position (FDR) is given by the gray dashed line (q ≈ 0.05).

(C) Hfq is crosslinked to single-stranded nucleotides within sRNAs. The secondary structure of 20 Hfq-dependent sRNAs was predicted using the UNAfold software package and nucleotides surrounding the site of maximal deletions were scored as base paired (+1) or unpaired (−1). The cumulative score for nucleotides from 20 Hfq-dependent sRNAs are plotted against their position relative to the maximal crosslinking site for three independent experiments. False discovery rate is given by the gray dashed line (q ≈ 0.05).