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A protein-RNA specificity code enables targeted activation of an endogenous human transcript

Nature Structural & Molecular Biology volume 21, pages 732–738 (2014)Cite this article

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Abstract

Programmable protein scaffolds that target DNA are invaluable tools for genome engineering and designer control of transcription. RNA manipulation provides broad new opportunities for control, including changes in translation. PUF proteins are an attractive platform for that purpose because they bind specific single-stranded RNA sequences by using short repeated modules, each contributing three amino acids that contact an RNA base. Here, we identified the specificities of natural and designed combinations of those three amino acids, using a large randomized RNA library. The resulting specificity code reveals the RNA binding preferences of natural proteins and enables the design of new specificities. Using the code and a translational activation domain, we designed a protein that targets endogenous cyclin B1 mRNA in human cells, increasing sensitivity to chemotherapeutic drugs. Our study provides a guide for rational design of engineered mRNA control, including translational stimulation.

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Figure 1: RNA recognition by the PUF proteins.
Figure 2: A quantitative TRM recognition code.
Figure 3: Prediction and distribution of specificity in nature.
Figure 4: Modifications of PUF scaffolds according to the TRM code.
Figure 5: Engineered specificity of PUF proteins.
Figure 6: Manipulation of translation with a modified PUF scaffold.

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Acknowledgements

We thank L. Vanderploeg for help with figures and M. Preston and S. Waghray for careful editing. This work was supported by US National Institutes of Health grant GM050942 to M.W. U2OS and HeLa cells were kind gifts from S. Miyamoto and R. Raines (both at University of Wisconsin–Madison), respectively.

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Authors and Affiliations

  1. Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA

    Zachary T Campbell, Cary T Valley & Marvin Wickens

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  1. Zachary T Campbell
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  2. Cary T Valley
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  3. Marvin Wickens
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Contributions

Z.T.C. and C.T.V. performed the experiments. Z.T.C., M.W. and C.T.V. wrote the manuscript.

Corresponding author

Correspondence to Marvin Wickens.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Specificity coefficients and generality of the TRM code.

(A) The ranking of TRM specificity is shown based on the percent enrichment of the dominant base at position +2 multiplied by the inverse sum of non-WT identities at the +1 and +3 bases. The specificity coefficient thus includes both the preference for the new base at the targeted site as well as the “offtarget” effects at flanking positions. Higher specificity coefficients indicate greater selectivity for a switch in identity only at the “targeted” base (in this case, +2). (B) The mean specificities for G, U, and A were calculated and compared using a two-tailed Student's T-test (error bars represent s.d.). Exclusion of the wild-type TRM from the G-specific group does not eliminate the level of significance when comparing G and A TRMs. (C) The specificities of natural and designed TRMs were compared, as in Panel (A). Natural proteins are slightly more specific (average 0.37 versus designed average 0.24).

Supplementary Figure 2 Analysis of cytosine binding.

(A) Ranking of TRMs by percentage of binding elements with C at position 2. TRMs previously described as preferential C-binders are SR-Y, AR-Y, and CR-Y in the context of human PUM (Dong, S. et al. Specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains. J. Biol. Chem. 286, 26732-26742 (2011). and Filipovska, A., Razif, M.F., Nygard, K.K. & Rackham, O. A universal code for RNA recognition by PUF proteins. Nat. Chem. Biol. 7, 425-427 (2011)) (B) Correlation between specificity and C-binding preferences. The relative degree of non-specific binding was defined as the sum of all non-consensus bases for a TRM at position two and was plotted against the frequency of cytosine at position 2.

Supplementary Figure 3 Relationships between TRM composition and degeneracy at flanking sites.

Prevalence of mismatches at the flanking nucleotides +1 (A) and +3 (B). Prevalence of mismatches at the +1 (C) and +3 (D) positions and physiochemical properties of edge on-residues. Significance values were determined by two-tailed Student's t-test. Error bars, s.d. (n = 3 independent colonies).

Supplementary Figure 4 Effects of TRM substitutions on flanking bases.

(A) The binding arrangement of a canonical binding element is shown as a schematic. The four bases examined in the figure are shown in red ovals opposite the PUF repeats (boxes). Quantification across all enriched binding elements with single substitutions at the -1,+1,+2, and +3 bases are shown in panels B-E, respectively. G, A, U, and C are shown in yellow, green, red, and blue, respectively.

Supplementary Figure 5 Identification of Dictyostelium TRMs.

(A) The PUF proteins from Dictyostelium were aligned to PUM2 for identification of TRM combinations (red). (B) Predictions for RNA binding derived from TRM code reported in Fig. 2.

Supplementary Figure 6 Wild-type PUM2 binding to various sequence variants.

RNA mutants are shaded in brown according to the key. RNA sequences are provided for variant sites. Red nucleotides indicate sites that differ from the wild-type sequence. Binding activity measurements were conducted in the yeast-three hybrid system. Error bars are s.d. from three individual colonies.

Supplementary Figure 7 Properties of the Neo-PUF and Neo-activator.

(A) Expression of myc-tagged transfected proteins in U2OS cells probed by immunoblot analysis. Acronyms are as follows - Cyclin B1 refers to full length Cyclin B1, neo-PUF refers to FBF-2 bearing the repeat 3 NQ-H substitution, RNADEF is the neo-PUF containing an RNA binding defective allele of FBF-2 with the H326A substitution, PAB is PAB1p RRMs 1-3, RNADEF-PAB is the neo-PUF containing the H326A mutation fused to PAB, and neo-activator is FBF-2 bearing the repeat 3 NQ-H substitution characterized in the main text fused to PAB. (B) RT-PCR analysis of neo-PUF binding to either to the cyclin B1 transcript (CCNB1) or a negative control (CCNA2) in vivo. U2OS cells were transfected with equivalent amounts of the indicated vectors and transcripts were isolated by RNA immuno-precipitation and RT-PCR. (C) Growth rate (inferred from measurement of metabolic flux) for U2OS cells transformed with either Cyclin B1 or the neo-activator was increased relative to vector alone or an RNA binding defective PUF–PAB chimera. Significance values were determined by twotailed Student's t-test (* denotes P < 0.05, ** denotes P < 0.01). Error bars are s.d. from three cell cultures. (D) U2OS cells were treated with taxol for 12 hours to induce arrest. The drug was removed and the cells were allowed to recover in fresh media for four hours. The relative percentage of cells remaining in mitosis was determined by immunostaining for phosopho histone H3. Significance values were determined by two-tailed Student's t-test (* denotes P < 0.05, ** denotes P < 0.01). Error bars are s.d. from three cell cultures.

Supplementary Figure 8 Uncropped blot images.

(A-B) Related to Fig. 6

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Campbell, Z., Valley, C. & Wickens, M. A protein-RNA specificity code enables targeted activation of an endogenous human transcript. Nat Struct Mol Biol 21, 732–738 (2014). https://doi.org/10.1038/nsmb.2847

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