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Evaluating ribosomal frameshifting in CCR5 mRNA decoding

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The Original Article was published on 09 July 2014

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Fig. 1: Evaluation of the original evidence for CCR5 frameshifting.
Fig. 2: Additional approaches to CCR5 −1 PRF detection.

Data availability

The data used to support our findings are either publicly available or were generated in this study and are included in the source data. Source data are provided with this paper.

References

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Acknowledgements

We thank A. T. Belew for his courage in alerting key outside individuals in May 2017 to problems with his work and recently in providing us with crucial information about the original plasmids. This work was supported by grants from the NIH (R35GM118070 and R01AI133348) to J.S.K., the Wellcome Trust (106207) to A.E.F., a SFI-HRB-Wellcome Trust Investigator in Science award (210692/Z/18) to P.V.B., and the Science Foundation Ireland and the Irish Research Council (13/IA/1853 and IRCLA/2019/74n) to J.F.A. A.-L.S. was supported by DFG STE 2509/2−1. S.J.K. was supported by an Irish Research Council studentship. Y.A.K. was supported by an award of the Winston Churchill Foundation of the USA, a Graduate Research Fellowship from the National Science Foundation and the Knight-Hennessy Scholarship. Y.A.K. thanks A. S. Khan for support.

Author information

Authors and Affiliations

Authors

Contributions

The splicing work, which was initiated in 2016, was performed by A.-L.S. and J.S.K. Two teams—one involving G.L. and J.F.A., and the other involving Y.A.K., K.B., H.S. and A.E.F.—semi-independently performed the frameshifting analysis. S.J.K. and P.V.B., with input from A.E.F., performed the ribosome profiling analysis. After the initial independent work of the teams involved, Y.A.K. and J.F.A. coordinated their combination. Y.A.K. and G.L. had major roles in preparing the manuscript with contributions and refinements from all other authors.

Corresponding authors

Correspondence to Jeffrey S. Kieft, Andrew E. Firth or John F. Atkins.

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The authors declare no competing interests.

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Extended data figures and tables

Extended Data Fig. 1 Alignment of mammalian CCR5 sequences for the putative −1 PRF region in human.

Sequence alignment of CCR5 CDS regions obtained from tblastn hits to human CCR5, trimmed to only include the frameshift region. The red box indicates the putative slippery site. See Supplementary Table 1b for a list of the accession numbers used.

Extended Data Fig. 2 Luciferase values for each experiment.

a, Absolute Renilla luciferase values for CCR5 DNA transfection experiments performed in HeLa cells. b, Absolute firefly luciferase values for CCR5 DNA transfection experiments performed in HeLa cells. c, Absolute Renilla luciferase values for CCR5 DNA transfection experiments performed in HEK293T cells. d, Absolute firefly luciferase values for CCR5 DNA transfection experiments performed in HEK293T cells. e, Absolute Renilla luciferase values for CCR5 DNA transfection experiments performed in HeLa cells. f, Absolute firefly luciferase values for CCR5 DNA transfection experiments performed in HeLa cells. g, Absolute Renilla luciferase values for CCR5 DNA transfection experiments performed in HEK293T cells. h, Absolute firefly luciferase values for CCR5 DNA transfection experiments performed in HEK293T cells i, Absolute Renilla luciferase values for retrotransposon transfection experiments performed in HeLa cells. j, Absolute firefly luciferase values for retrotransposon transfection experiments performed in HeLa cells. k, Absolute Renilla luciferase values for retrotransposon transfection experiments performed in HEK293T cells. l, Absolute firefly luciferase values for retrotransposon transfection experiments performed in HEK293T cells. m, Absolute Renilla luciferase values for CCR5 RNA transfection experiments performed in HeLa cells. n, Absolute firefly luciferase values for CCR5 RNA transfection experiments performed in HeLa cells.

Supplementary information

Supplementary Information

This file contains Supplementary Methods.

Reporting Summary

Supplementary Figure

This file contains the uncropped gels.

Supplementary Table 1

Oligonucleotides and accession numbers.

Source data

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Khan, Y.A., Loughran, G., Steckelberg, AL. et al. Evaluating ribosomal frameshifting in CCR5 mRNA decoding. Nature 604, E16–E23 (2022). https://doi.org/10.1038/s41586-022-04627-y

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