Review Article

RNA-based recognition and targeting: sowing the seeds of specificity

  • Nature Reviews Molecular Cell Biology volume 18, pages 215228 (2017)
  • doi:10.1038/nrm.2016.174
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Published:

Abstract

RNA is involved in the regulation of multiple cellular processes, often by forming sequence-specific base pairs with cellular RNA or DNA targets that must be identified among the large number of nucleic acids in a cell. Several RNA-based regulatory systems in eukaryotes, bacteria and archaea, including microRNAs (miRNAs), small interfering RNAs (siRNAs), CRISPR RNAs (crRNAs) and small RNAs (sRNAs) that are dependent on the RNA chaperone protein Hfq, achieve specificity using similar strategies. Central to their function is the presentation of short 'seed sequences' within a ribonucleoprotein complex to facilitate the search for and recognition of targets.

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Acknowledgements

The authors are grateful to B. Luisi, A. Eulalio, G. Wagner and members of the authors' laboratories for discussions and comments on the manuscript. The authors also thank S. Geibel for help with the figures.

Author information

Affiliations

  1. Institute of Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/D15, D-97080 Würzburg, Germany.

    • Stanislaw A. Gorski
    •  & Jörg Vogel
  2. Helmholtz Institute for RNA based Infection Research (HIRI), University of Würzburg, D-97080 Würzburg, Germany.

    • Jörg Vogel
  3. Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

    • Jennifer A. Doudna
  4. Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.

    • Jennifer A. Doudna
  5. California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA.

    • Jennifer A. Doudna
  6. Department of Chemistry, University of California, Berkeley, California 94720, USA.

    • Jennifer A. Doudna
  7. Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

    • Jennifer A. Doudna
  8. Innovative Genomics Initiative, University of California, Berkeley, California 94720, USA.

    • Jennifer A. Doudna

Authors

  1. Search for Stanislaw A. Gorski in:

  2. Search for Jörg Vogel in:

  3. Search for Jennifer A. Doudna in:

Competing interests

J.A.D. is executive director of the Innovative Genomics Initiative at the University of California, Berkeley (UC Berkeley) and the University of California, San Francisco (UCSF). J.A.D. is a co-founder of Editas Medicine, Intellia Therapeutics and Caribou Biosciences and a scientific adviser to Caribou, Intellia, eFFECTOR Therapeutics and Driver. Funding has been received from the Howard Hughes Medical Institute (HHMI), the US National Institutes of Health, the US National Science Foundation, Roche, Pfizer, the Paul Allen Institute and the Keck Foundation. J.A.D. is employed by HHMI and works at the UC Berkeley. UC Berkeley and HHMI have patents pending for CRISPR technologies on which she is an inventor.

Corresponding authors

Correspondence to Jörg Vogel or Jennifer A. Doudna.

Glossary

Loop–loop kissing interactions

Watson–Crick base pairing between the loop nucleotides of two RNA stem loops.

Adaptive immunity

A specific response to an infection by a pathogen based on prior exposure to that pathogen.

RNA-induced silencing complex

(RISC). A ribonucleoprotein complex of an Argonaute protein and an RNA.

Scissile bond

A covalent bond that can be broken by an enzymatic reaction.

PAZ domain

(PIWI–Argonaute–Zwille domain). A domain present in Argonaute proteins that is involved in binding to the 3′ end of the guide.

PIWI domain

(P-element-induced wimpy testis domain). A domain present in Argonaute proteins that contains an RNase H-like active site.

A-form helix

A secondary structure motif found in RNA in which bases are tilted with respect to the helix axis.

Entropy penalty

The thermodynamic cost associated with a loss of conformational entropy on the immobilization of a molecule in a fixed configuration.

High-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation

(HITS-CLIP). A sequencing method based on the ultraviolet crosslinking of RNA–protein complexes that is used to identify RNA ligands of RNA-binding proteins.

Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation

(PAR-CLIP). A sequencing method that uses photoactivatable ribonucleosides to crosslink RNA and protein to identify RNAs associated with a particular RNA-binding protein.

Crosslinking, ligation and sequencing of hybrids

(CLASH). A sequencing method used to identify RNAs and their targets by ligating them together when they are bound to a specific RNA-binding protein.

HNH domain

A nuclease domain within Cas9 that is related to McrA-like restriction endonucleases.

RuvC domain

A nuclease domain within Cas9 that is related to the RuvC endonuclease that cuts Holliday junctions during homologous recombination.

Total internal reflection microscopy

(TIRFM).A microscopy technique that uses an evanescent wave to specifically excite fluorophore-labelled molecules close to a surface.

Sm/Lsm superfamily

A large family of proteins present in all three domains of life and involved in RNA processing and degradation.

Shine–Dalgarno sequence

A 5–10-nucleotide sequence upstream of the initiation codon involved in defining where bacterial translation initiates.

Chemical footprinting

Methods used to map RNA secondary and tertiary structures based on the accessibility of nucleotides to specific chemicals.

Small-angle X-ray scattering

(SAXS). An X-ray scattering method that provides information on the size and shape of biological molecules in solution.