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From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo

Nature Reviews Genetics volume 23, pages 229–243 (2022)Cite this article

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Abstract

Genome-wide sequencing has led to the discovery of thousands of long non-coding RNA (lncRNA) loci in the human genome, but evidence of functional significance has remained controversial for many lncRNAs. Genetically engineered model organisms are considered the gold standard for linking genotype to phenotype. Recent advances in CRISPR–Cas genome editing have led to a rapid increase in the use of mouse models to more readily survey lncRNAs for functional significance. Here, we review strategies to investigate the physiological relevance of lncRNA loci by highlighting studies that have used genetic mouse models to reveal key in vivo roles for lncRNAs, from fertility to brain development. We illustrate how an investigative approach, starting with whole-gene deletion followed by transcription termination and/or transgene rescue strategies, can provide definitive evidence for the in vivo function of mammalian lncRNAs.

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Fig. 1: Dissecting functionality of the Xist locus using multiple strategies.
Fig. 2: The Tug1 locus highlights the complexity present at lncRNA loci.
Fig. 3: Physiological roles of lncRNAs discovered by gene targeting.
Fig. 4: lncRNA Airn transcription over the Igf2r promoter causes Igf2r silencing.
Fig. 5: Multiple mouse models unveil that the lncRNA Maenli controls the limb-specific En1 regulator by the act of transcription.
Fig. 6: Coupling LOF mouse models with transgene rescue to distinguish between lncRNA cis and trans activity.
Fig. 7: LOF strategies to disentangle the lncRNA mechanism of action in vivo.

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Acknowledgements

The authors thank S. Carpenter, D. Lim, M. Sauvageau and Q.J. Hudson for critical review and insights during the writing process. J.L.R. is the Leslie Orgel and Marvin Caruthers professor of RNA science and Howard Hughes Medical Institute (HHMI) faculty scholar. D.A. is supported by the Deutsche Forschungsgemeinschaft (Project-ID: 403584255—TRR 267). The authors are supported by HHMI and NIGMS PO GM099117.

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  1. These authors contributed equally: Daniel Andergassen, John L. Rinn.

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  1. Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich, Germany

    Daniel Andergassen

  2. Department of Biochemistry and BioFrontiers, University of Colorado Boulder, Boulder, CO, USA

    John L. Rinn

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Andergassen, D., Rinn, J.L. From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat Rev Genet 23, 229–243 (2022). https://doi.org/10.1038/s41576-021-00427-8

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