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Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation

Nature Biotechnology volume 30, pages 453–459 (2012)Cite this article

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Abstract

The ability to specifically upregulate genes in vivo holds great therapeutic promise. Here we show that inhibition or degradation of natural antisense transcripts (NATs) by single-stranded oligonucleotides or siRNAs can transiently and reversibly upregulate locus-specific gene expression. Brain-derived neurotrophic factor (BDNF) is normally repressed by a conserved noncoding antisense RNA transcript, BDNF-AS. Inhibition of this transcript upregulates BDNF mRNA by two- to sevenfold, alters chromatin marks at the BDNF locus, leads to increased protein levels and induces neuronal outgrowth and differentiation both in vitro and in vivo. We also show that inhibition of NATs leads to increases in glial-derived neurotrophic factor (GDNF) and ephrin receptor B2 (EPHB2) mRNA. Our data suggest that pharmacological approaches targeting NATs can confer locus-specific gene upregulation effects.

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Figure 1: Genomic organization of the human BDNF locus.
Figure 2: Antisense-mediated regulation of sense mRNA and protein.
Figure 3: Bdnf upregulation increases neuronal outgrowth.
Figure 4: Bdnf-AS regulates Bdnf mRNA and protein in vivo.
Figure 5: Blocking of Bdnf-AS, in vivo, causes an increase in neuronal survival and proliferation.
Figure 6: Removal of BDNF-AS resulted in the modification of chromatin marks.

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Acknowledgements

Q.-R. Liu from the National Institute of Drug Abuse kindly provided us with constructs that contain three splice variants of the human BDNF-AS transcript. We thank C. Coito, P. Frost, J. Hsiao and O. Khorkova at OPKO-CURNA for helpful discussions. The US National Institutes of Health (5R01NS063974 and 5RC2AG036596) funded this work. A significant portion of this study was carried out when the investigators were employed at The Scripps Research Institute and/or the Karolinska Institutet.

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  1. Miguel A Lopez-Toledano & Marcel P van der Brug

    Present address: Present Addresses: Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, Florida, USA (M.A.L.-T.) and Genentech Inc., S. San Francisco, California, USA (M.P.v.d.B.).,

Authors and Affiliations

  1. Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA

    Farzaneh Modarresi, Mohammad Ali Faghihi, Roya Pedram Fatemi, Marco Magistri, Shaun P Brothers & Claes Wahlestedt

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  1. Farzaneh Modarresi
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Contributions

F.M., M.A.F., M.A.L.-T., R.P.F. and M.M. each contributed experimental data to this work. M.P.v.d.B. performed RNA deep sequencing of brain samples. F.M., M.A.F., M.A.L.-T., R.P.F., M.M., S.P.B. and C.W. all contributed to the concepts behind the work; each were also responsible for contributions to the text of this article.

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Correspondence to Claes Wahlestedt.

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Competing interests

C.W. is a consultant for OPKO-CURNA. M.P.V.d.B. is an employee of Genentech.

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Supplementary Table 1, Supplementary Figures 1–17 and Supplementary Data 1,2 (PDF 1290 kb)

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Modarresi, F., Faghihi, M., Lopez-Toledano, M. et al. Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30, 453–459 (2012). https://doi.org/10.1038/nbt.2158

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