Article | Published:

Topoisomerases facilitate transcription of long genes linked to autism

Nature volume 501, pages 5862 (05 September 2013) | Download Citation

Abstract

Topoisomerases are expressed throughout the developing and adult brain and are mutated in some individuals with autism spectrum disorder (ASD). However, how topoisomerases are mechanistically connected to ASD is unknown. Here we find that topotecan, a topoisomerase 1 (TOP1) inhibitor, dose-dependently reduces the expression of extremely long genes in mouse and human neurons, including nearly all genes that are longer than 200 kilobases. Expression of long genes is also reduced after knockdown of Top1 or Top2b in neurons, highlighting that both enzymes are required for full expression of long genes. By mapping RNA polymerase II density genome-wide in neurons, we found that this length-dependent effect on gene expression was due to impaired transcription elongation. Interestingly, many high-confidence ASD candidate genes are exceptionally long and were reduced in expression after TOP1 inhibition. Our findings suggest that chemicals and genetic mutations that impair topoisomerases could commonly contribute to ASD and other neurodevelopmental disorders.

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Gene Expression Omnibus

Data deposits

Data from Microarray, RNA-seq and ChIPseq experiments have been deposited in the Gene Expression Omnibus under accession number GSE43900.

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Acknowledgements

We thank M. Vernon at the UNC Expression Profiling Core for assistance with microarray experiments and with data analysis, H. Kelkar for pilot bioinformatics support, P. Mieczkowski and A. Brandt at the UNC High Throughput Sequencing Facility for advice and assistance with Illumina library preparation and sequencing and T. Kafri and P. Zhang at the UNC Lenti-shRNA Core for assistance with preparation of lentiviral vectors. This work was supported by grants to M.J.Z. and B.D.P. from The Angelman Syndrome Foundation, The Simons Foundation (SFARI 10-3625) and The National Institute of Mental Health (R01MH093372). I.F.K. and A.M.M. were supported by Joseph E. Wagstaff Postdoctoral Research Fellowships from the Angelman Syndrome Foundation. J.M.C. was supported by a grant from the American Cancer Society (117571-PF-09-124-01-DDC). J.M.C., J.S. and T.M. were supported by a grant from the National Institutes of Health (NIH) (R01GM101974). B.L.P. was supported by a NIH postdoctoral training grant (T32HD040127). S.J.C. was supported by a grant from National Institute of Child Health and Human Development (NICHD) (R01HD068730). The expression profiling and bioinformatics cores were funded by grants from the National Institute of Neurological Disorders and Stroke (P30NS045892) and NICHD (P30HD03110).

Author information

Author notes

    • Hsien-Sung Huang

    Present address: Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.

Affiliations

  1. Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA

    • Ian F. King
    • , Angela M. Mabb
    • , Hsien-Sung Huang
    • , Brandon L. Pearson
    • , Benjamin D. Philpot
    •  & Mark J. Zylka
  2. Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA

    • Chandri N. Yandava
    • , Benjamin D. Philpot
    •  & Mark J. Zylka
  3. Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06032, USA

    • Jack S. Hsiao
    •  & Stormy J. Chamberlain
  4. Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA

    • J. Mauro Calabrese
    • , Joshua Starmer
    • , Joel S. Parker
    •  & Terry Magnuson
  5. Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA

    • Joel S. Parker
    •  & Terry Magnuson
  6. UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA

    • Benjamin D. Philpot
    •  & Mark J. Zylka

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Contributions

I.F.K., H.-S.H., A.M.M., J.S.H., S.J.C., B.D.P. and M.J.Z. conceived and designed experiments. I.F.K. performed RNA-seq and ChIP-seq experiments with mouse neurons. I.F.K., C.N.Y., J.M.C., J.S. and J.S.P. analysed data from genome-wide experiments and from published datasets. J.M.C. performed SNP filtering of RNA-seq data and J.S. performed statistical analysis of RNA-seq data. A.M.M. performed lentiviral shRNA knockdown experiments. J.S.H. and S.J.C. performed all experiments with iPSC-derived human neurons. B.L.P. assessed propensity of compounds to kill neurons and damage DNA. T.M. provided bioinformatics support. I.F.K., H.-S.H. and A.M.M. performed microarray experiments. I.F.K. and M.J.Z. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Benjamin D. Philpot or Mark J. Zylka.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Data 1

    This file contains a Table of all genes differentially expressed with topotecan treatment of cultured mouse cortical neurons.

  2. 2.

    Supplementary Data 2

    This file contains the functional annotation clustering data for topotecan upregulated and downregulated genes.

  3. 3.

    Supplementary Data 3

    This file contains the expression information for topotecan treated neurons for all ASD candidate genes considered in this study.

About this article

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DOI

https://doi.org/10.1038/nature12504

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