Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons

Sarah A. McClymont, Paul W. Hook, Alexandra I. Soto, Xylena Reed, William D. Law, Samuel J. Kerans, Eric L. Waite, Nicole J. Briceno, Joey F. Thole, Michael G. Heckman, Nancy N. Diehl, Zbigniew K Wszolek, Cedric D. Moore, Heng Zhu, Jennifer A. Akiyama, Diane E. Dickel, Axel Visel, Len A. Pennacchio, Owen A Ross, Michael A. BeerAndrew S. McCallion

Research output: Contribution to journalArticle

Abstract

The progressive loss of midbrain (MB) dopaminergic (DA) neurons defines the motor features of Parkinson disease (PD), and modulation of risk by common variants in PD has been well established through genome-wide association studies (GWASs). We acquired open chromatin signatures of purified embryonic mouse MB DA neurons because we anticipated that a fraction of PD-associated genetic variation might mediate the variants’ effects within this neuronal population. Correlation with >2,300 putative enhancers assayed in mice revealed enrichment for MB cis-regulatory elements (CREs), and these data were reinforced by transgenic analyses of six additional sequences in zebrafish and mice. One CRE, within intron 4 of the familial PD gene SNCA, directed reporter expression in catecholaminergic neurons from transgenic mice and zebrafish. Sequencing of this CRE in 986 individuals with PD and 992 controls revealed two common variants associated with elevated PD risk. To assess potential mechanisms of action, we screened >16,000 proteins for DNA binding capacity and identified a subset whose binding is impacted by these enhancer variants. Additional genotyping across the SNCA locus identified a single PD-associated haplotype, containing the minor alleles of both of the aforementioned PD-risk variants. Our work posits a model for how common variation at SNCA might modulate PD risk and highlights the value of cell-context-dependent guided searches for functional non-coding variation.

Original languageEnglish (US)
Pages (from-to)874-892
Number of pages19
JournalAmerican Journal of Human Genetics
Volume103
Issue number6
DOIs
StatePublished - Dec 6 2018

Fingerprint

Dopaminergic Neurons
Chromatin
Parkinson Disease
Mesencephalon
Zebrafish
Genome-Wide Association Study
DNA-Binding Proteins
Introns
Haplotypes
Transgenic Mice
Action Potentials
Alleles
Neurons

Keywords

  • alpha-synuclein (SNCA)
  • ATAC-seq
  • chromatin accessibility
  • dopaminergic neurons
  • enhancer
  • Parkinson disease
  • regulatory variation

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

McClymont, S. A., Hook, P. W., Soto, A. I., Reed, X., Law, W. D., Kerans, S. J., ... McCallion, A. S. (2018). Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons. American Journal of Human Genetics, 103(6), 874-892. https://doi.org/10.1016/j.ajhg.2018.10.018

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons. / McClymont, Sarah A.; Hook, Paul W.; Soto, Alexandra I.; Reed, Xylena; Law, William D.; Kerans, Samuel J.; Waite, Eric L.; Briceno, Nicole J.; Thole, Joey F.; Heckman, Michael G.; Diehl, Nancy N.; Wszolek, Zbigniew K; Moore, Cedric D.; Zhu, Heng; Akiyama, Jennifer A.; Dickel, Diane E.; Visel, Axel; Pennacchio, Len A.; Ross, Owen A; Beer, Michael A.; McCallion, Andrew S.

In: American Journal of Human Genetics, Vol. 103, No. 6, 06.12.2018, p. 874-892.

Research output: Contribution to journalArticle

McClymont, SA, Hook, PW, Soto, AI, Reed, X, Law, WD, Kerans, SJ, Waite, EL, Briceno, NJ, Thole, JF, Heckman, MG, Diehl, NN, Wszolek, ZK, Moore, CD, Zhu, H, Akiyama, JA, Dickel, DE, Visel, A, Pennacchio, LA, Ross, OA, Beer, MA & McCallion, AS 2018, 'Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons', American Journal of Human Genetics, vol. 103, no. 6, pp. 874-892. https://doi.org/10.1016/j.ajhg.2018.10.018
McClymont, Sarah A. ; Hook, Paul W. ; Soto, Alexandra I. ; Reed, Xylena ; Law, William D. ; Kerans, Samuel J. ; Waite, Eric L. ; Briceno, Nicole J. ; Thole, Joey F. ; Heckman, Michael G. ; Diehl, Nancy N. ; Wszolek, Zbigniew K ; Moore, Cedric D. ; Zhu, Heng ; Akiyama, Jennifer A. ; Dickel, Diane E. ; Visel, Axel ; Pennacchio, Len A. ; Ross, Owen A ; Beer, Michael A. ; McCallion, Andrew S. / Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons. In: American Journal of Human Genetics. 2018 ; Vol. 103, No. 6. pp. 874-892.
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AU - Reed, Xylena

AU - Law, William D.

AU - Kerans, Samuel J.

AU - Waite, Eric L.

AU - Briceno, Nicole J.

AU - Thole, Joey F.

AU - Heckman, Michael G.

AU - Diehl, Nancy N.

AU - Wszolek, Zbigniew K

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AU - Zhu, Heng

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AU - Dickel, Diane E.

AU - Visel, Axel

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