asd_3utr_mpra_analysis

This is the code from the paper titled : A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo

Authors: 

Tomas Lagunas Jr.^1,2,3, Stephen P. Plassmeyer^1,2, Anthony D. Fischer^1,2, Ryan Z. Friedman^1,3, Michael A. Rieger^1,2,3, Din Selmanovic^1,2, Simona Sarafinovska^1,2, Yvette K. Sol^1,2, Michael J. Kasper^1,2, Stuart B. Fass^1,2, Alessandra F. Aguilar Lucero⁴, Joon-Yong An^5,6, Stephan J. Sanders⁴, Barak A. Cohen¹, Joseph D. Dougherty^1,2

Affiliations:

¹Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave, Saint Louis MO, 63108, USA.

²Department of Psychiatry, Washington University School of Medicine.

³Division of Biology and Biomedical Sciences, Washington University School of Medicine.

⁴Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neuroscience, University of California, San Francisco, CA 94518

⁵Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Republic of Korea 

⁶School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul 02841, Republic of Korea

Abstract

The function of regulatory elements is highly dependent on the cellular context, and thus for understanding the function of elements associated with psychiatric diseases these would ideally be studied in neurons in a living brain. Massively Parallel Reporter Assays (MPRAs) are molecular genetic tools that enable functional screening of hundreds of predefined sequences in a single experiment. These assays have not yet been adapted to query specific cell types in vivo in a complex tissue like the mouse brain. Here, using a test-case 3′UTR MPRA library with genomic elements containing variants from autism patients, we developed a method to achieve reproducible measurements of element effects in vivo in a cell type-specific manner, using excitatory cortical neurons and striatal medium spiny neurons as test cases. This targeted technique should enable robust, functional annotation of genetic elements in the cellular contexts most relevant to psychiatric disease.