A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo

Tomas Lagunas; Stephen P. Plassmeyer; Anthony D. Fischer; Ryan Z. Friedman; Michael A. Rieger; Din Selmanovic; Simona Sarafinovska; Yvette K. Sol; Michael J. Kasper; Stuart B. Fass; Alessandra F. Aguilar Lucero; Joon Yong An; Stephan J. Sanders; Barak A. Cohen; Joseph D. Dougherty

doi:10.1038/s42003-023-05483-w

A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo

Tomas Lagunas
, Stephen P. Plassmeyer
, Anthony D. Fischer
, Ryan Z. Friedman
, Michael A. Rieger
, Din Selmanovic
, Simona Sarafinovska
, Yvette K. Sol
, Michael J. Kasper
, Stuart B. Fass
, Alessandra F. Aguilar Lucero
, Joon Yong An
, Stephan J. Sanders
, Barak A. Cohen
, Joseph D. Dougherty^*

^*Corresponding author for this work

School of Biosystem and Biomedical Science

Research output: Contribution to journal › Article › peer-review

8 Citations (Scopus)

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.

Original language	English
Article number	1151
Journal	Communications Biology
Volume	6
Issue number	1
DOIs	https://doi.org/10.1038/s42003-023-05483-w
Publication status	Published - 2023 Dec

Bibliographical note

Publisher Copyright:
© 2023, The Author(s).

ASJC Scopus subject areas

Medicine (miscellaneous)
General Biochemistry,Genetics and Molecular Biology
General Agricultural and Biological Sciences

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Cite this

Lagunas, T., Plassmeyer, S. P., Fischer, A. D., Friedman, R. Z., Rieger, M. A., Selmanovic, D., Sarafinovska, S., Sol, Y. K., Kasper, M. J., Fass, S. B., Aguilar Lucero, A. F., An, J. Y., Sanders, S. J., Cohen, B. A., & Dougherty, J. D. (2023). A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo. Communications Biology, 6(1), Article 1151. https://doi.org/10.1038/s42003-023-05483-w

Lagunas, T, Plassmeyer, SP, Fischer, AD, Friedman, RZ, Rieger, MA, Selmanovic, D, Sarafinovska, S, Sol, YK, Kasper, MJ, Fass, SB, Aguilar Lucero, AF, An, JY, Sanders, SJ, Cohen, BA & Dougherty, JD 2023, 'A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo', Communications Biology, vol. 6, no. 1, 1151. https://doi.org/10.1038/s42003-023-05483-w

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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.",

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AU - Selmanovic, Din

AU - Sarafinovska, Simona

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A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo

Abstract

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