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Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis

View ORCID ProfileRyan M. Mulqueen, View ORCID ProfileBrooke A. DeRosa, View ORCID ProfileCasey A. Thornton, View ORCID ProfileZeynep Sayar, View ORCID ProfileKristof A. Torkenczy, Andrew J. Fields, View ORCID ProfileKevin M. Wright, View ORCID ProfileXiaolin Nan, View ORCID ProfileRamesh Ramji, Frank J. Steemers, View ORCID ProfileBrian J. O’Roak, View ORCID ProfileAndrew C. Adey
doi: https://doi.org/10.1101/637256
Ryan M. Mulqueen
1Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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Brooke A. DeRosa
1Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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Casey A. Thornton
1Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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Zeynep Sayar
2Knight Cancer Institute’s Cancer Early Detection Advanced Research Center (CEDAR), Oregon Health & Science University, Portland, OR, USA
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Kristof A. Torkenczy
1Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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Andrew J. Fields
1Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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Kevin M. Wright
3Vollum Institute, Oregon Health & Science University, Portland, OR, USA
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Xiaolin Nan
2Knight Cancer Institute’s Cancer Early Detection Advanced Research Center (CEDAR), Oregon Health & Science University, Portland, OR, USA
4Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
5Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
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Ramesh Ramji
6Illumina Inc, San Diego, CA, USA
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Frank J. Steemers
6Illumina Inc, San Diego, CA, USA
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Brian J. O’Roak
1Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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  • For correspondence: adey@ohsu.edu oroak@ohsu.edu
Andrew C. Adey
1Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
2Knight Cancer Institute’s Cancer Early Detection Advanced Research Center (CEDAR), Oregon Health & Science University, Portland, OR, USA
5Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
7Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
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  • For correspondence: adey@ohsu.edu oroak@ohsu.edu
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Abstract

Development is a complex process that requires the precise modulation of regulatory gene networks controlled through dynamic changes in the epigenome. Single-cell-omic technologies provide an avenue for understanding the mechanisms of these processes by capturing the progression of epigenetic cell states during the course of cellular differentiation using in vitro or in vivo models1. However, current single-cell epigenomic methods are limited in the information garnered per individual cell, which in turn limits their ability to measure chromatin dynamics and state shifts. Single-cell combinatorial indexing (sci-) has been applied as a strategy for identifying single-cell-omic originating libraries and removes the necessity of single-cell, single-compartment chemistry2. Here, we report an improved sci-assay for transposase accessible chromatin by sequencing (ATAC-seq), which utilizes the small molecule inhibitor Pitstop 2™ (scip-ATAC-seq)3. We demonstrate that these improvements, which theoretically could be applied to any in situ transposition method for single-cell library preparation, significantly increase the ability of transposase to enter the nucleus and generate highly complex single-cell libraries, without altering biological signal. We applied sci-ATAC-seq and scip-ATAC-seq to characterize the chromatin dynamics of developing forebrain-like organoids, an in vitro model of human corticogenesis4. Using these data, we characterized novel putative regulatory elements, compared the epigenome of the organoid model to human cortex data, generated a high-resolution pseudotemporal map of chromatin accessibility through differentiation, and measured epigenomic changes coinciding with a neurogenic fate decision point. Finally, we combined transcription factor motif accessibility with gene activity (GA) scores to directly observe the dynamics of complex regulatory programs that regulate neurogenesis through developmental pseudotime. Overall, scip-ATAC-seq increases information content per cell and bolsters the potential for future single-cell studies into complex developmental processes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 15, 2019.
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Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis
Ryan M. Mulqueen, Brooke A. DeRosa, Casey A. Thornton, Zeynep Sayar, Kristof A. Torkenczy, Andrew J. Fields, Kevin M. Wright, Xiaolin Nan, Ramesh Ramji, Frank J. Steemers, Brian J. O’Roak, Andrew C. Adey
bioRxiv 637256; doi: https://doi.org/10.1101/637256
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Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis
Ryan M. Mulqueen, Brooke A. DeRosa, Casey A. Thornton, Zeynep Sayar, Kristof A. Torkenczy, Andrew J. Fields, Kevin M. Wright, Xiaolin Nan, Ramesh Ramji, Frank J. Steemers, Brian J. O’Roak, Andrew C. Adey
bioRxiv 637256; doi: https://doi.org/10.1101/637256

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