Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells

Lee, J.; Lu, Y.; Wang, J.; Li, J.; Fisher, S.; Nordren, C. E.; Rosario, J.; Anderson, S.; Ulyanova, A.; Brem, S.; Chen, H. I.; Wolf, J.; Grady, M. S.; Healy, M.; Kim, J.; Eberwine, J.

doi:10.1101/780387

bioRxiv · 10.1101/780387

Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells

Lee, J.·Lu, Y.·Wang, J.·Li, J.·Fisher, S.·Nordren, C. E.·Rosario, J.·Anderson, S.·Ulyanova, A.·Brem, S.·Chen, H. I.·Wolf, J.·Grady, M. S.·Healy, M.·Kim, J.·Eberwine, J.

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Abstract

Assays examining the open-chromatin landscape in single cells require isolation of the nucleus, resulting in the loss of spatial/microenvironment information. Here we describe CHEX-seq (CHromatin EXposed) for identifying single-stranded open-chromatin DNA regions in paraformaldehyde-fixed single cells. CHEX-seq uses light-activated DNA probes that binds to single-stranded DNA in open chromatin. In situ laser activation of the annealed probes 3-Lightning Terminator in selected cells permits the probe to act as a primer for in situ enzymatic copying of single-stranded DNA that is then sequenced. CHEX-seq is benchmarked with human K562 cells and its utility is demonstrated in dispersed primary mouse and human brain cells, and immunostained cells in mouse brain sections. Further, CHEX-seq queries the openness of mitochondrial DNA in single cells. Evaluation of an individual cells chromatin landscape in its tissue context enables \"spatial chromatin analysis\".\n\nOne Sentence SummaryA new method, CHEX-seq (CHromatin eXposed), identifies the open-chromatin landscape in single fixed cells thereby allowing spatial chromatin analysis of selected cells in complex cellular environments.

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Lee, J., Lu, Y., Wang, J., Li, J., Fisher, S., Nordren, C. E., Rosario, J., Anderson, S., Ulyanova, A., Brem, S., Chen, H. I., Wolf, J., Grady, M. S., Healy, M., Kim, J., Eberwine, J.. 2019-09-24. Single Cell Spatial Chromatin Analysis of Fixed Immunocytochemically Identified Neuronal Cells. https://doi.org/10.1101/780387

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