CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential

Youtao Lu, Jaehee Lee, Jifen Li, Srinivasa Rao Allu, Jinhui Wang, HyunBum Kim, Kevin L. Bullaughey, Stephen A. Fisher, C. Erik Nordgren, Jean G. Rosario, Stewart A. Anderson, Alexandra V. Ulyanova, Steven Brem, H. Isaac Chen, John A. Wolf, M. Sean Grady, Sergei A. Vinogradov, Junhyong Kim and James Eberwine ()
Additional contact information
Youtao Lu: University of Pennsylvania
Jaehee Lee: University of Pennsylvania
Jifen Li: University of Pennsylvania
Srinivasa Rao Allu: University of Pennsylvania
Jinhui Wang: University of Pennsylvania
HyunBum Kim: University of Pennsylvania
Kevin L. Bullaughey: University of Pennsylvania
Stephen A. Fisher: University of Pennsylvania
C. Erik Nordgren: University of Pennsylvania
Jean G. Rosario: University of Pennsylvania
Stewart A. Anderson: Children’s Hospital of Philadelphia
Alexandra V. Ulyanova: University of Pennsylvania
Steven Brem: University of Pennsylvania
H. Isaac Chen: University of Pennsylvania
John A. Wolf: University of Pennsylvania
M. Sean Grady: University of Pennsylvania
Sergei A. Vinogradov: University of Pennsylvania
Junhyong Kim: University of Pennsylvania
James Eberwine: University of Pennsylvania

Nature Communications, 2023, vol. 14, issue 1, 1-19

Abstract: Abstract Genomic DNA (gDNA) undergoes structural interconversion between single- and double-stranded states during transcription, DNA repair and replication, which is critical for cellular homeostasis. We describe “CHEX-seq” which identifies the single-stranded DNA (ssDNA) in situ in individual cells. CHEX-seq uses 3’-terminal blocked, light-activatable probes to prime the copying of ssDNA into complementary DNA that is sequenced, thereby reporting the genome-wide single-stranded chromatin landscape. CHEX-seq is benchmarked in human K562 cells, and its utilities are demonstrated in cultures of mouse and human brain cells as well as immunostained spatially localized neurons in brain sections. The amount of ssDNA is dynamically regulated in response to perturbation. CHEX-seq also identifies single-stranded regions of mitochondrial DNA in single cells. Surprisingly, CHEX-seq identifies single-stranded loci in mouse and human gDNA that catalyze porphyrin metalation in vitro, suggesting a catalytic activity for genomic ssDNA. We posit that endogenous DNA enzymatic activity is a function of genomic ssDNA.

Date: 2023
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DOI: 10.1038/s41467-023-43158-6

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