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

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

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-s...

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Bibliographic Details
Published in:Nature communications Vol. 14; no. 1; p. 7346
Main Authors: Lu, Youtao, Lee, Jaehee, Li, Jifen, Allu, Srinivasa Rao, Wang, Jinhui, Kim, HyunBum, Bullaughey, Kevin L., Fisher, Stephen A., Nordgren, C. Erik, Rosario, Jean G., Anderson, Stewart A., Ulyanova, Alexandra V., Brem, Steven, Chen, H. Isaac, Wolf, John A., Grady, M. Sean, Vinogradov, Sergei A., Kim, Junhyong, Eberwine, James
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 14-11-2023
Nature Publishing Group
Nature Portfolio
Subjects:
45
45/23
631/1647/2217
631/337/100/101
631/378/340
Brain
Catalytic activity
Chromatin
Copying
Deoxyribonucleic acid
DNA
DNA - genetics
DNA biosynthesis
DNA probes
DNA Repair
DNA Replication
DNA, Single-Stranded - genetics
DNA-Binding Proteins - metabolism
Enzymatic activity
Genomics
Homeostasis
Humanities and Social Sciences
Humans
Mitochondrial DNA
multidisciplinary
Nucleotide sequence
Porphyrins
Science
Science (multidisciplinary)
Single-stranded DNA
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Summary: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. The in situ single-stranded open chromatin landscape is dynamically regulated in single cells. In their efforts to understand brain cells’ functional dynamics and to complement the other single-cell chromatin approaches, the authors present a method named CHEX-seq (CHromatin EXposed).
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content type line 23
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-023-43158-6