CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
14 11 2023
14 11 2023
Historique:
received:
30
05
2023
accepted:
02
11
2023
medline:
16
11
2023
pubmed:
15
11
2023
entrez:
14
11
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37963886
doi: 10.1038/s41467-023-43158-6
pii: 10.1038/s41467-023-43158-6
pmc: PMC10645931
doi:
Substances chimiques
DNA, Single-Stranded
0
DNA
9007-49-2
DNA-Binding Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
7346Subventions
Organisme : NIAAA NIH HHS
ID : DP1 AA028409
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH110185
Pays : United States
Organisme : NHGRI NIH HHS
ID : RM1 HG010023
Pays : United States
Organisme : NIMH NIH HHS
ID : U01 MH098953
Pays : United States
Informations de copyright
© 2023. The Author(s).
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