HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation

Cell Rep. 2020 Jun 2;31(9):107705. doi: 10.1016/j.celrep.2020.107705.

Abstract

5-Hydroxymethylcytosine (5hmC) binding, ES-cell-specific (HMCES) crosslinks to apurinic or apyrimidinic (AP, abasic) sites in single-strand DNA (ssDNA). To determine whether HMCES responds to the ssDNA abasic site in cells, we exploited the activity of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3A (APOBEC3A). APOBEC3A preferentially deaminates cytosines to uracils in ssDNA, which are then converted to abasic sites by uracil DNA glycosylase. We find that HMCES-deficient cells are hypersensitive to nuclear APOBEC3A localization. HMCES relocalizes to chromatin in response to nuclear APOBEC3A and protects abasic sites from processing into double-strand breaks (DSBs). Abasic sites induced by APOBEC3A slow both leading and lagging strand synthesis, and HMCES prevents further slowing of the replication fork by translesion synthesis (TLS) polymerases zeta (Polζ) and kappa (Polκ). Thus, our study provides direct evidence that HMCES responds to ssDNA abasic sites in cells to prevent DNA cleavage and balance the engagement of TLS polymerases.

Keywords: APOBEC; DNA damage; DNA repair; HMCES; abasic site; damage tolerance; replication stress; translesion synthesis.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • 5-Methylcytosine / analogs & derivatives
  • 5-Methylcytosine / metabolism
  • Cell Line
  • Cell Nucleus / metabolism
  • Chromatin / metabolism
  • Cytidine Deaminase / genetics
  • Cytidine Deaminase / metabolism*
  • DNA Breaks, Double-Stranded*
  • DNA Replication
  • DNA, Single-Stranded / metabolism
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / antagonists & inhibitors
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / genetics
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / metabolism
  • DNA-Binding Proteins / antagonists & inhibitors
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • DNA-Directed DNA Polymerase / chemistry
  • DNA-Directed DNA Polymerase / genetics
  • DNA-Directed DNA Polymerase / metabolism
  • Deamination
  • Endonucleases / antagonists & inhibitors
  • Endonucleases / genetics
  • Endonucleases / metabolism
  • Humans
  • Multifunctional Enzymes / antagonists & inhibitors
  • Multifunctional Enzymes / genetics
  • Multifunctional Enzymes / metabolism
  • Proteins / genetics
  • Proteins / metabolism*
  • RNA Interference
  • RNA, Small Interfering / metabolism
  • Uracil / metabolism
  • Uracil-DNA Glycosidase / metabolism

Substances

  • Chromatin
  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • HMCES protein, human
  • Multifunctional Enzymes
  • Proteins
  • RNA, Small Interfering
  • 5-hydroxymethylcytosine
  • Uracil
  • 5-Methylcytosine
  • DNA polymerase zeta
  • DNA-Directed DNA Polymerase
  • POLK protein, human
  • Endonucleases
  • Uracil-DNA Glycosidase
  • APOBEC3A protein, human
  • Cytidine Deaminase
  • APEX2 protein, human
  • DNA-(Apurinic or Apyrimidinic Site) Lyase