Journal Article

Breakage of cytoplasmic chromosomes by pathological DNA base excision repair

Pellman, David, Cui, Yuxiang, Tang, Shangming, Stokasimov, Ema

2022

Overview

Chromothripsis is a catastrophic mutational process that promotes tumorigenesis and causes congenital disease 1 – 4 . Chromothripsis originates from aberrations of nuclei called micronuclei or chromosome bridges 5 – 8 . These structures are associated with fragile nuclear envelopes that spontaneously rupture 9 , 10 , leading to DNA damage when chromatin is exposed to the interphase cytoplasm. Here we identify a mechanism explaining a major fraction of this DNA damage. Micronuclei accumulate large amounts of RNA–DNA hybrids, which are edited by adenine deaminases acting on RNA (ADAR enzymes) to generate deoxyinosine. Deoxyinosine is then converted into abasic sites by a DNA base excision repair (BER) glycosylase, N -methyl-purine DNA glycosylase 11 , 12 (MPG). These abasic sites are cleaved by the BER endonuclease, apurinic/apyrimidinic endonuclease 12 (APE1), creating single-stranded DNA nicks that can be converted to DNA double strand breaks by DNA replication or when closely spaced nicks occur on opposite strands 13 , 14 . This model predicts that MPG should be able to remove the deoxyinosine base from the DNA strand of RNA–DNA hybrids, which we demonstrate using purified proteins and oligonucleotide substrates. These findings identify a mechanism for fragmentation of micronuclear chromosomes, an important step in generating chromothripsis. Rather than breaking any normal chromosome, we propose that the eukaryotic cytoplasm only damages chromosomes with pre-existing defects such as the DNA base abnormality described here. DNA damage during chromothripsis is caused by deoxyinosine formation on accumulated RNA–DNA hybrids in micronuclei that are then recognized by N -methyl-purine DNA glycosylase and cleaved by apurinic/apyrimidinic endonuclease.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 13 / 13/1 / 13/106 / 13/44 / 13/89 / 14/1 / 14/34 / 14/63 / 38/22 / 38/77 / 631/208/1405 / 631/337/1427/1429 / 631/337/1427/1979 / 631/337/1645/1944 / 631/80/103 / Adenine / Antibodies / Base excision repair / Cell cycle / Cell division / Chromatin / Chromosomes / Cyclin-dependent kinases / Cytoplasm / Damage accumulation / Deoxyribonucleic acid / DNA / DNA biosynthesis / DNA damage / DNA repair / Endonuclease / Enzymes / Genomes / Humanities and Social Sciences / Hybrids / Labeling / Micronuclei / multidisciplinary / Nuclear membranes / Oligonucleotides / Repair / Ribonucleic acid / RNA / Science / Science (multidisciplinary) / Single-stranded DNA / Substrates / Tumorigenesis