DNA Damage Tolerance Mechanisms Revealed from the Analysis of Immunoglobulin V Gene Diversification in Avian DT40 Cells.

Takuya Abe,Dana Branzei,Kouji Hirota

doi:10.3390/genes9120614

Takuya Abe, Dana Branzei + Show 1 more

Open Access

https://doi.org/10.3390/genes9120614

Copy DOI

Abstract

DNA replication is an essential biochemical reaction in dividing cells that frequently stalls at damaged sites. Homologous/homeologous recombination (HR)-mediated template switch and translesion DNA synthesis (TLS)-mediated bypass processes release arrested DNA replication forks. These mechanisms are pivotal for replication fork maintenance and play critical roles in DNA damage tolerance (DDT) and gap-filling. The avian DT40 B lymphocyte cell line provides an opportunity to examine HR-mediated template switch and TLS triggered by abasic sites by sequencing the constitutively diversifying immunoglobulin light-chain variable gene (IgV). During IgV diversification, activation-induced deaminase (AID) converts dC to dU, which in turn is excised by uracil DNA glycosylase and yields abasic sites within a defined window of around 500 base pairs. These abasic sites can induce gene conversion with a set of homeologous upstream pseudogenes via the HR-mediated template switch, resulting in templated mutagenesis, or can be bypassed directly by TLS, resulting in non-templated somatic hypermutation at dC/dG base pairs. In this review, we discuss recent works unveiling IgV diversification mechanisms in avian DT40 cells, which shed light on DDT mode usage in vertebrate cells and tolerance of abasic sites.

Highlights

Cellular DNA is continuously damaged by chemical and physical agents from both endogenous metabolic processes and exogenous insults
immunoglobulin variable (IgV) diversification, activation-induced deaminase (AID) converts dC to dU, which in turn is excised by uracil DNA glycosylase and yields abasic sites within a defined window of around 500 base pairs
One mode is mediated through homologous recombination (HR), continuous replication using a newly synthesized sister strand [10,12,13]

Summary

Introduction

Cellular DNA is continuously damaged by chemical and physical agents from both endogenous metabolic processes and exogenous insults. Replicative DNA polymerases replicate genomic DNA with extraordinarily high accuracy, making only a single error per 106 nucleotides synthesized in vivo [1] Due to this enzymatic property, replicative polymerases cannot accommodate nucleotides at damaged templates and arrest replication [2]. One mode is mediated through homologous recombination (HR), continuous replication using a newly synthesized sister strand [10,12,13] A second mode is translesion DNA synthesis (TLS), which employs specialized DNA polymerases, including polymerase η and polymerase ζ, to permit continuous replication beyond newly synthesized sister strand [10,12,13] (Figure 1A). (TLS), which employs specialized DNA polymerases, including polymerase η and polymerase ζ, to permit continuous replication beyond the damaged template [14,15,16,17,18] (Figure 1B)

B: TLS polymerases mediated TLS

Templated Mutagenesis by Gene Conversion

Nontemplated

Nontemplated Somatic Hypermutation

Summary and Perspective

Method