van Der Sluijs et al. "DNA polymerase kappa is the primary translesion synthesis polymerase for aldehyde ICLs"
Authors/Creators
-
1.
Princess Máxima Center
-
2.
Oncode Institute
-
3.
Hubrecht Institute for Developmental Biology and Stem Cell Research
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4.
University Medical Center Utrecht
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5.
Leiden University Medical Center
Description
Paired-end raw 150 base-pair Illumina short-read sequencing data corresponding to four experimental replicate libraries: MutSeq 8, MutSeq 9, Mutseq 9 - depletion, and Mutseq 10 - depletion.
Abstract:
DNA interstrand crosslinks (ICLs) are highly cytotoxic lesions that block essential cellular processes like replication and transcription. Endogenous ICLs can be induced by reactive aldehydes produced during normal cellular metabolism. Defective repair of these aldehyde-induced ICLs is associated with Fanconi anemia (FA), a cancer predisposition syndrome. We previously showed that acetaldehyde-induced ICLs are repaired by the Fanconi anemia (FA) pathway and a novel excision-independent pathway. Here, we demonstrate that ICLs induced by acrolein, another cellular aldehyde, are also repaired by both pathways, establishing the generality of aldehyde ICL repair. Focusing on the FA pathway, we identify DNA polymerase kappa (Polκ) as the primary translesion synthesis (TLS) polymerase responsible for the insertion step during lesion bypass of unhooked aldehyde ICLs. This function requires Polκ's catalytic activity and PCNA interaction domains but is independent of Rev1 interaction. In contrast, Polκ has a minor non-catalytic role in the extension step of cisplatin ICL repair that is dependent on Rev1 interaction. Our work reveals a key role for Polκ in aldehyde ICL repair and provides mechanistic insights into how different ICL structures determine the choice of TLS polymerases during repair.
Notes
The following Tables 1-3 below provide information on the barcodes and sample conditions for all samples used to generate the pooled libraries in this study. Some barcodes were used for different sample conditions and contexts, hence the necessity to refer to these tables. Left and right flanking sequences and corresponding reference plasmid are provided for generation of mutation profiles with the SIQ program (van Schendel et al. 2022). Processed reads from corresponding barcodes/samples were mapped to the matching plasmid reference with bwamem2 (Vasimuddin et al. 2019).
Table 1: Mutseq 8 and Mutseq 9 Library Barcodes and Sample Conditions.
|
Condition |
Left Flank |
Right Flank |
ID |
Barcode |
Reference |
|
Pt |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B1 |
CAGTTAGT |
CTRL.fa |
|
AA-red |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B2 |
AATAGGAT |
CTRL.fa |
|
Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
B3 |
AACACGTG |
Ctrl-Acr-red.fa |
|
AA-nat |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B4 |
TGTAAAGG |
CTRL.fa |
|
Acr-nat |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B5 |
GAATCTAG |
CTRL.fa |
|
mono-AA |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B6 |
GAGTTCTC |
CTRL.fa |
|
mono-Acr |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B7 |
AACTGAGC |
CTRL.fa |
|
Ctrl |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B8 |
GCAAGTAC |
CTRL.fa |
|
Ctrl-Acr |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
B9 |
GATTCGTA |
Ctrl-Acr-red.fa |
|
AA-nat DMSO |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
A1 |
TAGGTGTT |
CTRL.fa |
|
Acr-nat DMSO |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
A2 |
AGCTACGT |
CTRL.fa |
|
AA-nat p97i |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
A3 |
TCCTATAT |
CTRL.fa |
|
Acr-nat p97i |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
A4 |
CAACTGTG |
CTRL.fa |
Table 2: Mutseq 9 - depletion Library Barcodes and Sample Conditions.
|
Condition |
Left Flank |
Right Flank |
ID |
Barcode |
Reference |
|
Mock Pt |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B1 |
CAGTTAGT |
CTRL.fa |
|
Mock AA-red |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B2 |
AATAGGAT |
CTRL.fa |
|
Mock Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
B3 |
AACACGTG |
Ctrl-Acr-red.fa |
|
Mock Ctrl |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B4 |
TGTAAAGG |
CTRL.fa |
|
Mock Ctrl-Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
B5 |
GAATCTAG |
Ctrl-Acr-red.fa |
|
∆Rev1 Pt |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B6 |
GAGTTCTC |
CTRL.fa |
|
∆Rev1 AA-red |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B7 |
AACTGAGC |
CTRL.fa |
|
∆Rev1 Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
B8 |
GCAAGTAC |
Ctrl-Acr-red.fa |
|
∆Rev1 Ctrl |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B9 |
GATTCGTA |
CTRL.fa |
|
∆Rev1 Ctrl-Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
B10 |
TAGTAGGA |
Ctrl-Acr-red.fa |
|
∆PolK Pt |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
A1 |
TAGGTGTT |
CTRL.fa |
|
∆PolK AA-red |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
A2 |
AGCTACGT |
CTRL.fa |
|
∆PolK Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
A3 |
TCCTATAT |
Ctrl-Acr-red.fa |
|
∆PolK Ctrl |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
A4 |
CAACTGTG |
CTRL.fa |
|
∆PolK Ctrl-Acr |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
A5 |
GTTGTAGG |
Ctrl-Acr-red.fa |
Table 3: Mutseq 10 - depletion Barcodes and Sample Conditions.
|
Condition |
Left Flank |
Right Flank |
ID |
Barcode |
Reference |
|
Mock Pt |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B1 |
CAGTTAGT |
CTRL.fa |
|
Mock AA-red |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B5 |
GAATCTAG |
CTRL.fa |
|
Mock Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
A1 |
TAGGTGTT |
Ctrl-Acr-red.fa |
|
Mock Ctrl |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B8 |
GCAAGTAC |
CTRL.fa |
|
Mock Ctrl-Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
A6 |
AGCCGACG |
Ctrl-Acr-red.fa |
|
∆Rev1 Pt |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B2 |
AATAGGAT |
CTRL.fa |
|
∆Rev1 AA-red |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B6 |
GAGTTCTC |
CTRL.fa |
|
∆Rev1 Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
A2 |
AGCTACGT |
Ctrl-Acr-red.fa |
|
∆Rev1 Ctrl |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B9 |
GATTCGTA |
CTRL.fa |
|
∆Rev1 Ctrl-Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
A8 |
CGAAACGC |
Ctrl-Acr-red.fa |
|
∆PolK Pt |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B4 |
TGTAAAGG |
CTRL.fa |
|
∆PolK AA-red |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B7 |
AACTGAGC |
CTRL.fa |
|
∆PolK Acr-red |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
A5 |
GTTGTAGG |
Ctrl-Acr-red.fa |
|
∆PolK Ctrl |
AGACAGCCCTCTTCC |
TCTTCTTTCGTGCGC |
B10 |
TAGTAGGA |
CTRL.fa |
|
∆PolK Ctrl-Acr |
AGACAGCCCTCTCAC |
GCTTCTTTCGTGCGC |
A9 |
GTCAGACC |
Ctrl-Acr-red.fa |
Files
all_barcodes.txt
Files
(155.7 MB)
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Additional details
Funding
- European Research Council
- ERC Consolidator Grant ERC-CoG 101003210
Dates
- Updated
-
2025-07-23