RAD54L2 counters TOP2-DNA adducts to promote genome stability (Etoposide treated RPE1 CRISPR screens in TP53 and RAD53L2 knock outs)

The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anti-cancer agents such as etoposide operate by stabilising TOP2ccs, ultimately generating genotoxic TOP2-DNA protein crosslinks that require processing and repair. Here, we identify RAD54-like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with TDP2 and TOP2 (ZATT/ZNF451) and independent of tyrosyl-DNA phosphodiesterase 2 (TDP2). Our work suggests a model wherein RAD54L2 recognises sumoylated-TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer-therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery., CRISPR screens were performed as described in the manuscript. Comparisons of guide abundances in treated and untreated samples were made with DrugZ. 
All comparisons are of DMSO vs Etoposide treated cells., , # CRISPR screen data

Counts and analyses of CRISPR screens.

## Description of the data and file structure

File names prefixes indicate which library was used in the crispr screen:

* gattinara.* – Screens conducted with the Broad Gattinara library
* SPJ_DDR_v2.* – Screens conducted with the custom SPJ DDR v2 library (see doi.org/10.7554/eLife.55325)

And suffixes indicate the type of data:

* *.drugz_output.tsv – Results from analyses using DrugZ. Comparisons were of DMSO vs etoposide treated cells of the same genotype. See DrugZ paper for details of the algorithm and precise definitions of the statistics reported (). Columns defined below:
* GENE: Gene symbol, as used in the counts files.
* sumZ: Un-normalised summed Z-scores per gene.
* numObs: Number of observations (guides) per gene.
* normZ: Normalised summed Z-score.
* pval_synth: p-value of synthetic lethality (i.e. the combination of guides targeting the named gene and the treatment cause...