GEO series

RAD51 proximity mapping reveals spatial constraints on homology search during DNA double-stranded break repair

GSE304074 Homo sapiens Genome binding/occupancy profiling by high throughput sequencing 118 samples Submitted 2026/07/15 Platform GPL24676Platform GPL34281

Summary

DNA double-stranded breaks (DSBs) are an especially toxic form of damage that can be reversed without loss of genetic information by homology-directed repair (HDR), which copies from an intact template molecule. Finding a correct template within millions to billions of other DNA bases is termed homology search and is mediated by the protein RAD51. A major challenge in understanding homology search is the lack of tools to monitor search itself, rather than the end-stage outcome of HDR. We developed RAD51 proximity identification sequencing (RaPID-seq), a highly sensitive in cellulo method that marks all DNA searched by RAD51, regardless of whether it is chosen as the final template. We find that HDR in human cells is hierarchical. Only DSB-proximal sequences are searched, and even identical sequences outside the proximal window are not efficiently interrogated. Final recombination is unlocked by template homology but only at proximal sequences. We further find that RAD51 efficiently searches exogenously introduced DNA templates, such as those commonly used during genome editing, even those with no homology to the DSB site. Such highly abundant exogenous templates compete with search of endogenous genome templates. Our data reveal the invisible process of homology search and shed new light on fundamental mechanisms underlying genome editing.

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Direct links to NCBI, no account and no request form: the whole study as GSE304074_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 118 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1298870 and SRA study SRP604718. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

40 conditions, each sampled once — no replicated groups

Read from the first 40 of 118 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.

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