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| Status |
Public on Jul 27, 2020 |
| Title |
DNA polymerase stalling at structured DNA predicts the stability of short tandem repeats |
| Organism |
synthetic construct |
| Experiment type |
Other
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| Summary |
Short tandem repeats (STRs) significantly contribute to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their low complexity and repetitive nature induces DNA polymerase slippage and stalling, leading to length variation and base substitutions. However, the characterisation of DNA synthesis through STR loci has been restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour. In order to understand the interplay between the ability of a given STR to impair DNA synthesis and its genomic stability, we developed a high-throughput polymerase extension assay that allows monitoring the kinetics of DNA synthesis at all STR permutations in different lengths in parallel. We have used the assay to map at single-nucleotide resolution the movement of a prototypical A-family replicative DNA polymerase (T7 DNA polymerase) through the repeats over time. From this data we can infer the secondary structure adopted by a given STR from the precise manner in which it stalls polymerase and link this to slippage and point mutation during DNA synthesis.
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| Overall design |
Deep sequencing of the replication intermediates observed during primer extension reactions using a library of repeated sequences.
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| Contributor(s) |
Murat P, Guilbaud G, Sale JE |
| Citation(s) |
32819438 |
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| Submission date |
Jan 29, 2020 |
| Last update date |
Aug 31, 2020 |
| Contact name |
Julian E Sale |
| E-mail(s) |
jes@mrc-lmb.cam.ac.uk
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| Organization name |
MRC Laboratory of Molecular Biology
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| Department |
PNAC
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| Street address |
Cambridge Biomedical Campus, Francis Crick Ave
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| City |
Cambridge UK |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL21616 |
Illumina HiSeq 4000 (synthetic construct) |
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| Samples (24)
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| GSM4288585 |
Extended products, t = 0.5 min, replicate 1 |
| GSM4288586 |
Extended products, t = 1 min, replicate 1 |
| GSM4288587 |
Extended products, t = 2 min, replicate 1 |
| GSM4288588 |
Extended products, t = 30 min, replicate 1 |
| GSM4288589 |
Extended products, t = 4 min, replicate 1 |
| GSM4288590 |
Extended products, t = 0.5 min, replicate 2 |
| GSM4288591 |
Extended products, t = 1 min, replicate 2 |
| GSM4288592 |
Extended products, t = 2 min, replicate 2 |
| GSM4288593 |
Extended products, t = 30 min, replicate 2 |
| GSM4288594 |
Extended products, t = 4 min, replicate 2 |
| GSM4288595 |
Parental library, replicate 1-1 |
| GSM4288596 |
Parental library, replicate 1-2 |
| GSM4288597 |
Parental library, replicate 2-1 |
| GSM4288598 |
Parental library, replicate 2-2 |
| GSM4288599 |
Stalled products, t = 0.5 min, replicate 1 |
| GSM4288600 |
Stalled products, t = 1 min, replicate 1 |
| GSM4288601 |
Stalled products, t =2 min, replicate 1 |
| GSM4288602 |
Stalled products, t = 30 min, replicate 1 |
| GSM4288603 |
Stalled products, t = 4 min, replicate 1 |
| GSM4288604 |
Stalled products, t = 0.5 min, replicate 2 |
| GSM4288605 |
Stalled products, t = 1 min, replicate 2 |
| GSM4288606 |
Stalled products, t = 2 min, replicate 2 |
| GSM4288607 |
Stalled products, t = 30 min, replicate 2 |
| GSM4288608 |
Stalled products, t = 4 min, replicate 2 |
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| Relations |
| BioProject |
PRJNA603735 |
| SRA |
SRP245847 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144458_RAW.tar |
6.6 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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