Automated modeling of protein accumulation at DNA damage sites using qFADD.py Journal Article uri icon

Overview

abstract

  • Abstract; Eukaryotic cells are constantly subject to DNA damage, often with detrimental consequences for the health of the organism. Cells mitigate this DNA damage through a variety of repair pathways involving a diverse and large number of different proteins. To better understand the cellular response to DNA damage, one needs accurate measurements of the accumulation, retention, and dissipation timescales of these repair proteins. Here, we describe an automated implementation of the “quantitation of fluorescence accumulation after DNA damage” method that greatly enhances the analysis and quantitation of the widely used technique known as laser microirradiation, which is used to study the recruitment of DNA repair proteins to sites of DNA damage. This open-source implementation (“qFADD.py”) is available as a stand-alone software package that can be run on laptops or computer clusters. Our implementation includes corrections for nuclear drift, an automated grid search for the model of a best fit, and the ability to model both horizontal striping and speckle experiments. To improve statistical rigor, the grid-search algorithm also includes automated simulation of replicates. As a practical example, we present and discuss the recruitment dynamics of the early responder PARP1 to DNA damage sites.

publication date

  • January 1, 2022

has restriction

  • hybrid

Date in CU Experts

  • August 30, 2022 3:18 AM

Full Author List

  • Bowerman S; Mahadevan J; Benson P; Rudolph J; Luger K

author count

  • 5

Other Profiles

Electronic International Standard Serial Number (EISSN)

  • 2633-903X

Additional Document Info

volume

  • 2

number

  • e8