A computational pipeline to visualize DNA-protein binding states using dSMF data

Here, we present a pipeline to map states of protein-binding DNA in vivo. Our pipeline infers as well as quantifies cooperative binding. Using dual-enzyme single-molecule footprinting (dSMF) data, we show how our workflow identifies binding states at an enhancer in Drosophila S2 cells. Data from cel...

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Detalles Bibliográficos
Autores principales: Rao, Satyanarayan, Ramachandran, Srinivas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9026571/
https://www.ncbi.nlm.nih.gov/pubmed/35463472
http://dx.doi.org/10.1016/j.xpro.2022.101299
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author Rao, Satyanarayan
Ramachandran, Srinivas
author_facet Rao, Satyanarayan
Ramachandran, Srinivas
author_sort Rao, Satyanarayan
collection PubMed
description Here, we present a pipeline to map states of protein-binding DNA in vivo. Our pipeline infers as well as quantifies cooperative binding. Using dual-enzyme single-molecule footprinting (dSMF) data, we show how our workflow identifies binding states at an enhancer in Drosophila S2 cells. Data from cells lacking endogenous DNA methylation are a prerequisite for this pipeline. For complete details on the use and execution of this protocol, please refer to Rao et al. (2021) and Krebs et al. (2017).
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spelling pubmed-90265712022-04-23 A computational pipeline to visualize DNA-protein binding states using dSMF data Rao, Satyanarayan Ramachandran, Srinivas STAR Protoc Protocol Here, we present a pipeline to map states of protein-binding DNA in vivo. Our pipeline infers as well as quantifies cooperative binding. Using dual-enzyme single-molecule footprinting (dSMF) data, we show how our workflow identifies binding states at an enhancer in Drosophila S2 cells. Data from cells lacking endogenous DNA methylation are a prerequisite for this pipeline. For complete details on the use and execution of this protocol, please refer to Rao et al. (2021) and Krebs et al. (2017). Elsevier 2022-04-12 /pmc/articles/PMC9026571/ /pubmed/35463472 http://dx.doi.org/10.1016/j.xpro.2022.101299 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Rao, Satyanarayan
Ramachandran, Srinivas
A computational pipeline to visualize DNA-protein binding states using dSMF data
title A computational pipeline to visualize DNA-protein binding states using dSMF data
title_full A computational pipeline to visualize DNA-protein binding states using dSMF data
title_fullStr A computational pipeline to visualize DNA-protein binding states using dSMF data
title_full_unstemmed A computational pipeline to visualize DNA-protein binding states using dSMF data
title_short A computational pipeline to visualize DNA-protein binding states using dSMF data
title_sort computational pipeline to visualize dna-protein binding states using dsmf data
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9026571/
https://www.ncbi.nlm.nih.gov/pubmed/35463472
http://dx.doi.org/10.1016/j.xpro.2022.101299
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