A computational pipeline to visualize DNA-protein binding states using dSMF data
Summary: 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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722001794 |
| _version_ | 1817989220039393280 |
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| author | Satyanarayan Rao Srinivas Ramachandran |
| author_facet | Satyanarayan Rao Srinivas Ramachandran |
| author_sort | Satyanarayan Rao |
| collection | DOAJ |
| description | Summary: 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). |
| first_indexed | 2024-04-14T00:44:23Z |
| format | Article |
| id | doaj.art-7d11cf6285574effb7b959b82911c493 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-14T00:44:23Z |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-7d11cf6285574effb7b959b82911c4932022-12-22T02:22:05ZengElsevierSTAR Protocols2666-16672022-06-0132101299A computational pipeline to visualize DNA-protein binding states using dSMF dataSatyanarayan Rao0Srinivas Ramachandran1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA; Corresponding authorDepartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA; Corresponding authorSummary: 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).http://www.sciencedirect.com/science/article/pii/S2666166722001794BioinformaticsSequence analysisGenomicsMolecular Biology |
| spellingShingle | Satyanarayan Rao Srinivas Ramachandran A computational pipeline to visualize DNA-protein binding states using dSMF data STAR Protocols Bioinformatics Sequence analysis Genomics Molecular Biology |
| 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 | Bioinformatics Sequence analysis Genomics Molecular Biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722001794 |
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