Fine-Resolution Mapping of TF Binding and Chromatin Interactions
Summary: Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (shor...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2018-03-01
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| Series: | Cell Reports |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S221112471830233X |
| _version_ | 1828424666433191936 |
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| author | Jenia Gutin Ronen Sadeh Nitzan Bodenheimer Daphna Joseph-Strauss Avital Klein-Brill Adi Alajem Oren Ram Nir Friedman |
| author_facet | Jenia Gutin Ronen Sadeh Nitzan Bodenheimer Daphna Joseph-Strauss Avital Klein-Brill Adi Alajem Oren Ram Nir Friedman |
| author_sort | Jenia Gutin |
| collection | DOAJ |
| description | Summary: Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (short-fragment-enriched, low-input, indexed MNase ChIP), which combines enzymatic fragmentation of chromatin and on-bead indexing to address these desiderata. SLIM-ChIP reproduces a high-resolution binding map of yeast Reb1 comparable with existing methods, yet with less input material and full compatibility with high-throughput procedures. We demonstrate the robustness and flexibility of SLIM-ChIP by probing additional factors in yeast and mouse. Finally, we show that SLIM-ChIP provides information on the chromatin landscape surrounding the bound transcription factor. We identify a class of Reb1 sites where the proximal −1 nucleosome tightly interacts with Reb1 and maintains unidirectional transcription. SLIM-ChIP is an attractive solution for mapping DNA binding proteins and charting the surrounding chromatin occupancy landscape at a single-cell level. : Mapping transcription factors binding to DNA by chromatin immunoprecipitation sequencing is a key step in studying transcriptional programs. Gutin et al. introduce SLIM-ChIP, a simple, automation compatible protocol, that provides insights about the chromatin landscape at the bound sites. Using this protocol, they discover promoter architectures that enforce unidirectional transcription. Keywords: Reb1, CTCF, ChIP-seq, chromatin, transcription factor, DNA-binding, promoter directionality, nucleosomes |
| first_indexed | 2024-12-10T16:21:18Z |
| format | Article |
| id | doaj.art-d8f8baa4f4f64a3a895cab4ae35da467 |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-12-10T16:21:18Z |
| publishDate | 2018-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-d8f8baa4f4f64a3a895cab4ae35da4672022-12-22T01:41:49ZengElsevierCell Reports2211-12472018-03-01221027972807Fine-Resolution Mapping of TF Binding and Chromatin InteractionsJenia Gutin0Ronen Sadeh1Nitzan Bodenheimer2Daphna Joseph-Strauss3Avital Klein-Brill4Adi Alajem5Oren Ram6Nir Friedman7School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, IsraelSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Corresponding authorSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, IsraelSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, IsraelSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, IsraelInstitute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, IsraelInstitute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, IsraelSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Corresponding authorSummary: Transcription factor (TF) binding to DNA is crucial for transcriptional regulation. There are multiple methods for mapping such binding. These methods balance between input requirements, spatial resolution, and compatibility with high-throughput automation. Here, we describe SLIM-ChIP (short-fragment-enriched, low-input, indexed MNase ChIP), which combines enzymatic fragmentation of chromatin and on-bead indexing to address these desiderata. SLIM-ChIP reproduces a high-resolution binding map of yeast Reb1 comparable with existing methods, yet with less input material and full compatibility with high-throughput procedures. We demonstrate the robustness and flexibility of SLIM-ChIP by probing additional factors in yeast and mouse. Finally, we show that SLIM-ChIP provides information on the chromatin landscape surrounding the bound transcription factor. We identify a class of Reb1 sites where the proximal −1 nucleosome tightly interacts with Reb1 and maintains unidirectional transcription. SLIM-ChIP is an attractive solution for mapping DNA binding proteins and charting the surrounding chromatin occupancy landscape at a single-cell level. : Mapping transcription factors binding to DNA by chromatin immunoprecipitation sequencing is a key step in studying transcriptional programs. Gutin et al. introduce SLIM-ChIP, a simple, automation compatible protocol, that provides insights about the chromatin landscape at the bound sites. Using this protocol, they discover promoter architectures that enforce unidirectional transcription. Keywords: Reb1, CTCF, ChIP-seq, chromatin, transcription factor, DNA-binding, promoter directionality, nucleosomeshttp://www.sciencedirect.com/science/article/pii/S221112471830233X |
| spellingShingle | Jenia Gutin Ronen Sadeh Nitzan Bodenheimer Daphna Joseph-Strauss Avital Klein-Brill Adi Alajem Oren Ram Nir Friedman Fine-Resolution Mapping of TF Binding and Chromatin Interactions Cell Reports |
| title | Fine-Resolution Mapping of TF Binding and Chromatin Interactions |
| title_full | Fine-Resolution Mapping of TF Binding and Chromatin Interactions |
| title_fullStr | Fine-Resolution Mapping of TF Binding and Chromatin Interactions |
| title_full_unstemmed | Fine-Resolution Mapping of TF Binding and Chromatin Interactions |
| title_short | Fine-Resolution Mapping of TF Binding and Chromatin Interactions |
| title_sort | fine resolution mapping of tf binding and chromatin interactions |
| url | http://www.sciencedirect.com/science/article/pii/S221112471830233X |
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