7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Abstract Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited res...
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| Format: | Article |
| Language: | English |
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BMC
2019-10-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-6088-0 |
| _version_ | 1828943704502566912 |
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| author | Jonas Ibn-Salem Miguel A. Andrade-Navarro |
| author_facet | Jonas Ibn-Salem Miguel A. Andrade-Navarro |
| author_sort | Jonas Ibn-Salem |
| collection | DOAJ |
| description | Abstract Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. Results While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals at loop anchor regions close to the directly bound site. We use the position and shape of ChIP-seq signals around CTCF motif pairs to predict whether they interact or not. We implemented this approach in a prediction method, termed Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C). We applied 7C to all CTCF motif pairs within 1 Mb in the human genome and validated predicted interactions with high-resolution Hi-C and ChIA-PET. A single ChIP-seq experiment from known architectural proteins (CTCF, Rad21, Znf143) but also from other TFs (like TRIM22 or RUNX3) predicts loops accurately. Importantly, 7C predicts loops in cell types and for TF ChIP-seq datasets not used in training. Conclusion 7C predicts chromatin loops which can help to associate TF binding sites to regulated genes. Furthermore, profiling of hundreds of ChIP-seq datasets results in novel candidate factors functionally involved in chromatin looping. Our method is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC. |
| first_indexed | 2024-12-14T04:19:12Z |
| format | Article |
| id | doaj.art-b7c2181126584be78605a8f18500a472 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T04:19:12Z |
| publishDate | 2019-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b7c2181126584be78605a8f18500a4722022-12-21T23:17:25ZengBMCBMC Genomics1471-21642019-10-0120111510.1186/s12864-019-6088-07C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifsJonas Ibn-Salem0Miguel A. Andrade-Navarro1Faculty of Biology, Johannes Gutenberg University of MainzFaculty of Biology, Johannes Gutenberg University of MainzAbstract Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. Results While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are co-immunoprecipitated and sequenced. This produces minor ChIP-seq signals at loop anchor regions close to the directly bound site. We use the position and shape of ChIP-seq signals around CTCF motif pairs to predict whether they interact or not. We implemented this approach in a prediction method, termed Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C). We applied 7C to all CTCF motif pairs within 1 Mb in the human genome and validated predicted interactions with high-resolution Hi-C and ChIA-PET. A single ChIP-seq experiment from known architectural proteins (CTCF, Rad21, Znf143) but also from other TFs (like TRIM22 or RUNX3) predicts loops accurately. Importantly, 7C predicts loops in cell types and for TF ChIP-seq datasets not used in training. Conclusion 7C predicts chromatin loops which can help to associate TF binding sites to regulated genes. Furthermore, profiling of hundreds of ChIP-seq datasets results in novel candidate factors functionally involved in chromatin looping. Our method is available as an R/Bioconductor package: http://bioconductor.org/packages/sevenC.http://link.springer.com/article/10.1186/s12864-019-6088-0Chromatin interactionsThree-dimensional genome architectureTranscription factorsChIP-seq3C4C |
| spellingShingle | Jonas Ibn-Salem Miguel A. Andrade-Navarro 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs BMC Genomics Chromatin interactions Three-dimensional genome architecture Transcription factors ChIP-seq 3C 4C |
| title | 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs |
| title_full | 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs |
| title_fullStr | 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs |
| title_full_unstemmed | 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs |
| title_short | 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs |
| title_sort | 7c computational chromosome conformation capture by correlation of chip seq at ctcf motifs |
| topic | Chromatin interactions Three-dimensional genome architecture Transcription factors ChIP-seq 3C 4C |
| url | http://link.springer.com/article/10.1186/s12864-019-6088-0 |
| work_keys_str_mv | AT jonasibnsalem 7ccomputationalchromosomeconformationcapturebycorrelationofchipseqatctcfmotifs AT miguelaandradenavarro 7ccomputationalchromosomeconformationcapturebycorrelationofchipseqatctcfmotifs |