Comprehensive Genome-wide Protein-DNA Interactions Detected at Single Nucleotide Resolution
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Summary
ChIP-exo is described, where an exonuclease trims ChIP DNA to a precise distance from the crosslinking site to reveal diverse tendencies governing in vivo DNA binding specificity that include sequence variants, functionally distinct motifs, motif clustering, secondary interactions, and combinatorial modules within a compound motif.
- Type
- article
- Published
- 2011-12-09
- Cited by
- 806
- References
- 51
- Access
- Open access
- OpenAlex
- https://openalex.org/W1989419347
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:9736454
Keywords
Biology, Genome, Computational biology, DNA, Genetics
References
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Cited by
- Loss of Maternal CTCF Is Associated with Peri-Implantation Lethality of Ctcf Null Embryos
- RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data
- Genome-wide identification of nucleosome positioning determinants in schizosaccharomyces pombe
- Mechanisms of Antisense Transcription Initiation from the 3′ End of the GAL10 Coding Sequence In Vivo
- Fixated on fixation: using ChIP to interrogate the dynamics of chromatin interactions
- Host genetic studies in adult pulmonary tuberculosis.
- CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
- Endogenous Hot Spots of De Novo Telomere Addition in the Yeast Genome Contain Proximal Enhancers That Bind Cdc13
- Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast
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- Chromatin immunoprecipitation and chromatin immunoprecipitation with massively parallel sequencing on mouse embryonic tissue.
- Predicting In Vivo Transcription Factor Occupancy from In Vitro Binding
- The impact of the microbiota on transcriptional regulation in the vertebrate intestine
- Structural Determinants of DNA-binding Specificity for Hox Proteins
- Tipping the Balance: Factors That Influence the ER Signaling Network in Breast Cancer
- The Dynamic Nucleosome: Multiple Aspects of Positioning the +1 Nucleosome
- Transcriptional regulation of the mannosyltransferase-encoding gene pigm in inherited glycosylphosphatidylinositol (GPI) deficiency
- Genome-Wide Studies of Transcriptional Regulation in Human Liver Cells by High-throughput Sequencing
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