ChIP-seq and Beyond: new and improved methodologies to detect and characterize protein-DNA interactions

By Terrence S. Furey. Nature reviews genetics, 2012

762 citations recorded by the source corpus.

Chromatin immunoprecipitation experiments followed by sequencing (ChIP–seq) detect protein–DNA binding events and chemical modifications of histone proteins. Challenges in the standard ChIP–seq protocol have motivated recent enhancements in this approach, such as reducing the number of cells that are required and increasing the resolution. Complementary experimental approaches — for example, DNaseI hypersensitive site mapping and analysis of chromatin interactions that are mediated by particular proteins — provide additional information about DNA-binding proteins and their function. These data are now being used to identify variability in the functions of DNA-binding proteins across genomes and individuals. In this Review, I describe the latest advances in methods to detect and functionally characterize DNA-bound proteins.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e9435949640903e9325ad825a32168545ca9718b

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In Molecular Biology

1. Jian Peng
2. Mona Singh
3. Bonnie Berger
4. Andy Gardner
5. F. M. Ausubel
6. B. Slatko
7. Jinbo Xu
8. Sheng Wang

Citations in the corpus

• Computational solutions for omics data (2013, background): “…for a range of functional genomics experiments (for example, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP–seq) 158 to detect protein–DNA interactions, ultraviolet crosslinking and immunoprecipitation followed by sequencing (CLIP–seq) and related techniques…”
• Overview of Next Generation Sequencing Technologies (2018, background): “A large number of applications are supported, including targeted and de novo DNA and RNA sequencing, transcriptome sequencing, microbial sequencing, copy number variation detection, small RNA and miRNA sequencing, and CHIP-seq (chromatin immunoprecipitation sequencing; Furey, 2012).”