ChIP-Seq: advantages and challenges of a maturing technology

By P. Park. Nature reviews genetics, 2009

2,157 citations recorded by the source corpus.

Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes. Owing to the tremendous progress in next-generation sequencing technology, ChIP–seq offers higher resolution, less noise and greater coverage than its array-based predecessor ChIP–chip. With the decreasing cost of sequencing, ChIP–seq has become an indispensable tool for studying gene regulation and epigenetic mechanisms. In this Review, I describe the benefits and challenges in harnessing this technique with an emphasis on issues related to experimental design and data analysis. ChIP–seq experiments generate large quantities of data, and effective computational analysis will be crucial for uncovering biological mechanisms.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ad07a438761a4ec34dfa78191f94dedd60d714af

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Citations in the corpus

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections (2014, background): “The targets of a known TF can be identified experimentally with relatively high accuracy through chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) [15].”
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection (2010, neutral): “Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a technique that provides quantitative, genome-wide mapping of target protein binding events [1,2].”
Target specificity of the CRISPR-Cas9 system (2014, neutral): “Chromatin immunoprecipitation (ChIP) is a widely used technique for assaying genomewide binding of proteins on DNA in vivo [53].”
diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates (2013, background): “This has provided us with unprecedented details [2] of protein-DNA interactions at genes, as well as intergenic regions, in comparison with its predecessor, ChIP-chip.”
Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics (2010, methodology): “Cross-linking of intact cells (predominantly with formaldehyde) stabilizes protein-DNA complexes prior to selective immunoprecipitation, which has been used among others to map histone modifications or the in vivo position of transcription factors along target genes (70–72).”
High‐throughput DNA sequencing – concepts and limitations (2010, background): “Given the immense diversity, we have not discussed these applications in depth here; other reviews with a stronger focus on specific applications and data analysis are available [24, 82–88].”
Statistical Design and Analysis of RNA Sequencing Data (2010, background): “2008), epigenetic events (P ark 2009), copy number variants (A lkan et al .”
Measuring reproducibility of high-throughput experiments (2011, background): “We now state the background of ChIP-Seq data in more detail and refer to Park (2009) for a recent review.”