Overview - What is chromatin immunoprecipitation sequencing (ChIP-seq)?
One of the most popular techniques for exploring DNA-protein interaction is ChIP-Seq or ChIP sequencing. ChIP-Seq combines chromatin immunoprecipitation (ChIP) with next-generation sequencing (NGS) to identify the genomic loci of DNA-protein binding sites. ChIP-Seq can be used to investigate any protein of interest and locate potential binding sites in the entire genome of a specific organism. The method is applicable to research on histone modifications, DNA methylation, nucleosome positioning and functional elements of the genome.
ChIP-Seq experiments have helped improve the understanding of normal and abnormal transcription and gene regulation, cell cycle checkpoint control, DNA synthesis, DNA repair, immune response, signal transduction, embryonic development, viral protein-human genome associations and much more.
Applications - What are the advantages of ChIP-Seq?
The immunoprecipitation and NGS-based technique is ideal for exploring DNA and histone modifications, as well as DNA-transcription factor links, because the method:
- Generates high resolution data with a low signal-to-noise ratio
- Functions for samples with low-input DNA
- Interrogates DNA targets for protein-binding sites or is applied for chromatin modifications in the entire genome
- Suited for nearly any organism
- Can be used to explore any chromatin-associated protein of interest
Workflow - Methods & Technologies for ChIP-Seq
Chromatin is a DNA packaging complex that is mainly composed of nucleic acids and histones. During chromatin immunoprecipitation (ChIP), DNA-binding proteins are crosslinked to DNA found in chromatin complexes in vivo. The cross-linked DNA fragments are sheared, and protein-bound DNA fragments are selectively immunoprecipitated by using antibodies that are specific to the protein of interest. Subsequently, the immunoprecipitated DNA fragments are most often analysed with microarrays (ChIP-Chip) or NGS (ChIP-Seq).
ChIP-Chip vs. ChIP-Seq
ChIP-Chip uses micorarrays to analyse DNA-protein binding sites. The technique can provide a global view of DNA-protein interactions in a relatively inexpensive manner. ChIP-Seq is increasingly displacing ChIP-Chip, as the next-generation sequencing-based method offers several advantages over ChIP-Chip. ChIP-Seq is applicable to nearly any organism and requires less input DNA for more sensitive and more specific protein-binding-site identification compared to ChIP-Chip. Due to its higher sensitivity, ChIP-Seq is also more efficient at discovering unknown protein binding sites.
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