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ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.
Overall ChIP-seq has risen to be a very efficient method for determining these factors, but there is a rivaling method known as ChIP-on-chip. ChIP-on-chip , also known as ChIP-chip, is an experimental technique used to isolate and identify genomic sites occupied by specific DNA-binding proteins in living cells.
Introduced in 2007, ChIP sequencing (ChIP-seq) is a technology that uses chromatin immunoprecipitation to crosslink the proteins of interest to the DNA but then instead of using a micro-array, it uses the more accurate, higher throughput method of sequencing to localize interaction points. [13]
Recent advances in chromatin immunoprecipitation followed by sequencing have provided powerful ways to identify genome-wide profiling of DNA-binding proteins and histone modifications. [ 1 ] [ 2 ] The application of ChIP-seq methods has reliably discovered transcription factor binding sites and histone modification sites.
Wilbanks and colleagues [3] is a survey of the ChIP-seq peak callers, and Bailey et al. [4] is a description of practical guidelines for peak calling in ChIP-seq data. Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq [ 5 ] or m6Aseq [ 6 ] for detection of post-transcriptional RNA ...
ChIP-loop combines 3C with ChIP-seq to detect interactions between two loci of interest mediated by a protein of interest. [ 2 ] [ 46 ] The ChIP-loop may be useful in identifying long-range cis -interactions and trans interaction mediated through proteins since frequent DNA collisions will not occur.
The ChIA-PET method combines ChIP-based methods, [2] and Chromosome conformation capture (3C) based methods, [3] to extend the capabilities of both approaches. ChIP-Sequencing (ChIP-Seq) is a popular method used to identify transciption factor binding sites (TFBS) while 3C has been used to identify long-range chromatin interactions.
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. [9] ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. [9] In epigenomics, this is often used to assess histone modifications (such as ...