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or chemically (Micrococcal nuclease (MNase) enzyme). The protein-DNA

complex is precipitated using antibodies produced particularly for the

desired protein. Acid treatment is employed for the release of precipitated

DNA, which is then detected by either sequencing, microarray or amplified

via polymerase chain reaction (PCR) (Park, 2009).

12.5.1.2 CHIP-SEQUENCING (CHIP-SEQ)

ChIP assay coupled with the next-generation sequencing methods is an

effective approach for locating the different sites across the whole genome

where DNA binds with transcription factors and other proteins. The use of

next-generation sequencing (NGS) on ChIP has provided useful data on gene

regulatory events involved in a variety of biological processes. ChIP-Seq

may be utilized for global mapping of protein-DNA interacting regions

genome-wide. Unlike arrays and other epigenome-related methods, which

are biased by the use of probes produced from known sequences, ChIP-Seq

does not require any previous information. ChIP-Seq uses massively parallel

sequencing to do genome-wide profiling, yielding millions of counts across

many samples enabling a cost-effective, precise, and impartial examination

of epigenetic profile (Park, 2009).

12.5.1.3 CHIP PCR

In this protocol analysis of protein-bound DNA sequences are immuno­

precipitated then the DNA fragments are detected and/or quantified in

ChIP-PCR with specific primers using TaqMan or Sybr Green Technologies.

In this technique, histone modifications and/or protein binding to a known

selected of desired loci in the genome are investigated using PCR. ChIP­

qPCR allows rapid and quantitative comparisons of a particular area within

the genome across numerous samples. This approach is less expensive and

faster than whole-genome sequencing.

12.5.1.4 CHIP MICROARRAY (CHIP-CHIP)

ChIP microarray (ChIP-Chip), or genome-wide mapping, integrates chro­

matin immunoprecipitation (ChIP) with DNA microarray for discovering

cellular protein-DNA associations. The antibody pulled down DNA is labeled