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DOI: 10.1201/9781003355205-6

C h a p t e r 6

Chromatin

Immunoprecipitation

Sequencing

6.1  INTRODUCTION TO CHROMATIN IMMUNOPRECIPITATION

In complex organisms like multicellular eukaryotes, each somatic cell in the body carries

exactly the same genome (set of DNA molecules) but gene expression varies from a type

of cells to another. A genome is formed of a set of chromosomes found in pairs in most

eukaryotic cells. These cells are called diploids. A chromosome is a DNA molecule formed

by the four basic nucleotides of the nucleobases: adenine (A), cytosine (C), guanine (G),

and thymine (T). The lengths of chromosomes of an organism vary and each chromosome

includes a different set of genes that code for different proteins. For the set of chromosomes

to fit the nucleus, each chromosome includes multiple repeated units around 147 bp in

length. These repeated units of DNA sequences wrapped around eight units (octamer) of

histone proteins forming structures called nucleosomes. A histone octamer is formed of

four different core histone units (H2A, H2B, H3, and H4). Nucleosomes are connected by

other family of histones called linker histone H1, which is highly susceptible to modifica-

tions. A chromosome and packing proteins (histones) are together called chromatin, and

when we mention a chromatin segment, we refer to a piece of raw DNA with histones.

Some environmental factors may lead to changes in chromatin causing the so-called

epigenetic changes that involve covalent modifications to chromatin structure. These epi-

genetic chromatin modifications include DNA methylation, histone modification (acetyla-

tion, phosphorylation, methylation, and ubiquitylation), and chromatin remodeling. Such

modifications affect gene expression without altering the DNA sequence and they deter-

mine the expression status of the protein-coding RNA (mRNAs) and other non-coding

RNA molecules. In general, epigenetic changes include any process that alters gene expres-

sion without changing the DNA sequence and leads to modifications that can be transmit-

ted to daughter cells. A wide variety of illnesses including cancers and many other health