Cell News

The Structure and Function of Chromatin

Chromatin is a complex of macromolecules composed of DNA, RNA, and protein, which is found inside the nucleus of eukaryotic cells. Chromatin exists in two forms: heterochromatin (condensed) and euchromatin (extended). The primary protein components of chromatin are histones that help to organize DNA into “bead-like” structures called nucleosomes by providing a base on which the DNA can be wrapped around. A nucleosome consists of 147 base pairs of DNA that is wrapped around a set of 8 histones called an octomer. The nucleosome can be further folded to produce the chromatin fiber. Chromatin fibers are coiled and condensed to form chromosomes. Chromatin makes it possible for a number of cell processes to occur including DNA replication, transcription, DNA repair, genetic recombination, and cell division.

DNA in the nucleus is packaged with proteins to form chromatin. The fundamental repeating unit of chromatin is the nucleosome which is composed of approximately two turns of DNA wrapped around a protein core of two molecules of each of the core histones H2A, H2B, H3 and H4. Investigations on chromatin assembly in vitro implicate chromatin assembly factor 1 (CAF1) as a chaperone for histones H3/H4 and nucleosome assembly protein 1 (NAP1) as a chaperone for histones H2A/H2B. Chromatin assembly factor-1 (CAF-1) is a protein complex – including Chaf1a (p150), Chaf1b (p60), and p48 subunits in humans, or Cac1, Cac2, and Cac3, respectively, in yeast- that assembles histone tetramers onto replicating DNA during the S phase of the cell cycle.

Chromatin Assembly Factor 1 (CAF1) and Nucleosome Assembly Protein 1 (NAP1)

Chromatin assembly factor 1 (CAF1) Chaf1a (p150)
Chaf1b (p60)
Nucleosome assembly protein 1 (NAP1) NAP1L1
NAPL2
NAPL3
NAPL4
NAPL5
NAPL6

Core Histones Products

Family Subfamily Members
H2A H2AF H2AFB1H2AFB2H2AFB3H2AFJH2AFVH2AFXH2AFYH2AFY2, H2AFZ
H2A1 HIST1H2AAHIST1H2AB, HIST1H2ACHIST1H2AGHIST1H2AIHIST1H2AKHIST1H2ALHIST1H2AM
H2A2 HIST2H2AA3HIST2H2AC
H2B H2BF H2BFMH2BFSH2BFWT
H2B1 HIST1H2BAHIST1H2BBHIST1H2BCHIST1H2BDHIST1H2BGHIST1H2BHHIST1H2BJ, HIST1H2BKHIST1H2BNHIST1H2BO
H2B2 HIST2H2BE
H3 H3A1 HIST1H3AHIST1H3BHIST1H3CHIST1H3DHIST1H3EHIST1H3GHIST1H3H
H3A2 HIST2H3C
H3A3 HIST3H3
H4 H41 HIST1H4BHIST1H4DHIST1H4HHIST1H4I
H44 HIST4H4

More Epigenetics Antibodies

The Structure and Function of Chromatin

Chromatin, Chromosomes and Chromatids

People often confuse these three terms: chromatin, chromosome, and chromatid. While all of those three structures are composed of DNA and proteins within the nucleus, each is uniquely defined.

As mentioned above, chromatin is composed of DNA and histones that are packaged into thin, stringy fibers. The chromatin undergoes further condensation to form the chromosome. So the chromatin is a lower order of DNA organization, while chromosomes are the higher order of DNA organization.

Chromosomes are single-stranded groupings of condensed chromatin. During the cell division processes of mitosis and meiosis, chromosomes replicate to ensure that each new daughter cell receives the correct number of chromosomes. A duplicated chromosome is double-stranded and has the familiar X shape. The two strands are identical and connected at a central region called the centromere.

A chromatid is either of the two strands of a replicated chromosome. Chromatids connected by a centromere are called sister chromatids. At the end of cell division, sister chromatids separate and become daughter chromosomes in the newly formed daughter cells.

The Function of Chromatin

DNA Packaging

This is the most fundamental function of chromatin: compactification of long DNA strands.The length of DNA in the nucleus is far greater than the size of the compartment in which it is stored. To fit into this compartment the DNA has to be condensed in some manner. Packing ratio is used to describe the degree to which DNA is condensed. To achieve the overall packing ratio, DNA is not packaged directly into structure of chromatin. Instead, it contains several hierarchies of organization.

The first level of packing is achieved by the winding of DNA around the nucleosome, which gives a packing ratio of about 6. This structure is invariant in both the euchromatin and heterochromatin of all chromosomes. The second level of packing is the wrapping of beads in a 30 nm fiber that is found in both interphase chromatin and mitotic chromosomes. This structure increases the packing ratio to about 40. The final packaging occurs when the fiber is organized in loops, scaffolds and domains that give a final packing ratio of about 1,000 in interphase chromatin and about 10,000 in mitotic chromosomes.

Transcription Regulation

Transcription is a process in which the genetic information stored in DNA is read by proteins and then transcribed into RNA, and the RNA will later be translated into functional proteins. If the chromatin gets strengthened and restricts access to the read proteins, there are no transcription occurs. Euchromatin, an extended type of chromatin, can conduct the process of transcription. While heterochromatin, the condensed type of chromatin, is packed too tightly for DNA to be read by proteins.

Fluctuations between open and closed chromatin may contribute to the discontinuity of transcription, or transcriptional bursting. Other factors may probably be involved, such as the association and dissociation of transcription factor complexes with chromatin. The phenomenon, as opposed to simple probabilistic models of transcription, can account for the high variability in gene expression occurring between cells in isogenic population

Chromatin and DNA Repair

The packaging of DNA into the chromatin presents a barrier to all DNA-based processes. Due to the high dynamic arrangement of proteins and DNA, chromatin can readily change its shape and structure. Chromatin relaxation occurs rapidly at the site of a DNA damage, which allows the repair proteins to bind to DNA and repair it.

Reference:

1. Comings D E. The structure and function of chromatin [M]. Advances in human genetics. Springer US, 1972: 237-431.

2. Widom J. Structure, dynamics, and function of chromatin in vitro [J]. Annual review of biophysics and biomolecular structure, 1998, 27(1): 285-327.

3. Mercer T R, Mattick J S. Structure and function of long noncoding RNAs in epigenetic regulation [J]. Nature structural & molecular biology, 2013, 20(3): 300-307.