What is Chromatin?

Deoxyribonucleic acid (DNA) is a polymer made of two polynucleotide chains that coil around one another to form a double helix and which contains the genetic material necessary for all known creatures, including many viruses, to develop, function, grow, and reproduce. Nucleic acids include DNA and ribonucleic acid (RNA). Nucleic acids are one of the four main categories of macromolecules that are necessary for all known forms of life, along with proteins, lipids, and complex carbohydrates (polysaccharides).

Chromatin

• Eukaryotic chromosomes are housed in a distinct cellular structure known as the nucleus.
• To fit DNA into the nucleus, a significant amount of its length must be compressed.
• The binding of DNA to numerous different cellular proteins results in the compacting of DNA.
• The packing is finished by the nucleoprotein complex known as chromatin, a highly structured DNA-protein complex.
• Chromatin is a dynamic structure that can change during a cell’s lifetime in terms of both form and composition (cell cycle).
• At the metaphase stage, chromosomes are extremely condensed, and during interphase, very dispersed structures are present.

Chromosome

Single-stranded collections of compacted chromatin make up chromosomes. Chromosomes replicate during the cell division processes of mitosis and meiosis to guarantee that each new daughter cell has the appropriate amount of chromosomes. A duplicated chromosome bears the well-known X shape and is double-stranded. The centromere is a central area where the two strands are linked and are of equal length.

Chromatid

A chromatid can be one of a replicated chromosome’s two strands. Sister chromatids are chromatids connected by a centromere. Sister chromatids split at the conclusion of cell division to create daughter chromosomes in the newly created daughter cells.

Chromatin Composition and Packaging

Histones

1. Histones make up the vast bulk of the proteins in chromatin.
2. Small, positively charged proteins known as histones come in five main varieties: H1, H2A, H2B, H3, and H4.
3. High concentrations of the basic amino acids arginine and lysine are found in high concentrations in histones.
4. These positively charged amino acids provide the histones a net positive charge, which makes it easier for them to connect to the negatively charged DNA.
5. DNA and histone are both equally abundant in chromatin.
6. Eukaryotic chromosomes also include a wide range of non-histone chromosomal proteins.
7. Sometimes one of the main histone proteins is replaced in chromatin by variant histones with alternative amino acid sequences.
8. Even among animals that are distantly related, the amino acid sequences of histones H2A, H2B, H3, AND H4 are remarkably conserved.
9. These amino acid sequences’ evolutionary constancy strongly suggests that histones play the same fundamental function in arranging the DNA in chromosomes throughout all eukaryotes.
10. All histones are eventually related to one another in terms of evolution, according to structural analyses that indicate the histone classes indeed have a common tertiary structure.

Role of H1

1. Histone H1 causes the chromatin to condense at the next level.
2. H1 is not a component of the core particle, in contrast to the other histones.
3. H1 attaches to 20–22 bp of DNA at the points where the strands enter and exit the octamer.
4. H1 binds to both the middle of the DNA segment encircling core histones and the linker DNA at one end of the nucleosome.
5. H1 acts as a clamp around the nucleosome octamer and serves to confine the DNA into position.
6. The chromatosome is the collective name for the core particle and the H1 histone that it associates with.

Nucleosomes

1. When chromatin is separated from a cell’s nucleus and seen with an electron microscope, it looks like beads strung together.
2. The nucleosome is created when DNA and protein are broken down by nuclease enzymes.
3. The nucleosome is the simplest level of chromatin and the basic structural and functional unit of chromatin.
4. A nucleosome is a core particle created when DNA is wrapped around an octamer of eight histone proteins approximately twice (2 copies each of H2A, H2B, H3, H4).
5. Between 145 and 147 bp of DNA are in direct touch with the histone octamer.
6. The DNA is six times more compact in this format.

Linker DNA

1. About 167 bp of DNA are included in each chromatosome (147 bp around the nucleosome +20 bp bound by H1).
2. Chromosomes are spaced apart from one another along the DNA molecule at regular intervals by linker DNA.
3. Different cell types have different linker DNA sizes, however, in most cells, linker DNA is between 30 and 40 bp in length.

30nm Chromatin Fiber

• The nucleosomes group together to form the 30nm chromatin fiber, a structure with a diameter of around 30nm.
• For the 30nm z, two models are possible.
• They are:
  • Solenoid model: In this concept, a linear array of nucleosomes is wound into a solenoid of higher order, a left-handed helix with about six nucleosomes on each turn.
  • Helix model: Nucleosomes are grouped in this model in the shape of a ribbon that twists or supercoils.

Three Stages of Chromatin Organization

1. Nucleosomes also referred to as “beads on a string” structures, are created when DNA is wrapped around histone proteins (euchromatin).
2. A 30-nanometer fiber made of many histones and nucleosome arrays at their most solid state (heterochromatin).
3. The 30-nm fiber’s higher-level DNA supercoiling produces the metaphase chromosome (throughout mitosis and meiosis).

Different creatures do not adhere to this structure. For example, eukaryotic cells and protozoa do not compress their chromatin into visible chromosomes at all, avian red blood cells and spermatozoa have more densely packed chromatin than most trypanosomatids. In order to shape their DNA, prokaryotic cells have an entirely distinct architecture (the prokaryotic chromosome is equal and is called a genophore and is confined within the nucleoid region).

The cell cycle stages serve as the foundation for the chromatin system’s straightforward structure. Because chromatin is physically free during interphase, DNA and RNA polymerases can access it and copy and replicate the DNA. The precise genes that are present in the DNA determine the basic structure of chromatin during interphase. In a structure known as euchromatin, DNA contains genes that are loosely packed and strongly tied to RNA polymerases, whereas heterochromatin, which contains sections with dormant genes, is typically more densely packed and linked to structural proteins. The structural proteins in chromatin that are altered epigenetically by acetylation and methylation also change the shape of restricted chromatin, which affects gene expression.

Cell-Cycle Structural Organization

1. Interphase: While the DNA is being squeezed into the nucleus during the interphase of mitosis, the structure of chromatin is adjusted to permit straightforward access of transcription and DNA repair components to the DNA. Depending on how much access to the DNA is required, the structure changes. Euchromatin must transmit the looser structure to genes that need fixed access from RNA polymerase.
2. Metaphase: The chromatin structure in metaphase is significantly different from that in interphase. It is designed to be physically strong and manageable, forming the traditional chromosome shape seen in karyotypes. According to current theories, the compressed chromatin is composed of loops of 30 nm fiber supporting a protein core. It still lacks a clear definition. For this step of the division, chromatin strength is crucial to prevent DNA damage from shear as the daughter chromosomes are divided. As the chromatin approaches the centromere, its organization alters to maximize strength, mostly due to alternate histone H1 equivalents. Also keep in mind that while the majority of the chromatin is tightly compressed during mitosis, there are a few small areas that are not. These regions frequently connect to the promoter regions of genes that resided in that cell type prior to chromatid entrance. Bookmarking, an epigenetic mechanism thought to be important for passing to daughter cells the “remember” of which genes were active earlier to enter into mitosis, is the lack of space in certain regions. Due to the fact that transcription ends during mitosis, this bookmarking process is necessary to aid in the dissemination of this memory.

Chromatin in Mitosis

1. Prophase: Chromatin fibers transform into coiled chromosomes during mitosis’ prophase. Two chromatids are joined or connected at a centromere on each duplicated chromosome.
2. Metaphase: The chromatin becomes incredibly thick during the metaphase. At the metaphase plate, the chromosomes align.
3. Anaphase: The sister chromatids, or paired chromosomes, split during anaphase and are dragged to the cell’s periphery by the spindle microtubules.
4. Telophase: Each brand-new daughter chromosome splits into its own nucleus during telophase. Chromatin fibers loosen up and become less compressed. Two genetically identical daughter cells are created after cytokinesis. There are an equal amount of chromosomes in each cell. Chromatin is created as the chromosomes continue to lengthen and uncoil.

Euchromatin and Heterochromatin

Depending on the cell’s stage in the cell cycle, the amount of condensed chromatin inside a cell might vary. Heterochromatin or euchromatin can be found in the nucleus. The cell goes through a phase of growth during the interphase of the cycle rather than separating. Euchromatin, a less compressed form of chromatin, makes up the majority of it. In euchromatin, more DNA is visible, enabling DNA transcription and replication. The DNA double helix unwinds and opens during transcription to enable the replication of the genes that code for proteins. In order for the cell to produce DNA, proteins, and organelles in preparation for cell division, DNA replication and transcription are necessary. Heterochromatin makes up a modest portion of the chromatin during interphase. Since this chromatin is tightly packed, gene transcription cannot take place. Dye stains on heterochromatin are darker than those on euchromatin.

Chromatin Function

At first, chromatin was thought to be the component that gave the cell nucleus its color. Later, it was discovered that it is one of the most significant DNA expression controllers and is not merely a coloring agent. The structure of chromosomes is crucial for DNA replication. DNA is packaged in chromatin and nucleosomes, forming a tightly closed structure that is inaccessible to the enzymes in charge of transcription, replication, and DNA repair.

Only a minimal level of gene expression is permitted due to the transcriptionally restrictive packing of DNA structure. The DNA can more easily be copied and transcribed for nucleosome structures that are open or damaged.

Some repressors and activators that interact with RNA to control gene activity during transcription alter the chromatin structure. Activators alter the nucleosome’s structure, stimulating the assembly of the RNA polymerase. Similar modulation of chromatin structure also takes place during replication, enabling the replication mechanism to exist at the replication origin.

The regulation of gene expression is another function of chromatin. By placing the genes next to silent heterochromatic chromatins, a phenomenon known as location effect variegation can cause the genes to become transcriptionally inactive. Up to 1000 kilobase pairs can separate silent heterochromatin chromatins from genes. Since it results in phenotypic diversity, this phenomenon is known as epigenetics.

FAQs on Chromatin

Question 1: What is chromatin made of?

Answer:

The term “chromatin” describes the DNA and protein mixture that makes up the chromosomes found in the cells of humans and other higher creatures. The enormous amount of DNA contained in a genome is packaged by many proteins, most notably histones, into a form that can fit inside the cell nucleus.

Question 2: Where is chromatin stored?

Answer:

Eukaryotic cells’ nuclei include a combination of macromolecules called chromatin, which is made up of DNA, RNA, and protein.

Question 3: What is the main function of chromatin?

Answer:

The primary role of chromatin is to condense lengthy DNA molecules into smaller volumes by packaging them into compact, dense structures.

Question 4: What are the two types of chromatin?

Answer:

There are two varieties of chromatin. One type, referred to as euchromatin, is less compressed and capable of transcription. Heterochromatin is the name of the second type, which is extremely compressed and not usually transcribed.

Question 5: What is half a chromosome called?

Answer:

One of a chromosome’s two identical halves that have been replicated in preparation for cell division is known as a chromatid. The centromere, a constrictive area of the chromosome, is where the two “sister” chromatids are linked.

Question 6: What is facultative chromatin?

Answer:

The cytological expression of epigenetic mechanisms that control gene expression is facultative heterochromatin. Histone H3 methylation and the presence of HP1 proteins distinguish constitutive heterochromatin from facultative heterochromatin, whose chromatin alterations are less well understood.