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Chromatin Organisation

Chromatin is the complex of DNA, histone proteins, and non-histone proteins that makes up the genetic material of eukaryotic cells. It is located inside the nucleus and serves as the structural framework that packages long DNA molecules into a compact, organized form that fits within the nucleus while allowing gene regulation, replication, and repair.

The term chromatin was first introduced by Walther Flemming (1882), derived from the Greek word chroma, meaning colour, as it stains intensely with basic dyes.

2. Chemical Composition of Chromatin

Chromatin is composed of:

• DNA (~30–40%)
• Histone proteins (~60%)
• Non-histone proteins (enzymes and regulatory proteins)
• RNA (small amount)

Histones are basic, positively charged proteins due to a high content of lysine and arginine. Non-histone proteins are acidic and play key roles in gene expression regulation and chromosome scaffolding.

3. Types of Chromatin

Chromatin exists in two major forms depending on its degree of condensation and transcriptional activity:

(a) Euchromatin

• Lightly stained, less condensed regions of chromatin.
• Transcriptionally active DNA — genes can be expressed.
• Found in the interior of the nucleus.
• Rich in gene sequences.
• Undergoes regular replication during the S-phase.

(b) Heterochromatin

• Densely stained, highly condensed regions.
• Transcriptionally inactive or silent DNA.
• Mostly located near the nuclear periphery.
• Replicates late in the S-phase.
• Found in centromeres, telomeres, and sometimes interspersed between euchromatin.

Heterochromatin is further classified as:

• Constitutive heterochromatin — permanently condensed, non-coding DNA (e.g., centromeres).
• Facultative heterochromatin — can switch between heterochromatin and euchromatin states depending on cell type or stage (e.g., Barr body or inactivated X chromosome).

4. Hierarchical Organisation of Chromatin Structure

The packaging of DNA into chromatin follows a multi-level hierarchical structure:

(a) Primary Structure – Nucleosome

• The fundamental repeating unit of chromatin is the nucleosome, discovered by Roger Kornberg (1974).
• Each nucleosome consists of:
  • A core particle of eight histone molecules (two each of H2A, H2B, H3, and H4).
  • ~146 base pairs of DNA wrapped around the histone octamer (1.65 turns).
  • A linker DNA segment (~20–80 bp) connecting adjacent nucleosomes.
  • H1 histone binds to the linker region and stabilizes the nucleosome.

This structure resembles “beads on a string” under an electron microscope.

(b) Secondary Structure – 30 nm Solenoid Fibre

• Nucleosomes further coil to form a 30 nm thick fibre known as the solenoid or zig-zag fibre.
• This structure is stabilized by histone H1 and non-histone scaffold proteins.
• It represents the chromatin fibre seen in interphase nuclei.

(c) Tertiary Structure – Looped Domains

• The 30 nm chromatin fibre forms looped domains (40–100 kb DNA) attached to a protein scaffold.
• These loops play an important role in gene regulation, bringing distant regulatory sequences close to promoters.

(d) Quaternary Structure – Higher-Order Coiling

• During mitosis, the looped domains are further coiled and folded to form metaphase chromosomes, the most compact form of chromatin.

5. Histone Code Hypothesis

Proposed by Strahl and Allis (2000), this hypothesis states that post-translational modifications (like methylation, acetylation, phosphorylation, ubiquitination) of histone tails act as a “code” that influences chromatin structure and gene expression.

For example:

• Histone acetylation → loosens chromatin → gene activation.
• Histone methylation → either activation or repression depending on the residue modified.

6. Functional Significance of Chromatin Organisation

1. Efficient DNA Packaging: Allows ~2 meters of DNA to fit into a nucleus of ~10 µm diameter.
2. Protection of DNA: Shields DNA from damage and enzymatic degradation.
3. Regulation of Gene Expression: Dynamic chromatin remodeling controls which genes are expressed.
4. Chromosome Segregation: Condensed chromatin ensures accurate segregation during mitosis and meiosis.
5. DNA Replication and Repair: Chromatin relaxation provides access to enzymes during replication and repair.

7. Chromatin Remodeling

Chromatin is a dynamic structure that can transition between condensed (inactive) and relaxed (active) states.
This is mediated by ATP-dependent chromatin remodeling complexes such as:

• SWI/SNF complex
• ISWI complex
• Mi-2/NuRD complex

These complexes reposition or evict nucleosomes to facilitate or repress transcription.

8. Nucleosome Positioning and Gene Regulation

The position of nucleosomes relative to promoter regions is critical for transcription:

• Promoter regions that are nucleosome-free allow transcription initiation.
• Repressive nucleosome positioning prevents access to RNA polymerase.

9. Differences Between Prokaryotic and Eukaryotic Chromatin

Feature	Prokaryotic DNA	Eukaryotic Chromatin
Location	Cytoplasm (nucleoid)	Nucleus
DNA-Protein Complex	Absent (no histones)	Present (histones + non-histones)
Structure	Naked, circular	Linear, wrapped around histones
Chromatin Forms	None	Euchromatin & Heterochromatin
Gene Regulation	Operon-based	Chromatin remodeling-based

Chromatin organisation is a key structural and functional adaptation of eukaryotic cells that balances DNA compaction with controlled gene accessibility. Understanding chromatin dynamics provides insight into gene regulation, cell differentiation, development, and diseases like cancer, where chromatin architecture is often altered.

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