DNA Packaging and Chromosome Structure: The Structural Basis of Cellular Information

DNA Packaging in Cells

Introduction to DNA Packaging

DNA packaging refers to the processes by which long DNA molecules are compacted to fit within the confines of a cell, and in eukaryotes, within the nucleus. Efficient packaging is essential for both protection and regulation of genetic material.

• Challenge: DNA molecules are much longer than the dimensions of the cell or nucleus, requiring complex packaging strategies.

• Key Terms: Chromosome, Nucleosome, Chromatin, Heterochromatin, Euchromatin, Centromeres, Telomeres, Repeated DNA, Nonrepeated DNA, Tandem Repeated DNA (STR), Interspersed Repeated DNA, Exons, Introns.

DNA Packaging in Bacteria

Bacterial Chromosomes

Bacterial DNA is organized in chromosomes and plasmids. The main bacterial genome is called the bacterial chromosome, which is typically a single, circular DNA molecule.

• Chromosome Structure: Most bacteria have a single circular chromosome, though some species may have multiple, linear, or circular chromosomes.

• Nucleoid: The chromosome is localized to a region called the nucleoid.

• Protein Association: DNA is bound to small amounts of protein and is negatively supercoiled and folded.

Organization of Bacterial DNA

• Loops: Bacterial DNA forms loops held in place by RNA and protein/s.

• Enzymatic Treatment: Ribonuclease degrades RNA, releasing some loops; topoisomerase relaxes supercoils but does not affect loop structure.

Bacterial Nucleoid

The nucleoid is the region within the bacterial cell where the chromosome is concentrated. Electron micrographs show the nucleoid as a distinct area, and released DNA appears as a tangled mass outside the cell.

Bacterial Plasmids

In addition to the chromosome, bacteria may contain plasmids: small, circular DNA molecules capable of autonomous replication.

• Function: Plasmids often carry genes for cellular functions such as antibiotic resistance, metabolic pathways, and virulence.

• Replication: Plasmids are supercoiled and replicate independently, but their replication is often coordinated with the chromosome.

Types of Plasmids

• F (Fertility) Factors: Involved in bacterial conjugation.

• R (Resistance) Factors: Carry genes for drug resistance.

• Col (Colicinogenic) Factors: Encode proteins that kill other bacteria.

• Virulence Factors: Enhance pathogenicity by encoding toxins.

• Metabolic Plasmids: Encode enzymes for specific metabolic reactions.

• Cryptic Plasmids: No known function.

DNA Packaging in Eukaryotes

Chromatin and Chromosomes

Eukaryotic DNA is associated with proteins to form chromatin. During cell division, chromatin condenses into visible chromosomes.

• Chromatin: DNA-protein complex that allows efficient packaging and regulation.

• Chromosome: Highly condensed chromatin visible during mitosis and meiosis.

Histones and Nucleosomes

Histones are small, basic proteins rich in lysine and arginine, which bind to negatively charged DNA. The basic unit of chromatin structure is the nucleosome.

• Types of Histones: H1, H2A, H2B, H3, H4. H1 is present in half the amount of the others and is associated with linker DNA.

• Nucleosome Structure: Consists of a histone octamer (2x H2A, 2x H2B, 2x H3, 2x H4) with 146 base pairs of DNA wrapped around it. Linker DNA connects nucleosomes.

Evidence for Nucleosomes

• Partial digestion of chromatin with nucleases produces DNA fragments at 200-bp intervals, indicating regular nucleosome spacing.

Chromatin Fiber Formation

Nucleosomes are packed together to form chromatin fibers. The "beads-on-a-string" structure is about 10 nm in diameter, while the more compact 30-nm fiber is facilitated by histone H1.

• Higher-Order Packing: 30-nm fibers are further folded into loops (50,000–100,000 bp) held by cohesin proteins and attached to a protein scaffold.

Chromatin Types: Euchromatin and Heterochromatin

Chromatin exists in two forms:

• Heterochromatin: Highly compacted, transcriptionally inactive, visible as dark regions in micrographs.

• Euchromatin: Less compacted, transcriptionally active, diffuse appearance.

Histone Modification and Chromatin Remodeling

Cells regulate chromatin structure and gene activity by modifying histones:

• Methylation: Addition of methyl groups to lysine residues by histone methyltransferases; can activate or repress transcription.

• Acetylation: Addition of acetyl groups by histone acetyltransferases (HATs); generally associated with gene activation.

• Deacetylation: Removal of acetyl groups by histone deacetylases (HDACs); associated with gene repression.

Effects: Acetylation leads to looser packing; methylation leads to tighter packing.

Special Chromosomal Regions

Centromeres

Centromeres are constricted regions of chromosomes bound by protein complexes, serving as sites for kinetochore formation and spindle attachment during cell division.

• DNA Sequence: Characterized by highly repetitive CEN sequences; centromeric chromatin contains a histone H3 variant called CENP-A.

Telomeres

Telomeres are found at chromosome ends, containing highly repetitive DNA sequences (e.g., TTAGGG in vertebrates) that protect chromosome ends from degradation and maintain stability during replication.

Chromosome Banding Patterns

Chromosomes can be identified by unique banding patterns produced by stains such as Giemsa, which reveal light and dark G bands, aiding in chromosome identification and karyotyping.

Types of DNA Sequences in the Genome

Repeated DNA Sequences

Genomes contain both repeated and nonrepeated DNA. Repeated DNA is classified as:

• Tandem Repeated DNA: Multiple copies arranged next to each other; accounts for 10–15% of mammalian genomes.

• Simple-Sequence Repeats: Short tandem repeats (<10 bases), also called satellite DNA.

• VNTRs: Variable number tandem repeats; minisatellites (10–100 bp) and microsatellites/STRs (short tandem repeats, 2–10 bp).

Application: STRs are used in DNA fingerprinting for paternity testing.

Interspersed Repeated DNA

Interspersed repeats are scattered throughout the genome, often as transposable elements (transposons). They account for 25–50% of mammalian genomes.

• LINEs: Long interspersed nuclear elements (6000–8000 bp), encode proteins for their own mobilization; ~20% of human genome.

• SINEs: Short interspersed nuclear elements (<500 bp), rely on other elements for movement; Alu sequences are the most common SINEs in humans (~10% of genome).

Organelle Genomes

Mitochondrial and Chloroplast DNA

Mitochondria and chloroplasts have their own circular chromosomes, devoid of histones. These organelles encode some of their own proteins but rely on nuclear genes for most functions.

• Human Mitochondrial Genome: 16,569 base pairs, encodes 37 genes (5% of needed RNAs and proteins).

• Chloroplast Genome: ~120,000 bp, ~120 genes; some protein subunits are encoded by the nuclear genome.

Summary Table: Types of Repeated DNA

Type	Structure	Length	Example	Function/Application
Tandem Repeats	Adjacent copies	1–2000 bp/unit	CAGCAGCAG	Satellite DNA, centromeres
VNTRs (Minisatellites)	Variable number	10–100 bp/unit	Minisatellite loci	DNA fingerprinting
STRs (Microsatellites)	Short repeats	2–10 bp/unit	STR loci	Paternity testing
LINEs	Dispersed	6000–8000 bp	LINE-1	Transposable elements
SINEs	Dispersed	<500 bp	Alu	Transposable elements

Key Equations

• Supercoiling: Linking number ($Lk$) = Twist ($Tw$) + Writhe ($Wr$)

• DNA Repeat Calculation: Total repeat length = Number of repeats × Length of repeat unit

Additional info: Chromatin structure and histone modifications are central to epigenetic regulation, affecting gene expression and cell identity.