Chapter 10: Molecular Structure of Chromosomes and Transposable Elements

Introduction

This chapter explores the molecular organization of chromosomes in both bacteria and eukaryotes, the mechanisms of chromosome compaction, and the role of transposable elements. Understanding these structures is fundamental to genetics, as chromosomes store, replicate, and transmit genetic information.

• Chromosomes are complexes of DNA and proteins that carry genetic information.

• Key functions of chromosomes include gene expression, replication, segregation, and compaction.

• Transposable elements (TEs) are DNA segments that can move to different chromosomal locations.

Organization of Bacterial Chromosomes

General Features

• Bacterial chromosomal DNA is typically a circular molecule a few million nucleotides long.

• Contains thousands of genes, mostly protein-coding.

• Intergenic regions are non-transcribed DNA between genes.

• Most bacteria have a single chromosome type, possibly in multiple copies.

• One origin of replication is required for DNA replication initiation.

• Repetitive sequences may be scattered throughout the chromosome.

Structure and Compaction

• The chromosome is located in the nucleoid, a region not bounded by a membrane, allowing direct contact with the cytoplasm.

• Nucleoid-associated proteins (NAPs) help compact and organize the chromosome, facilitate segregation, and regulate gene expression.

Loop Domains

• DNA is compacted ~1000-fold by forming loop domains (microdomains), each about 10,000 base pairs.

• In E. coli, there are 400–500 microdomains, further organized into macrodomains (800–1000 kb).

DNA Supercoiling

• Supercoiling is the additional coiling of DNA due to twisting forces, further compacting the chromosome.

• Negative supercoiling (underwinding) and positive supercoiling (overwinding) are possible; these forms are called topoisomers.

• In bacteria, DNA is mostly negatively supercoiled, aiding compaction and facilitating local strand separation for processes like transcription.

Enzymatic Control of Supercoiling

• DNA gyrase (topoisomerase II) introduces negative supercoils using ATP and can relax positive supercoils.

• DNA topoisomerase I relaxes negative supercoils.

• The balance of these enzymes maintains proper supercoiling.

DNA Gyrase Inhibitors

• Drugs such as quinolones (e.g., ciprofloxacin) and coumarins inhibit bacterial gyrase, serving as antibiotics.

• These drugs do not affect eukaryotic topoisomerases.

Organization of Eukaryotic Chromosomes

General Features

• Eukaryotes have one or more sets of linear chromosomes.

• Genes are interspersed with non-coding regions (introns, intergenic DNA).

• Three essential DNA sequence types:

  • Origins of replication: multiple per chromosome, required for DNA synthesis initiation.

  • Centromeres: regions for chromosome segregation during cell division.

  • Telomeres: specialized ends for replication and stability.

• Chromosomes in diploid species occur in sets (e.g., 2 sets in somatic cells).

• Chromosome size: tens to hundreds of millions of base pairs.

• Repetitive sequences are common, especially near centromeres and telomeres.

Genome Size and Complexity

• Eukaryotic genomes are much larger than bacterial genomes.

• Genome size does not correlate with organismal complexity; much of the variation is due to repetitive DNA rather than gene number.

• Example: Some amphibians (e.g., salamanders) have very large genomes.

Sequence Complexity

• Unique (non-repetitive) sequences: Found once or a few times; include most protein-coding genes and intergenic regions (about 41% of the human genome).

• Moderately repetitive sequences: Hundreds to thousands of copies; include rRNA, histone genes, regulatory sequences, and transposable elements.

• Highly repetitive sequences: Tens of thousands to millions of copies; short sequences (a few to several hundred nucleotides).

• Some are interspersed (e.g., Alu elements in humans, ~10% of the genome), others are in tandem arrays (e.g., AATAT repeats in Drosophila centromeres).

Table: Major Categories of Human Genome Sequences

Chromatin Structure in Eukaryotes

Chromatin and Compaction

• Chromatin is the DNA-protein complex in eukaryotic cells.

• Compaction is necessary to fit long DNA molecules into the small nucleus (e.g., 1 meter of DNA into a 2–4 μm nucleus).

• Compaction levels change during the cell cycle.

Nucleosomes

• The nucleosome is the fundamental repeating unit of chromatin.

• Composed of ~146–147 base pairs of DNA wrapped around a histone octamer (2 each of H2A, H2B, H3, H4).

• Linker DNA connects adjacent nucleosomes.

Histones

• Histones are basic proteins with many lysine and arginine residues, giving them a positive charge to bind negatively charged DNA.

• Each histone has a globular domain and a flexible, charged amino-terminal tail.

• Five types: H2A, H2B, H3, H4 (core histones), and H1 (linker histone).

• H1 binds to linker DNA and helps organize nucleosomes into higher-order structures.

Experimental Evidence for Nucleosome Structure

• Roger Kornberg proposed the nucleosome model in 1974, supported by biochemical, X-ray, and electron microscopy data.

• Markus Noll's DNase I digestion experiments showed that chromatin is cut into ~200 bp fragments, consistent with nucleosome spacing.

Higher-Order Chromatin Structure

• Nucleosomes fold into a 30 nm fiber, a more compact structure aided by H1.

• At moderate salt, H1 is removed, resulting in "beads-on-a-string"; at low salt, H1 remains, and nucleosomes pack into the 30 nm fiber.

• The zigzag model is one proposed structure for the 30 nm fiber.

Loop Domains and Further Compaction

• The 30 nm fiber forms loop domains (third level of compaction), further shortening DNA.

• CCCTC-binding factor (CTCF) binds to specific DNA sequences and, together with SMC proteins, forms chromatin loops.

• SMC proteins can dimerize and encircle DNA, forming and stabilizing loops.

Levels of Chromatin Compaction

• DNA double helix (2 nm)

• Nucleosomes (11 nm)

• 30 nm fiber

• Loop domains (300 nm)

• Further compaction (700 nm)

• Metaphase chromosome (1,400 nm)

Table: Levels of Chromatin Compaction

Chromosome Territories

• Each chromosome occupies a distinct region (territory) in the nucleus during interphase.

• Fluorescent staining shows that chromosomes do not intermingle randomly.

Heterochromatin vs. Euchromatin

• Heterochromatin: Highly compacted, transcriptionally inactive, further compacted loop domains.

• Euchromatin: Less condensed, transcriptionally active, 30 nm fiber forms loop domains.

Types of Heterochromatin

• Constitutive heterochromatin: Always compacted, permanently inactive, contains highly repetitive sequences (e.g., centromeres, telomeres).

• Facultative heterochromatin: Can switch between heterochromatin and euchromatin (e.g., X-chromosome inactivation).

Chromosome Structure During Cell Division

Compaction in M Phase

• During mitosis, chromosomes become highly condensed (metaphase chromosomes: 1,400 nm diameter).

• Condensed chromosomes are transcriptionally inactive.

Role of Protein Complexes

• Condensin: Promotes chromosome condensation; contains SMC proteins.

• Cohesin: Promotes sister chromatid cohesion; also contains SMC proteins.

• SMC proteins use ATP to change chromosome structure.

Condensin I and II

• Condensin II enters the nucleus during interphase and initiates condensation in early prophase.

• Condensin I is cytoplasmic until the nuclear envelope breaks down, then binds chromosomes to further compact loops.

• Condensin II forms a central scaffold; condensin I forms smaller loops within larger loops.

Cohesin and Sister Chromatid Cohesion

• After S phase, cohesin holds sister chromatids together along their length.

• During prophase, cohesin is removed from chromosome arms but remains at centromeres.

• At anaphase, centromeric cohesin is degraded, allowing chromatid separation.

Summary Table: Key Proteins in Chromosome Structure

Key Equations and Concepts

• Supercoiling: The linking number (L) of a closed-circular DNA is the sum of the number of base pairs per turn (T) and the number of supercoils (W):

• Negative supercoiling facilitates strand separation, important for replication and transcription.

Examples and Applications

• Antibiotics: Ciprofloxacin targets bacterial DNA gyrase, inhibiting DNA replication in bacteria but not in eukaryotes.

• Chromosome territories: Fluorescent in situ hybridization (FISH) can visualize chromosome territories in the nucleus.

• Facultative heterochromatin: X-chromosome inactivation in female mammals is an example of facultative heterochromatin.

Additional info: The chapter also covers the role of transposable elements in genome structure, though detailed mechanisms of transposition are not included in the provided slides. For a complete understanding, students should review the molecular mechanisms of transposition and its evolutionary significance.