Genome diversity and the organisation of DNA in chromosomes

Diversity in viral genomes

• Extremely diverse in size: 4–2,500 kb.

• Genome types:

  • DNA or RNA, single-stranded or double-stranded.

  • Linear or circular.

• Examples:

  • Bacteriophage λ: linear dsDNA, ~48.5 kb.

  • Influenza virus: segmented, negative-sense RNA.

Diversity in bacteria genomes

• Typical genome: 1–10 Mb, mostly circular DNA.

• Low proportion of non-coding DNA compared to eukaryotes (~10–15% non-coding).

• Often contain plasmids, small extrachromosomal DNA with accessory genes.

• Can have operons, clusters of functionally related genes controlled by a single promoter.

Diversity in eukaryote genomes

• Genome size highly variable (C-value paradox): not correlated with organismal complexity.

• Example ranges:

  • Yeast (S. cerevisiae): ~12 Mb, ~6,000 genes.

  • Humans: ~3,200 Mb, ~20,000–25,000 genes.

• Larger genomes contain highly repetitive DNA and transposable elements.

• Genome complexity is mostly in regulatory regions and chromatin organization.

Bacterial Genome compaction mechanisms

Chromosome organized into looped domains (50–100 kb loops in E. coli, ~4,500 kb total chromosome)

• supercoiling

• Nucleoid-associated proteins (NAPs)

• Chromosomal Interaction Domains (CIDs)

• SMC-like proteins

supercoiling

Negative supercoiling condenses DNA and helps in replication and transcription

Nucleoid-associated proteins (NAPs)

• E.g., H-NS, HU, Fis in E. coli.

• Bind DNA and stabilize loops.

Chromosomal Interaction Domains (CIDs)

Hi-C experiments show:

• Domains formed by looping.

• Boundaries correspond to highly transcribed genes.

• Disruption of transcription (e.g., rifampicin) abolishes these domains.

SMC-like proteins

Help align chromosome arms; promote large-scale organization

Bacterial Genome Compaction experimental example

• Hi-C in C. crescentus revealed square “domains” in contact maps.

• Moving highly expressed genes creates new boundaries.

C-value Paradox

• Observation: Genome size does not correlate with organismal complexity.

• Examples:

  • Fugu rubripes (~400 Mb, ~20,000 genes) vs. humans (~3,200 Mb, ~20,000 genes).

  • Plants often have enormous genomes due to repetitive DNA and polyploidy.

• Explanation: Most DNA in large genomes is non-coding or repetitive, not additional genes.

Classes of DNA in Eukaryotic Genomes

• Unique/Single-copy DNA

• Moderately repetitive DNA

• Highly repetitive DNA

• Transposable elements

• Special sequences

Unique/Single-copy DNA

• Includes most protein-coding genes.

• Example: human β-globin gene.

Moderately repetitive DNA

• Present in 10–1,000 copies.

• Examples: rRNA genes, tRNA genes.

Highly repetitive DNA

• Tandem repeats: satellite, minisatellite, microsatellite DNA.

• Often found at centromeres and telomeres.

Transposable sequences

• Retrotransposons and DNA transposons.

• Contribute to genome expansion.

Special sequences

• Centromeres: alpha-satellite DNA in humans.

• Telomeres: TTAGGG repeats in humans.

Core histones

H2A, H2B, H3, H4 → form nucleosome octamer.

Linker histone

H1 → stabilizes higher-order chromatin

histone modification

• Acetylation: loosens chromatin → transcriptionally active.

• Methylation: depends on site; e.g., H3K9me → heterochromatin, H3K4me → euchromatin.

Histone chaperones

e.g., CAF-1, HJURP (CENP-A deposition at centromeres)

nucleosome organisation in chromatid structure

• DNA wrapped around histone octamer (~147 bp DNA per nucleosome).

• Nucleosomes compact into 30-nm fiber, then looped domains.

Euchromatin

• less condensed DNA

• Active transcription of genes

• Histone marks: H3K4me, acetylation

• e.g. Gene-rich chromosome interiors

Heterochromatin

• highly condensed dna

• silent genes

• Histone marks: H3K9me, hypoacetylation

• e.g. Pericentromeric regions, inactive X chromosome

function of centromeres

• Site of kinetochore assembly → chromosome segregation during mitosis/meiosis.

• Bind CENP-A, a histone H3 variant.

• Flanked by heterochromatin to stabilize function.

CENP-A Deposition

• Mediated by histone chaperones.

• Precise regulation critical: excess CENP-A → ectopic centromeres → missegregation.

neocentromeres

• Functional centromeres forming at non-traditional sequences.

• Epigenetically inherited.

• Experimental example: human chromosome 10 deletion forms a neocentromere at a new site (marker deletion, mardel).

centromere epigenetic inheritance

• Centromere location maintained through histone modifications, not just DNA sequence.

• Rare loss of centromere → inactivation, though DNA remains unchanged.

telomere structure

• Repetitive TTAGGG (humans), G-rich 3′ overhang.

• Forms t-loops for protection.

telomere function

• Protect chromosome ends.

• Solve end-replication problem.

telomerase

• RNA + protein enzyme.

• Extends G-rich strand using RNA template.

• Complementary strand filled by conventional DNA polymerase.

Shelterin Complex (human)

• POT1: binds G-overhang.

• TPP1/TIN2: scaffold proteins.

• TRF1/TRF2: double-stranded telomere binding.

• RAP1: associated with TRF2.

• Mutations in Shelterin → telomere shortening or elongation.

• Recombination-based elongation occurs in some cells lacking telomerase.

Boundary Elements and Chromatin Domains

• Function: Prevent heterochromatin spreading into euchromatin.

• Examples:

  • Drosophila position-effect variegation of white+ gene.

  • S. pombe boundaries flanking centromeric heterochromatin.

Boundary Elements and Chromatin Domains mechanisms

• Binding of specific proteins (e.g., Swi6/HP1).

• Organizing chromatin into looped domains/TADs.

• Anchoring to nuclear periphery → heterochromatin formation.

Higher-order chromosome organization in nucleus

• Loops → TADs → chromosome territories.

• Chromosome territories: discrete nuclear domains.

• Gene-rich chromosomes often interior, gene-poor chromosomes periphery.

Rabl chromosome Configuration in nucleus

Centromeres cluster at one end, telomeres at the other post-mitosis

Transcription-dependent chromosome organization in nucleus

• Active transcription → expansion of chromosome territory.

• Silenced genes may relocate near pericentromeric heterochromatin (shown in Drosophila brown locus).

experimental examples of Chromosome Architecture in the Nucleus

• Hi-C: DNA-DNA interactions across genome; TADs visible as triangles.

• FISH: confirm co-localization of regions within TADs.

• Electron microscopy: heterochromatin at nuclear periphery.

Mitochondria genomes

• Circular DNA (~16 kb in humans).

• Encodes 13 proteins, 22 tRNAs, 2 rRNAs.

• Replicates independently of nuclear genome.

chloroplast genomes

• Circular DNA (~120–160 kb in plants).

• Encodes photosynthesis-related genes and ribosomal RNAs.