Genome Content and Organisation Notes

Genes and Genomes: An Overview

• Genome: Entire DNA content, including genes and intergenic regions.

• Transcriptome: Entire set of gene transcripts (mRNAs) in a cell.

• Proteome: Entire set of proteins encoded by a genome.

The Human Genome

• Size: 3.3 x 10^9 basepairs (over 3 billion).

• Chromosomes: 24 (22 autosomes, 2 sex chromosomes).

• Protein-coding exons: Roughly 2%.

• Number of genes: Approximately 20,000.

Mitochondrial Genome

• Size: 16,569 base pairs.

• Structure: One circular chromosome.

• Copies per mitochondrion: 10,000.

• Genes: 37 (13 protein-coding, 2 ribosomal RNA, 22 transfer RNAs).

Genome Size and Genetic Complexity

• No simple correlation between genome size (C value) and genetic complexity (gene number).

• C-value paradox: the amount of DNA in a haploid genome does not correlate with the complexity of the organism.

• Gene density and the proportion of coding vs. non-coding DNA are important factors.

Genome Content Percentages

• Exons: 2%

• Introns: 24%

• Large duplications: 5%

• Simple repeats: 3%

• Retrotransposons: 45%

• Other intergenic DNA: 21%

Repetitive vs. Non-Repetitive DNA

• Repetitive DNA: Sequences (5-5000 bp) present in multiple copies, usually non-coding.

  • Examples: centromeres, telomeres.

• Non-repetitive DNA: Unique sequences, one copy per haploid genome.

  • Includes >98% of protein-encoding genes, gene clusters.

Non-Repetitive DNA

• Protein-coding genes and genes encoding certain RNAs.

• Gene clusters/families: Sets of genes with similar functions (e.g., globin genes).

• Pseudogenes: Non-functional gene sequences similar to functional genes.

Gene Families

• Arise through duplication during evolution.

• Related on sequence level, perform similar functions.

• Example: Globin family (myoglobin vs. hemoglobin).

Pseudogenes

• Non-repetitive DNA components.

• Sequence similar to functional genes but do not produce functional products.

• Types: processed (from reverse transcription) and non-processed (from gene duplication or mutation).

Repetitive DNA Details

• Present in multiple copies.

• Located in specific regions (centromeres, telomeres).

• Often lack function.

Types of Repetitive DNA

• Highly repetitive: Satellite DNA, tandem repeats.

• Middle repetitive: Interspersed retrotransposons (SINEs, LINEs), multiple copy genes.

Repetition Frequency (f)

• Number of times a DNA sequence appears in a haploid genome.

• Different types of repetitive DNA have different f values.

• Highly repetitive: >10^6 (simple sequence).

• Middle repetitive: 10^3-10^5.

Repetitive DNA: Satellite DNA

• Satellite: e.g., human alphoid DNA repeat.

• Minisatellite: e.g., human telomeres (TTAGGG repeats).

• Microsatellite: Found in genes; e.g., CAG repeats in Huntington's disease.

Repetitive DNA: Interspersed Genome-Wide Repeats

• LINEs (Long Interspersed Nuclear Elements): e.g., human LINE-1.

• SINEs (Short Interspersed Nuclear Elements): e.g., human Alu sequence (10% of the human genome).

Summary of Genome Organization

• Cells contain nuclear and mitochondrial genomes.

• Genome size does not correlate well with genome complexity.

• Genomes are classified into repetitive and non-repetitive sequences.

• Non-repetitive sequences are the majority in higher mammals.

• Non-repetitive sequences have structural roles in genome organization.