11 Organisation of Genome

• Non-coding DNA sequences with important functions in eukaryotes

  • Introns
  • Centromeres
  • Telomeres
  • Promoters
  • Enhancers
  • Silencers
• Organisation of Genomes

  1. Nuclear genomes of eukaryotes differ greatly in size, number of genes, and gene density

  2. Number of chromosomes differs between species

  3. Certain organelles in eukaryotes possess small amounts of their own DNA

  4. Eukaryotic genomes generally have a higher proportion of non-coding DNA to coding DNA

  5. Bacteria have several plasmids in addition to a large, circular chromosome

  6. Bacteria exhibit genetic diversity through mutation and genetic transfer despite reproducing asexually

  7. Viral genomes vary in nature (DNA or RNA), single- or double-stranded, and may possess positive-sense or negative-sense RNA
• Knowledge of transposons, satellite DNA, pseudo-genes, and duplication of segments is not required
• Key structures and organization of prokaryotic and eukaryotic genomes

  • Size
  • Number of genes
  • Molecule
  • Number of origins of replication
  • Presence of Telomeres
  • Presence of Centromeres
  • Association with proteins involved in organisation of genome
  • Level of DNA packing/coiling
• The prokaryotic genome is located in the nucleoid region of the cell whereas most of the eukaryotic genome is located within the nucleus
• Eukaryotic genome features

  • Larger size (107-1011 base pairs)
  • More genes (7000 – 60 000)
  • Linear DNA molecules
  • Multiple origins of replication per chromosome
  • Telomeres present at both ends of the linear chromosome
  • Centromere present
  • Associate with a large number and type of histone proteins
  • Higher degree of DNA packing/coiling
• Genome


  The complete set of genetic material in a particular cell
• Prokaryotic genome features

  • Smaller size (105-107 base pairs)
  • Fewer genes (500 – 7500)
  • Double helical DNA molecule
  • One origin of replication per chromosome
  • No telomeres in chromosomes
  • No centromere present<|Associate with histone-like proteins<|Lower degree of DNA packing/coiling
• Formation of characteristic metaphase chromosome in a dividing cell


  Loops coil and fold further to produce characteristic metaphase chromosome in a dividing cell
• Presence of enhancers or silencers

  1. Prokaryotic genome: Present

  2. Eukaryotic genome: Present
• Non-coding regions in DNA

  • Prokaryotic genome: Not common (typically less than 15%)
  • Eukaryotic genome: Common (about 98%)
• Presence of introns

  1. Prokaryotic genome: Present but not as extensive as eukaryotes

  2. Eukaryotic genome: Present and more extensive than prokaryotes, introns are interspersed between exons of a gene
• Location of functionally-related genes on chromosomes

  1. Prokaryotic genome: Genes that encode proteins for the same metabolic pathway are grouped together in a single operon (e.g. lac Operon)

  2. Eukaryotic genome: Genes that encode functionally related proteins are usually located on different chromosomes
• Non-coding DNA sequences with important functions

  • Promoter
  • Introns
  • Terminator
  • Distal control elements
• Organisation of Genome Feature

  • Prokaryotic genome
  • Eukaryotic genome
• Control by promoter

  1. Prokaryotic genome: Promoter present, a single promoter controls the structural genes grouped in an operon

  2. Eukaryotic genome: Promoter present, each gene is under the control of its own individual promoter
• Terminator is a specific sequence of non-coding DNA located at the end of a gene
• Introns

  Non-coding DNA sequences interspersed between coding regions known as exons in eukaryotic genes
• RNA splicing is a process where introns are excised from the primary mRNA transcript and exons are spliced together to form mature mRNA
• Control elements

  • Specific non-coding DNA sequences that function to either initiate or terminate transcription via promoter and terminator respectively, and increase and decrease the rate of transcription via enhancer and silencer respectively
• The presence of introns within a gene allows the gene to potentially encode several different polypeptides
• Introns

  1. Introns are transcribed together with exons to form the primary mRNA transcript (pre-mRNA)

  2. Splice sites at both ends of each intron serve as signals for RNA splicing

  3. Introns are excised via RNA splicing before translation to form mature mRNA
• Terminator

  The transcribed terminator sequence on the RNA product serves as a termination signal to stop transcription, causing RNA polymerase to release the pre-mRNA and detach from the DNA template
• Promoter

  1. Specific non-coding DNA sequences located just upstream of the transcription start site of a gene

  2. Proteins involved in transcription initiation bind to the promoter, including RNA polymerase and general/basal transcription factors

  3. Essential for initiating transcription of a gene at the basal rate and recruiting RNA polymerase to the promoter

  4. Certain critical elements within the promoter, like the TATA box, determine the strength of the promoter and affect the rate of transcription
• Alternative RNA splicing allows a single pre-mRNA to produce different mature mRNAs, leading to one gene coding for more than one type of polypeptide
• Introns are not involved in the translation of an mRNA
• Centromeres consist of large arrays of non-coding repetitive tandem DNA sequences
• Silencers

  • DNA sequences bound by repressors, inhibit assembly of transcription initiation complex, decrease rate of gene transcription
• There are different mechanisms of transcription termination in eukaryotes, with less well-studied examples compared to prokaryotes
• Transcription termination

  RNA polymerase releases the pre-mRNA and detaches from the DNA template
• Centromeres are visible as constricted regions on chromosomes where spindle fibers attach during nuclear division
• Enhancers

  • DNA sequences bound by activators, promote assembly of transcription initiation complex, increase rate of gene transcription
• Transcription termination in eukaryotes

  RNA polymerase transcribes well past the end of the gene, involves polyadenylation signal sequence, and certain proteins cut the pre-mRNA to release it from the RNA polymerase
• Transcription termination in prokaryotes

  RNA polymerase transcribes the terminator sequence, a hairpin loop forms causing the RNA polymerase to pause and separate from the DNA
• Enhancers and silencers are regulatory elements that control transcription of genes
• Each sister chromatid has its own centromeric DNA sequences
• Centromeres and telomeres are essential features of eukaryotic chromosomes for functionality and structural integrity
• Centromeres facilitate chromatin organisation


  Enabling sister chromatids adhesion during mitosis (prophase and metaphase)
• Telomeres ensure genes are not lost/eroded with each round of DNA replication due to the end replication problem, preventing loss of vital genetic information
• Telomeres

  Non-coding regions of DNA consisting of a series of short tandem repeat sequences