BIO341 Gene Discovery Section 1 Background Genetics

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BIO341 - Gene DiscoverySection 1Background
Genetics

• Jasper Rees
• Department of Biochemistry, UWC
• www.biotechnology.uwc.ac.za/teaching/BIO341

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Course Objectives

• Genome level organisation of prokaryotes and
  eukaryotes
• Genome content
• Model organisms used in genomics
• Gene identification - homologies of known genes
• Gene identification of unknown genes
• Protein families
• Linking genes to functions and structures

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Course method

• Lectures
• Computer based exploration of research reviews
  and papers
• Computer analysis of sequence data
• Annotation of region of genomic sequence
• Analysis of a protein family (sequence/structure)

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Overview Section 1

• Genome Structure and organisation
• Prokaryotic genomes
• Eukaryotic nuclear genomes
• Eukaryotic organelle genomes
• Model Organisms
• Genome Sequencing Projects
• EST Projects
• Computational genomics and gene discovery

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Genome size and biological complexity
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Minimum Genome sizes
The minimum size of genome found in each class of
organisms (phyla) increases with the genetic and
biological complexity of the organisms. Lower
organisms have fewer genes and less DNA.
Smallest Prokaryote Mycoplasma 0.9
Mb Smallest Eukaryote Microsporida 3 Mb
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Prokaryotic genomes

• Small, compact, circular genomes
• Usually only one chromosome
• 105 - 107 bases long
• Single origin of replication
• Many promoters
• Genes arranged in transcriptional operons
  containing functionally related coding sequences
  (operons)
• Little DNA with no information content.

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E.coli Genome Organisation

• 4.7 Mb for E.coli K12
• Around 5000 genes
• Extensive reorganisation seen in E.coli 0157H7 -
  a highly pathogenic strain - with up to 20 of
  the genome being added or deleted.
• These variable sequences must include those that
  define the pathogenicity of this strain

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E.coli 0157 genome
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Prokaryote operon organisation

• Genes clustered into functional groups - operons
• One promoter regulates the cluster of genes
• mRNA is polycistronic
• Ribosomes translate the ORFs from 5 to 3

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Eukaryotic Nuclear Genomes

• Generally larger, though smallest eukaryotes are
  smaller than E.coli. 106 to 1011 bases
• Linear chromosomes, generally multiple
• Diploid or haploid for majority of life cycle
• Increased size of genomes goes with increased
  complexity of gene structure and transcription
• Increased size of genomes goes with increased
  amounts of non-coding and repetitive DNA (junk
  DNA)

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Eukaryote Chromosome structure and organisation

• Chromosomes are linear (one DNA molecule)
• Multiple replication origins
• One centromere per chromosome
• Telomers at ends
• DNA packaged into chromatin by histones and
  non-histones
• Contain mix of unique and repetitive sequences
• Coding and non-coding sequences

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Chromatin condensation

• Observed at mitosis and meiosis
• Results from packaging of chromatin
• Transcription stops
• Chromosomes visible in microscopy
• Separation of haploid chromosome sets occurs in
  nuclear division
• Packaging ratio about 100001

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Chromosome staining patterns of the human
karyotype
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Human Chromosome 16

• Typical human chromosome
• Approximately 100 Mbases
• Large heterochromatic centromeric region

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Chromatin structure

• Chromatin made up of 5 histones and many
  different non-histones
• Histones assemble with DNA into nucleosomes
• Nucleosomes pack into compact fibres
• Non-histones regulate packaging of nucleosomes
  and organise chromatin into large loops (50 - 200
  kb) for transcription.

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Centromers

• Simple DNA sequences
• Characterised in yeast into three conserved
  regions
• In mammalian centromers less well understood
• Site of attachment of spindles (microtubules) in
  cell division

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Telomers

• Short repetitive sequences at the ends of
  chromosomes
• Required for replication of ends of linear
  sequences
• Required to stabilise ends against nucleases
• Template dependent addition by Telomerase enzyme
• GT rich sequences form G Quartet structures

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Eukaryotic gene organisation

• One promoter for each gene (99 of genes)
• One open reading frame (ORF) only is translated
  for each mRNA
• Exons spliced together in nucleus
• Alternative splicing gives additional complexity
  of possible mRNA products (10 of genes?)
• Alternative poly A addition can give possible
  complexity (lt1 of genes)

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Human Chromosome 16 - DWNN gene shows complex
organisation
P0
P1
1
2
3
4
0
18
16
17
15
Gene - Chr 16.p21
P0 1.1kb
P1 1.1kb
P0 6.1kb - Exon 16
P0 6.1kb Exon 16
P1 6.1kb - Exon 16
P1 6.1kb Exon 16
DWNN gene is 35 000 bases long
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Eukaryotic organelle genomes

• Small, circular, prokaryote-like
• Encode very limited number of proteins and RNAs
• Generally two major transcription units
• Replication process like prokaryotes
• Evolutionary similarity to prokaryotes, more than
  the eukaryote nuclear genes
• Symbiosis theory proposed for their origin.

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Yeast Mitochondrial genome

• 84 kb
• tRNA and rRNA genes
• Some of the protein coding genes have introns
• Introns are self-splicing
• Total genetic content similar to human
  mitochondrial genome

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Human mitochondrial genome

• 16.6 kb
• 22 tRNAs
• 2 rRNAs
• 13 open reading frames
• One transcription unit
• Encodes small number of proteins required for
  mitochondrial function
• All other mitochondrial proteins are encoded by
  nuclear genes

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Human Mitochondrial RNA transcripts

• Transcribed from one strand
• tRNA sequences separate coding sequences
• Cleavage to produce tRNAs results in release of
  mRNAs