Genome and proteom

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Genome and proteom
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• 3 broad areas
• Genomes, transcriptomes, proteomes
• Applications of the human genome project
• (C) Genome evolution

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A) Genomes, transcriptomes, proteomes

• Genome projects
• - Human Genome Project (HGP) a history
• - Other genome projects why do it
• - Genome organisation
• insights from HGP
• Repeat elements
• Transposable elements
• Mitochondrial genomes
• Y chromosome
• Post-genomics
• -transcriptomes
• - proteomes

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(A) Genomes, transcriptomes and proteomes
genome
Entire DNA complement of any organism which
include organelle DNA
transcriptome
All RNA transcribed from genome of a cell or
tissue
proteome
all proteins expressed by a genome, cell or tissue
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Why study the genome?

• 3 main reasons
• description of sequence of every gene valuable.
  Includes regulatory regions which help in
  understanding not only the molecular activities
  of the cell but also ways in which they are
  controlled.
• identify characterise important inheritable
  disease genes or bacterial genes (for industrial
  use)
• Role of intergenic sequences e.g. satellites,
  intronic regions etc

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HGP

• Goal Obtain the entire DNA sequence of human
  genome
• Players
• International Human Genome Sequence Consortium
  (IHGSC)
• - public funding, free access to all, started
  earlier
• - used mapping overlapping clones method
• (B) Celera Genomics
• private funding, pay to view
• - started in 1998
• - used whole genome shotgun strategy

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Whose genome is it anyway?

• International Human Genome Sequence Consortium
  (IHGSC)
• - composite from several different people
  generated from 10-20 primary samples taken from
  numerous anonymous donors across racial and
  ethnic groups
• (B) Celera Genomics
• 5 different donors (one of whom was J Craig
  Venter himself !!!)

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Strategies for sequencing the human genome
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Figure 12.2 Arranging DNA Sequences
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Strategies for sequencing the human genome
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Whole-genome shotgun sequencing
Private company Celera used to sequence whole
human genome

• Whole genome randomly sheared three times
• Plasmid library constructed with 2kb inserts
• Plasmid library with 10 kb inserts
• BAC library with 200 kb inserts
• Computer program assembles sequences into
  chromosomes
• No physical map construction
• Only one BAC library
• Overcomes problems of repeat sequences

• Whole genome randomly sheared three times
• Plasmid library constructed with 2kb inserts
• Plasmid library with 10 kb inserts
• BAC library with 200 kb inserts
• Computer program assembles sequences into
  chromosomes
• No physical map construction
• Only one BAC library
• Overcomes problems of repeat sequences

Fig. 10.13 Genetics by Hartwell
Fig. 10.13
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sequencing larger genomes
Mapping phase
Genomes - Dr. MV Hejmad
Sequencing phase
http//www.DNAi.org
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Other genomes sequenced
1997 4,200 genes
2002 36,000 genes
1998 19,099 genes
Sept 2003 18,473 human orthologs
2002 38,000 genes
Science (26 Sep 2003)Vol301(5641)pp1854-1855
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Genomics World's smallest genome

• the smallest genome known is the DNA of a
  'nucleomorph' of Bigelowiella natans, a
  single-celled algae of the group known as
  chlorarachniophytes.
• 373,000 base pairs and a mere 331 genes
• The nucleomorph is an evolutionary vestige that
  was originally the nucleus of a eukaryotic cell.
  The eukaryotic cell swallowed a cyanobacterium to
  acquire a photosynthetic 'plastid' organelle, and
  that cell was in turn engulfed by another cell to
  produce B. natans as we know it. Now, most of the
  nucleomorph's genome is concerned with its own
  maintenance, and just 17 of its genes still exert
  any control over the plastid. Its small size
  suggests it is heading for evolutionary oblivion.

Proc. Natl Acad. Sci. USA 103, 95669571 (2006)
by G McFadden, University of Melbourne, Australia
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Organisation of human genome

• Mitochondrial genome

• Nuclear genome (3.2 Gbp)
• 24 types of chromosomes
• Y- 51Mb and chr1 -279Mbp

http//www.ncbi.nlm.nih.gov/Genomes/
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Nuclear genome organisation (human)
Genomes 2 by TA Brown pg 23
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Nuclear genome organisation (human)

• 1) Gene and gene related sequences
• Coding regions Exons (5)
• Non-coding regions
• RNA genes
• Introns
• Pseudogenes
• Gene fragments

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• Basic structure of a gene

Fig. 21.11
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Polypeptide-coding regions
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Non polypeptidecoding RNA encoding
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Nuclear genome organisation (human)
RNA genes -
Major classes of RNA involved in gene expression

• rRNA
• tRNA
• snRNA
• snoRNA

• 16S, 23S, 28S, 18S etc
• 22 types of mitochondrial 49 cytoplasmic
• U1,U2.U4,U5,U6 etc
• gt 100 types

• Other RNA classes
• microRNA
• XIST RNA
• Imprinting associated RNA
• Nervous system specific
• Antisense RNA
• Others

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introns
Non-coding regions..
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Pseudogenes (?)
Non-coding regions..

• A non functional copy of most or all of a gene
• Inactivated by mutations that may cause either
• inhibition of signal for initiation or
  transcription
• prevent splicing at exon-intron boundary
• premature termination of translation

Human Mol Gen 3 by Strachan Read pgs 262-264
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Pseudogenes (?)
Non-coding regions..

• Different classes include
• Non-processed
• contain non functional copies of genomic DNA
  sequence incl exons and introns
• arise from gene duplication events
• E.g. rabbit pseudogene ?b2

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rabbit pseudogene ?b2
Non-coding regions..

• Related to b1
• Usual exon and intron organisation

b1
?b2
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Pseudogenes - processed
Non-coding regions
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Nuclear genome organisation (human)
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Nuclear genome organisation (human)

• 2) Extragenic (intergenic) DNA
• (62 of genome)
• A) Unique or low copy number sequences
• B) Repetitive sequences ( 53)

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A) Unique or low copy number sequences

• Non coding, non repetitive and single copy
  sequences of no known function or significance

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B) Repetitive sequences

• Significance
• Evolutionary signposts
• Passive markers for mutation assays
• Actively reorganise gene organisation by
  creating, shuffling or modifying existing genes
• Chromosome structure and dynamics
• Provide tools for medical, forensic, genetic
  analysis

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• Eukaryotic genomes have repetitive DNA sequences
• Highly repetitive sequencesshort sequences (lt
  100 bp) repeated thousands of times in tandem
  not transcribed
• Short tandem repeats (STRs) of 15 bp are
  scattered around the genome and can be used in
  DNA fingerprinting.

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• Moderately repetitive sequences are repeated
  101,000 times.
• Includes the genes for tRNAs and rRNAs
• Single copies of the tRNA and rRNA genes are
  inadequate to supply large amounts of these
  molecules needed by cells, so genome has multiple
  copies in clusters
• Most moderately repeated sequences are
  transposons.

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• Transposons are of two main types in eukaryotes
• Retrotransposons (Class I) make RNA copies of
  themselves, which are copied into DNA and
  inserted in the genome.
• LTR retrotransposons have long terminal repeats
  of DNA sequences
• Non-LTR retrotransposons do not have LTR
  sequencesSINEs and LINEs are types of non-LTR
  retrotransposons

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• Transposons (or transposable elements) are DNA
  segments that can move from place to place in the
  genome.
• They can move from one piece of DNA (such as a
  chromosome), to another (such as a plasmid).
• If a transposon is inserted into the middle of a
  gene, it will be transcribed and result in
  abnormal proteins.

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DNA Sequences That Move (Part 2)
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• DNA transposons (Class II) do not use RNA
  intermediates.
• They are excised from the original location and
  inserted at a new location without being
  replicated.

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Table 12.3 Types of Sequences in Eukaryotic
Genomes
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Concept 12.4 The Human Genome Sequence Has Many
Applications

• By 2010 the complete haploid genome sequence was
  completed for more than ten individuals.
• Soon, a human genome will be sequenced for less
  than 1,000.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Some interesting facts about the human genome
• Protein-coding genes make up about 24,000 genes,
  less than 2 percent of the 3.2 billion base pair
  human genome.
• Each gene must code for several proteins, and
  posttranscriptional mechanisms (e.g., alternative
  splicing) must account for the observed number of
  proteins in humans.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Over 50 percent of the genome is transposons and
  other repetitive sequences.
• Most of the genome (97 percent) is the same in
  all people.
• Chimpanzees share 95 percent of the human genome.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Rapid genotyping technologies are being used to
  understand the complex genetic basis of diseases
  such as diabetes, heart disease, and Alzheimers
  disease.
• Haplotype maps are based on single nucleotide
  polymorphisms (SNPs)DNA sequence variations that
  involve single nucleotides.
• SNPs are point mutations in a DNA sequence.

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• SNPs that differ are not all inherited as
  independent alleles.
• A set of SNPs that are close together on a
  chromosome are inherited as a linked unit.
• A piece of chromosome with a set of linked SNPs
  is called a haplotype.
• Analyses of human haplotypes have shown that
  there are, at most, 500,000 common variations.
• .

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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Technologies to analyze SNPs in an individual
  genome include next-generation sequencing
  methods and DNA microarrays.
• A DNA microarray detects DNA or RNA sequences
  that are complementary to and hybridize with an
  oligonucleotide probe.
• The aim is to find out which SNPs are associated
  with specific diseases and identify alleles that
  contribute to disease.

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Figure 12.13 SNP Genotyping and Disease
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Concept 12.4 The Human Genome Sequence Has Many
Applications

• Genetic variation can affect an individuals
  response to a particular drug.
• A variation could make an drug more or less
  active in an individual.
• Pharmacogenomics studies how the genome affects
  the response to drugs.
• This makes it possible to predict whether a drug
  will be effective, with the objective of
  personalizing drug treatments.

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Figure 12.14 Pharmacogenomics
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https//genographic.nationalgeographic.com/