Chapter 19 Eukaryotic genomes organization, regulation and

							              Chapter 19
   Eukaryotic genomes: organization,
       regulation and evolution
http://www.studiodaily.com/main
       /searchlist/6850.html

   “The Inner life of the Cell”
           Gene expression…
• Is altered in response to environmental changes,
  both internal and external
• Is influenced by the structure of chromatin
   – Heterochromatin is highly compacted and is not
     transcribed
   – Euchromatin is less compacted and available for
     transcription
• Is most often regulated at the transcription stage
• Differential gene expression (cell differentiation)
  is the result of genes being turned “on” or “off” in
  different cells having the same genome
• Only 1.5% of human DNA codes for proteins
         Chromatin structure….
• Eukaryotic DNA associates with many histone proteins
  that form complex structures – the mass of histones =
  the mass of DNA
• Histones – highly conserved, small, basic proteins that
  shape the 1st level of chromatin structure:
   – The high [ ]’s of arganine and lysine make them +ly charged
   – Of the 5 types (H1,H2A,H2B,H3,H4) all but H1 are found in the
     nucleosome, the basic unit of DNA packing
   – Are evolutionarily conserved
   – Only leave DNA briefly during replication
• Interphase chromatin is attached to the nuclear lamina to
  keep chromosomes from tangling
    Eukaryotic DNA structure
• DNA + histones form
  nucleosomes (10nm
  fiber)
• Nucleosomes coil to form
  chromatin fiber (30nm
  fiber)
• 30nm fiber folds into
  looped domains (300nm
  fiber)
• Chromatin condenses
  further to form the
  metaphase
  chromosome (highly
  compacted 1400 nm)
 CONTROL POINTS in eukaryotic
      gene expression:
• Regulation of chromatin structure: histone acetylation
  and DNA methylation
• Transcription of the gene: transcription initiation
• RNA Processing: alternative RNA splicing
• mRNA export:
• mRNA degradation: polyA tail, miRNA, RNAi
• Translation of mRNA: regulatory proteins block initiation
  of translation
• Polypeptide processing: cleavage, modification and
  transport
• Protein Degradation: ubiquitin/proteasome activity
• Stages in which eukaryotic gene expression can be
  regulated are represented by the colored boxes
 Regulation of chromatin structure:
• Histone modification –
  acetyl groups added to
  histone tails relax
  chromatin and promote
  transcription
• DNA methylation can
  inactivate genes and be
  inherited by offspring–
  genomic imprinting works
  this way!
    Control of gene expression in
      eukaryotes: an overview
• http://highered.mcgraw-
  hill.com/olc/dl/120080/bio31.swf
The eukaryotic gene consists of
• the gene + RNA polymerase + a promoter
• Control elements – non-coding DNA that regulates
  transcription by binding to certain proteins. Distal
  elements called enhancers are very important
• Transcription factors:
   – General transcription factors result in low RNA production
   – Specific transcription factors can promote high levels of
     transcription. They may be:
       • Activators – protein that stimulates transcription
       • Repressors – proteins that inhibit gene expression
   – Activators and repressors may alter chromatin structure, thereby
     further influencing gene expression
Transcription of the gene:
  regulation of initiation
Prokaryotes have operons to control expression of
    genes with related functions…what about
                  eukaryotes?
• Functionally related eukaryotic genes are
  co-expressed because they have the
  same control elements that are activated
  by the same chemical signals
   Regulation of transcription
• http://wps.aw.com/bc_campbell_biology_7
  /0,9854,1704975-,00.html
            RNA processing:
• Alternative RNA
  splicing can generate
  different mRNA
  molecules from the
  same primary
  transcript – organisms
  can produce more
  than 1 polypeptide
  from a single gene!
The mRNA transcript:
        mRNA degradation:
• Eukaryotic mRNA can have a survival time
  measured in weeks…how is it degraded?
  – Shortening of the poly-A tail and removal of
    the 5’cap allows nucleases to degrade mRNA
  – microRNA’s can degrade mRNA or block its
    translation (called RNA interference)
mRNA degradation:
          mRNA translation
• Initiation of translation can be blocked by
  regulatory proteins that bind to the UTR’s
  and block the attachment of ribosomes to
  the mRNA
      Polypeptide processing:
• Any interference in the processing of the
  polypeptide can alter gene expression.
  Polypeptides are processed via
  – Cleavage
  – Chemical modifications
  – Protein transport to its target destination
      Degradation of protein:
• The lifespan of a protein varies and is
  strictly regulated by other proteins
• Proteins tagged with ubiquitin are
  recognized by proteosomes and degraded
Protein degradation:
    A review of gene expression:
     prokaryotes vs eukaryotes
• http://highered.mcgraw-
  hill.com/olc/dl/120077/bio25.swf
               Gene expression:
          prokaryotic     eukaryotic
•   Small genome, no specialization          •   Larger genome, cell specialization
•   Most of their DNA codes for protein or   •   Most of the DNA does not code for
    RNA’s, very little “junk”                    protein or RNA’s
•   Genome = DNA + few proteins in
    simple arrangement                       •   Genome = DNA w/many proteins
                                                 in complex arrangement
•   RNA processing not an option for
    controlling gene expression              •   RNA processing allows for several
•   mRNA has a short life span (minutes)         opportunities to regulate genes
                                             •   mRNA is long lived (days to
                                                 months)



•   Both alter gene expression in
    response to environment; in both,
    transcription initiation is the most
    important control point
 Cancer results from genetic changes that
         affect cell cycle control

• It is a disease in which cells escape
  control methods that normally regulate cell
  growth and division
• The agents of change can be random
  spontaneous mutations or carcinogens
• Cancer-causing genes, oncogenes, were
  originally discovered in retroviruses
          Proto-oncogenes:
• Proto-oncogenes code for proteins that
  stimulate normal cell growth and division
  They may turn into oncogenes by:
  – Translocation/transposition within the genome
  – Gene amplification
  – Point mutations within a control element or
    the gene that may lead to a protein that is
    more active or longer lived
Proto-oncogenes
            Tumor-suppressor genes

• Tumor-suppressor genes encode for proteins
  that help prevent uncontrolled cell division. They
  may function to:
  – Repair damaged DNA
  – Control cell adhesion
  – Act as components of cell-signaling pathways that
    inhibit the cell cycle
• A mutation in a tumor suppressor gene reduces
  the activity of its protein product, leads to
  excessive cell division and potentially cancer
 Some proteins encoded by proto-oncogenes and
 tumor-suppressor genes are components of cell
               signaling pathways
• The Ras proto-
  oncogene (G protein)
  is part of a cell cycle
  stimulating pathway.
  A mutation making
  this pathway
  abnormally active
  could result in cancer
• The product of the
  p53 gene (p53
  protein) inhibits the
  cell cycle and allows
  time for DNA repair
  mechanisms to
  operate. Deficiencies
  in this cell cycle
  inhibiting pathway
  could promote cancer
Control of the cell cycle: p53 and rb
• http://highered.mcgraw-
  hill.com/sites/0072437316/student_view0/
  chapter20/animations.html#
   The multistep model for cancer
           development:
• Cancer results from an accumulation of
  mutations, not just one
• Usually there is the presence of one active
  oncogene and the mutation of several tumor-
  suppressor genes
• Certain viruses can promote cancer by insertion
  of viral DNA into a cells genome
• Individuals who inherit a mutant oncogene or
  tumor-suppressor allele have an increased risk
  of developing cancer
Eukaryotic genomes have many noncoding
  DNA sequences in addition to genes
• Eukaryotes have fewer genes/DNA length
  than do prokaryotese
• Most of the DNA is noncoding (98.5%)
• Most intergenic DNA is repetitive DNA in
  the form of transposable elements and
  related sequences (44%)
• There are 2 types of transposable
  elements:
  – Transposons and retrotransposons
     Transposable elements:
• Transposons:       • Retrotransposons:
• Move within a      • Move within a
  genome via a DNA     genome via an RNA
  intermediate         intermediate
• Can move via:      • This is the most
  – Cut-and-paste      prevalent type
    methods
  – Copy and paste
    methods
        Simple sequence DNA
•   Short, noncoding DNA sequences
•   Tandemly repeated
•   Prominent in centromeres and telomeres
•   Play a structural role in the chromosome
          Multigene families:
• Collections of identical or very similar genes,
• A multigene family is a member of a family of
  related proteins encoded by a set of similar
  genes. Multigene families are believed to have
  arisen by duplication and variation of a single
  ancestral gene. Examples of multigene families
  include those that encode the actins,
  hemoglobins, immunoglobulins, and histones.
  The evolution of the Genome - a
        history of mutation!
• Polyploidy! A duplication of chromosome sets. One set
  functions normally, the other is free to diverge
• Duplication of individual DNA segments or genes which
  may then diverge to create new genes and gene
  products
• Rearrangement of gene parts:
   – Exon duplication
   – Exon shuffling
• The use of transposable elements that promote
  recombination, disrupt genes, or carry genes to new
  locations also contributes to genome evolution