Eukaryotic Genomes

1
Eukaryotic Genomes

• CHAPTER 19

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Structural Levels of DNA

• a single linear DNA double helix averages about 4
  cm in length
• DNA associates with proteins that condense it so
  it will fit in the nucleus
• DNA-protein complex chromatin
• chromatin looks like beads on a string when
  unfolded
• beads nucleosomes made up of histones
  (proteins) string DNA
• http//www.youtube.com/watch?v9kQpYdCnU14feature
  relmfu
• http//www.youtube.com/watch?vgbSIBhFwQ4sfeature
  relmfu

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• chromatin fiber (30 nm)
• created by interactions between adjacent
  nucleosomes and the linker DNA
• chromatin fiber (300 nm)
• created when the 30 nm chromatin fiber forms
  loops called looped domains attached to a protein
  scaffold made of nonhistones
• chromosome
• forms when the 300 nm chromatin fiber folds on
  itself

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Regulation of Chromatin Structure

• compactness of chromatin helps regulate gene
  expression
• heterochromatin highly compact so it is
  inaccessible to transcription enzymes
• euchromatin less compact allowing transcription
  enzymes access to DNA
• chemical modifications that can alter chromatin
  compactness
• histone acetylation (-COCH3) neutralizes the
  histones so they no longer bind to neighboring
  nucleosomes causing chromatin to have a looser
  structure

5
DNA Methylation

• addition of methyl groups to DNA bases (usually
  cytosine) inactivate DNA
• methylation patterns can be passed on
• after DNA replication, methylation enzymes
  correctly methylate the daughter strand
• accounts for genomic imprinting in mammals
  expression of either the maternal or paternal
  allele of certain genes during development
• (NOTE inheritance of chromatin modifications
  that do not involve a change in the DNA sequence
  is called epigenetic inheritance)
• http//www.youtube.com/watch?NR1vdfdnf1Wpg0Efe
  atureendscreen

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Cell Differentiation

• process of cell specialization (form function)
  during the development of an organism
• differences in cell types results from
  differential gene expression
• several control points at which gene expression
  can be regulated (turned on/off, accelerated,
  slowed down)
• most commonly regulated at transcription in
  response to an extracellular signal

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Regulation of Transcription Initiation

• general transcription factors proteins that
  form a transcription initiation complex on the
  promoter sequence (ex TATA box) allowing RNA
  polymerase to begin transcription
• control elements segments of noncoding DNA that
  help regulate transcription by binding certain
  proteins
• proximal control elements
• distal control elements (enhancers) - interact
  with specific transcription factors
• activators stimulate transcription by binding to
  enhancers
• repressors - inhibit transcription by binding
  directly to enhancers or by blocking activator
  binding to enhancers or other transcription
  machinery

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1. activators bind to enhancer with 3-binding sites
2. a DNA-bending protein brings the bound activators
   closer to the promoter
3. activators bind to general transcription factors
   mediator proteins, helping them to form a
   functional transcription initiation complex

• activators can also promote histone acetylation
  repressors can promote histone deacetylation

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Cell Type-Specific Transcription

• the of different genes far exceeds the of
  different control elements therefore, the
  particular combination of control elements is
  what is important in controlling transcription
  along with the available activators in the cell

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Co-expressed Genes

• most co-expressed genes are found scattered over
  different chromosomes
• to coordinate their gene expression, each gene is
  regulated by the same control elements these
  control elements are activated by the same
  chemical signals

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Post-Transcriptional Regulation

• alternative RNA-splicing regulatory proteins
  specific to a cell type control intron-exon
  choices, thereby producing different mRNA
  molecules from the same primary transcript

12

• methods of mRNA degradation
• enzymatic shortening of the poly-A tail triggers
  the removal of the 5' cap which is followed by
  the digestion of the mRNA by nucleases
• nucleotide sequences in the untranslated region
  at the 3' end regulate the length of time an mRNA
  remains intact
• microRNAs (miRNAs) small RNA molecules that
  bind to complementary sequences on mRNA causing
  degradation by associated proteins miRNAs may
  also block translation
• RNA interference (RNAi) pathway involve small
  interfering RNAs (siRNAs) that function in the
  same way as miRNAs

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• initiation of translation
• can be blocked by regulatory proteins that bind
  to specific sequences or structures within the
  untranslated region at the 5 end of the mRNA
  prevent the attachment of ribosomes
• translation will not begin if the poly-A tails
  are not long enough
• global control activation or inactivation of
  one or more of the protein factors required to
  initiate translation
• protein processing degradation
• regulation of the modification or transporting of
  a protein
• ubiquitin-tagged proteins are degraded by
  proteasomes

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Genes Associated With Cancer

• proto-oncogenes normal cellular genes that code
  for proteins that stimulate normal cell growth
  division
• can be converted to oncogenes (cancer-causing
  genes) by
• translocation proto-oncogene ends up near an
  active promoter or vice versa
• amplification increases of proto-oncogenes in
  cell
• point mutations in a promoter, enhancer, or the
  coding region itself
• tumor-suppressor genes encode proteins that
  help prevent uncontrolled cell growth
• mutations that decrease the normal activity of
  these genes may contribute to the onset of cancer

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Example ras gene p53 gene

• ras gene is a proto-oncogene
• it encodes a G protein that, in response to
  growth factors, triggers a cell signaling pathway
  that synthesizes a cell cycle stimulating protein
• mutations in this gene can lead to the production
  of a hyperactive G protein that continuously
  triggers this pathway even when growth factors
  are absent
• p53 gene is a tumor-suppressor gene
• it promotes the synthesis of cell cycle
  inhibiting proteins
• a mutation that knocks out this gene can lead to
  excessive cell growth cancer

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Model of Cancer Development

• changes that must occur at the DNA level for a
  cell to become fully cancerous
• appearance of at least one oncogene
• mutation or loss of several tumor-suppressor
  genes
• in most cases mutations must knock out both
  alleles to block tumor suppression

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Tumor Viruses

• can transform cells into cancer cells through the
  integration of viral nucleic acid into host cell
  DNA
• retroviruses may donate an oncogene to the cell
• integrated viral DNA may disrupt a
  tumor-suppressor gene or convert a proto-oncogene
  to an oncogene
• produce proteins that inactivate p53 and other
  tumor-suppressor proteins

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Predisposition to Cancer

• an individual inheriting an oncogene or a mutant
  allele of a tumor-suppressor gene is one step
  closer to accumulating the necessary mutations
  for cancer to develop
• (ex) breast cancer genes BRCA1 or BRCA2
• a woman who inherits one mutant BRCA1 allele has
  a 60 chance of developing breast cancer before
  the age of 50

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Eukaryotic vs. Prokaryotic Genomes

• Eukaryotes

• Prokaryotes

• larger genome but fewer genes in a given length
  of DNA
• more noncoding DNA (10,000 times as much as
  prokaryotes )
• most of the DNA does not encode protein or RNA
• genes contain introns so they are much longer
  than prokaryotic genes

• smaller genome but more genes in a given length
  of DNA
• less noncoding DNA
• most of the DNA codes for protein, tRNA, or rRNA
• genes are not interrupted by introns

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Human Genome

• 98.5 does not code for proteins, rRNAs, or
  tRNAs
• 24 is gene-related regulatory sequences and
  introns
• 44 is repetitive DNA made up of transposable
  elements related sequences

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Transposable Elements

• two types
• transposons move within a genome by means of a
  DNA intermediate
• can move by cut-and-paste or copy-and-paste
• retrotransposons move within a genome by means
  of an RNA intermediate
• always leave a copy at the original site because
  they are initially transcribed into an RNA
  intermediate
• to be inserted at another site, the RNA
  intermediate must be converted back to DNA by
  reverse transcriptase

22
Other Types of Repetitive DNA

• probably arose by mistakes that occurred during
  DNA replication or recombination
• accounts for about 15 of the human genome
• about 1/3 of this consists of large-segment
  duplications (10,000-300,000 base-pairs)
• long stretches of DNA that have been copied from
  one chromosomal location to another
• remaining 2/3 is simple sequence DNA copies of
  tandemly repeated short sequences like GTTAC
• most is located at chromosomal telomeres and
  centromeres indicating it has a structural role

23
Gene-Related DNA

• consists of coding noncoding DNA
• constitutes about 25 of the human genome
• about ½ of the total coding DNA consists of
  solitary genes
• remaining ½ occurs in multigene families
  collections of identical or similar genes
• (ex) identical gene family rRNA
• allows for quick production of millions of
  ribosomes
• (ex) non-identical families a-globin and
  ß-globin

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Evolution of Genomes

• extra sets of chromosomes can arise from
• errors during meiosis
• polyploidy extra sets of genes
• mutations can accumulate in the extra sets of
  genes
• unequal crossing-over
• can result in one chromosome with a deletion and
  another with a duplication
• errors during DNA replication
• slippage
• occurs when DNA template shifts with respect to
  the new complementary strand resulting in a
  region of the DNA not be copied or being copied
  twice

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• rearrangement of existing DNA sequences by
• exon duplication
• exon shuffling
• mixing matching of different exons either
  within a gene or between two nonallelic genes
  owing to errors in meiotic recombination
• transposable elements
• can promote recombination
• disrupt cellular genes or control elements
• carry entire genes or individual exons to new
  locations

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Evolution of Globin Genes

• all the a-globin and ß-globin genes likely
  evolved from one common ancestral globin gene
• the ancestral globin gene duplicated and diverged
  into a-globin and ß-globin ancestral genes
• the ancestral a-globin and ß-globin genes later
  duplicated several times and their copies
  diverged into the current family genes
• the divergences undoubtedly arose from
  accumulated mutations
• some of the gene duplications and subsequent
  divergences are also suspected to have produced
  new genes with novel, yet related functions