the human genome and genomics

• gene


  unit of heredity

  smallest unit to encode a protein (or RNA transcript)

  comprised of exons, introns and regulatory regions
• genome


  total genetic complement of a cell, virus or organism
• human genome

  nuclear and mitochondrial
• diploid (2n)

  somatic cells (not germ cells)

  22 autosome pairs

  2 sex chromosomes (XX or XY)

  1000s of mitochondrial genomes
• haploid (1n)


  gametes, one set of chromosomes

  half that of nuclear chromosomes of somatic cells

  not generally referring to mitochondrial genomes
• nuclear genome size (haploid)

  22 human autosomes plus X or Y

  ˜ 3,200,000,000 nucleotide base pairs
• mitochondrial genome


  human mitochondrial circular genome 16, 569 base pairs

  mitochondrion contains ˜ 10 genomes, with ˜ 10,000 mitochondria/cell
• largest human chromosome ˜ 260M bp

  smallest ˜ 47M bp

  haploid total ˜ 3200M bp of DNA
• y chromosome is easily lost in karyotypes because it doesn't encode for many things
• human mitochondrial genome

  • ˜ 10 copies/mitochondrion, ˜ 8-10,000/somatic cell
  • maternally inherited
  • egg is packed with mitochondrial DNA -> mitochondrial DNA at the end of the sperm tail, which is lost during fusion
  • gene dense
  • some mitochondrial proteins are coded from nuclear genes
  • codes for electron transport enzyme
  • DNA polymerase made/encoded in the nucleus
• composition of the nuclear genome

  • 37% genes (1.5% exons); ˜ 44% repetitive and transposons
  • LINEs (640Mb), LTR elements (250Mb), SINEs (420 Mb), DNA transposons (90 Mb) -> all repetitive sequence elements
  • intergenic DNA (2000 Mb) -> 'junk' DNA, function relatively unknown
• entire gene is transcribed

  • introns spliced out for translation
  • only exons kept
  • prokaryotes do NOT contain introns
  • ovalbumin gene -> 7 exons
  • hemoglobin β subunit -> 3 exons
• open reading frame (ORF)


  series of nucleotide triplets (codons) running from translation start to translation stop. more complicated in eukaryotes.

  signals in the DNA determine strand usage and where transcription/translation start and terminate

  6 possible ORFs, only 1 correct ORF

  • issues arise when introns aren't spliced (stop codon or other codons are left in causing translation issues)
• the dystrophin locus

  • gene consists of >80 exons and occupies ˜ 2.4 Mbp of DNA on the X chromosome (females with one copy are less affected than males with one copy)
  • alternative promotors and RNA splicing generate many dystrophin proteins in a tissue-specific manner
  • muscular dystrophy
• dystrophin

  1. structural protein of cytoskeleton underlying cell membrane
  2. contains an amino terminal ACTIN-BINDING domain (actin is a major constituent of the cell cytoskeleton), a large rod-like domain, a domain with 2 Ca++ binding sites, and a carboxyl terminal domain to interact with plasma membrane (integrate from outside to inside)
  3. helps connect muscle sarcolemma to plasma membrane glycoproteins (extracellular matrix communication?) -> helps normal muscle stiffening
  4. normal muscle cells are stiffer than those that lack dystrophin
• muscular dystrophy

  1. mosst common forms of 9 MD diseases:
  2. duchenne: lack of dystrophin expression
  3. becker: low or less functional dystrophin protein
  4. early stages (3-5 years) affect shoulders, upper arm, hips and thighs. weaknesses causes difficulty with movement
  5. by teens -> respiratory system and cardiac complications (potential mortality)
  6. X-linked recessive, maternally inherited. Heterozygous females present with minor muscle weakness and cramping
  7. 2/3 males obtain mutation from mother. 1/3 can be from new mutations
• muscular dystrophy diagnosis/prognosis

  • diagnosis
  • history/physical exam
  • early blood test - creatine kinase leaks out of damaged muscle. high blood levels suggestive, not diagnostic
  • muscle biopsy (PCR, histology, IHC)
  • prognosis
  • duchenne affects all voluntary muscles, the heart and respiratory muscles. survival rarely beyond early 30s
  • less severe for becker. patients can live full life with correctional therapies (exercise, physical therapy, orthopedic surgery, pacemaker)
• gene families

  • related genes with related functions
  • may arise by tandem gene amplification (close clustering, globin, GH)
  • can form from duplication then mutation
  • may be wide spread with unrelated intervening sequence and one numerous chromosomes (compound clusters, histones, HOX, aldolase, NF1)
• histone genes

  1. no introns
  2. multigene compound clusters
  3. genes are duplicated (H2a, H2b, H3, H4)
  4. highly conserved evolutionarily (except H1)

  • histone DNA wraps around proteins to form nucleosomes
  • essential
• transposons

  • repetitive sequence elements (LINEs, SINEs, and LTR elements, retroviruslike)
  • 45% of genome
  • was mobile in past, can no longer move

  1. retrotransposons: replicative (or copy) transposition. LINEs, SINEs and LTRs
  2. dna transposons: conservative transposition. cut and paste mechanism
  3. autonomous vs nonautonomous transposition
• major repetitive DNA sequence in human genome

  • centromere and telomere
  • telomere: TTAGGG minisatellite
  • centromere: pull chromosomes apart during replication. various satellite components
  • 0.1-20 kb of 6-64 bp repeated units
  • several MB in length tandemly repeated 5-170 bp sequences
  • <100 bp repeats dispersed in chromosomes