Organization eukaryotic genome


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Organization eukaryotic genome

  1. 1. Organization of the EukaryoticChromatin StructureNoncoding sequencesLevels of packingGene regulationChemical Modifications
  2. 2. Human Genome  20,000-30,000 genes  most of the DNA does NOT encode for a protein or RNA (is not a gene)
  3. 3. Coding & Noncoding Sequences
  4. 4. Classes of Noncoding Sequences  Introns  Regulatory sequences  Highly repetitive sequences:  Tandemly repetitive DNA (tandem repeats)  Interspersed repetitive DNA  Telomeres
  5. 5. Noncoding DNA Noncoding DNA Introns Repetitive DNA Regulatory sequences Telomere Tandemly Repetitive Interspersed DNA (e.g. VNTRs) Repetitive DNA (e.g. transposon)
  6. 6. Tandemly Repetitive DNA Short identical DNA sequences repeated in series Many types, often classified by length of the repeat Variable Number Tandem Repeats (VNTRs)  Number of repeat varies  Sequence can be repeated different number of times
  7. 7. Tandemly Repetitive DNAApplication Useful for DNA Fingerprinting and studying evolution OSC Lab: VNTR at the D1S80 locus  Length of repeat: 16 bp  Repeated sequence: GTGGTCCTCCTTCCTG  Number of repeats: 14-41  Total length: 200-700 bp
  8. 8. Example: Fragile X Syndrome First triplet repeat identified was the one in Fragile X syndrome Repeat sequence: CGG triplet on X chromosome Normal fragile X allele: repeated 30x in the 5’ untranslated region of the first exon Fragile X syndrome: repeat is over 100x The most common single known cause of intellectual disability and autism
  9. 9. Example: Huntington’s Disease  Neurodegenerative Repeats Disease disorder that affects < 27 - muscle coordination and 27 – 35 - Repeat Median Age at leads to cognitive decline 36 – 39 +/- Size Onset * (years) and psychiatric problems 39 66 (72-59) > 39 + 40 59 (61-56)  Repeat sequence: CAG 41 54 (56-52)  Individuals affected with 42 49 (50-48) HD typically have at least 43 44 44 (45-42) 42 (43-40) 36 repeats or greater. 45 37 (39-36) 46 36 (37-35) 47 33 (35-31)Specific numbers of CAG repeat correlates to disease. Walker FO (2007). "Huntingtons disease".Lancet 369 (9557): 218–28. Normal HD gene CAG repeats range from 10 - 27 repeats. A few 48 32 (34-30)normal individuals have intermediate HD gene CAG repeats of 27-35 repeats. 49 28 (32-25)A current review of 1,049 persons (the majority of whom were symptomatic) has provided adetermination of the likelihood of an age-of-onset for a given CAG repeat size for repeats between 50 27 (30-24)39 50 repeats (Brinkman et al., 1997; Am. J. Hum. Genet. 60:1202-1210). *Age by which 50% of individuals will be affected
  10. 10. Comparing Prokaryotic andEukaryotic DNA Prokaryote EukaryoteDNA Circular LinearLocation of Not in nucleus Contained inDNA Nucleoid region nucleusDNA bound No. Naked. Yeswith proteins?
  11. 11. Chromosome Structure 2 arms, divided at centromere:  p arm – petit arm  q arm – long arm Centromeres:  region where sister chromatids are connected  made up of repetitive sequences
  12. 12. Activity: DNA Packing Materials:  Thread  Scissors  pill covers Instructions:  Cut out 20 m of thread  Put the thread in the pill cover
  13. 13. DNA Packing Animation Try to ignore the strange music
  14. 14. Levels of DNA packing 1st level: nucleosome 2nd level: solenoid / chromatin 3rd level: looped domain 4th level: metaphase chromosome
  15. 15.
  16. 16. Histones Proteins around which DNA coils to form chromatin Contain positively charged R-groups which bind to the negatively charged DNA (phosphate groups)  DNA backbone has a negative charge  histones have a positive charge 5 types  Core: H2A, H2B, H3, H4  Linker: H1
  17. 17. First level of packing: Nucleosome Nucleosome = DNA + core histones DNA wrapped twice around an octamer of core histones consisting of:  2 of each core histone: H2A, H2B, H3, H4  Note: H1 is not part of the nucleosome, but is attached to the DNA near the nucleosome 10 nm in diameter
  18. 18.
  19. 19. Beads-on-a-string A nucleosome looks like a bead (histone) with string wrapped around it (DNA) Beads-on-string Consists of histone octamer and DNA
  21. 21. Second level of packing: Solenoids / chromatin Solenoid: H1 histones aggregate causing 6 nucleosomes to coil together 30 nm in diameter stack on top of each other forming the chromatin fiber
  22. 22.
  23. 23. Third level of packing:looped domains Chromatin fibers forms loops which attach to nonhistone proteins Nonhistone proteins form a scaffold 300 nm in diameter
  24. 24.
  25. 25. Fourth level of packing:Metaphase Chromosome Looped domains coil and fold, further compacting chromatin Result in the characteristic metaphase chromosome seen in karyotypes Such packing occurs during mitosis
  26. 26. DNA Packing Video
  27. 27. Tutorial Discovery of chromosome packaging
  28. 28. Gene Regulation Topics Review cell cycle Metaphase chromosome in mitosis Interphase chromatin in G1, S, G2  DNA replication  transcription
  29. 29. Gene Regulation Defined The ability to control whether a gene is actively being transcribed or not This regulation can occur at the:  Structural level (e.g. supercoiling of DNA)  Molecular level (e.g. negative feedback to suppress enzymatic activity)
  30. 30. Cell Cycle
  31. 31. Supercoiling For a gene to be expressed (transcribed), the chromosome at that region must be uncoiled Different levels of supercoiling affects transcription Allows control over which genes are expressed
  32. 32. Mitosis: PMAT  DNA is “inactive” because it is in the most condensed form (metaphase chromosome)  thus information is inaccessible
  33. 33. Interphase Chromatin Much less condensed than during mitosis Scaffold may be less defined (e.g. attach to inside of nuclear envelope) But order still exists:  Each chromosome occupies a restricted area with the nucleus  Nucleosome structure stays intact throughout cell cycle  Most still maintain the solenoid and looped domain structures
  34. 34. Interphase Chromatin  Different levels of packing on various regions of the same chromosome  Euchromatin: loosely packed region on chromatin, active transcription  Heterochromatin: densely packed region on chromatin, inactivatedEu = true; Hetero = different
  35. 35. Chromatin Structure duringTranscription
  36. 36.
  37. 37. MaCS onlyThe following sections are for the MaCS grade 12 biology class only
  38. 38. Epigenetics Study of heritable changes in gene expression caused by mechanisms other than the DNA sequence Modifications often affect both chromatin structure and gene regulation Modifications include:  DNA methylation  Histone acetylation
  39. 39. Methylation Attachment of methyl groups (-CH3) to DNA bases, usually at cytosine Occurs after DNA is replicated (S-phase) In general, methylation occurs on genes that are not expressed  Methylation suppresses gene expression  Removing methylation turns genes “on”
  40. 40. Histone AcetylationAttachment of acetyl group (-COCH3) to histones Acetylation changes histone shape reducing its grip on the DNA Results in more loosely packed DNA, available for transcription  Acetylation activates gene expression  Deacetylation suppresses gene expression
  41. 41. Summary of Modificationsaffecting chromatin structure and gene regulation
  42. 42. Summary of Modificationsaffecting chromatin structure and gene regulation
  43. 43. Genomic Imprinting Imprinting: suppression of genes so that only 1 allele is expressed  Established in germline cells  Maintained in all somatic cells derived from the parent cell Most genes are not imprinted: both alleles are expressed Imprinted genes:  Expressions regulated by epigenetic factors  Inactivated gene can be either maternal or paternal  Genes are expressed from the non-imprinted allele
  44. 44.
  45. 45. Epigenetics Videos PBS NOVA Now “Epigenetics” (13:03) BeginBeforeBirth “What makes us who we are?” (4:11) BBC Horizon “The Ghost in Your Genes” (49:06)