Chromosome structure


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this lecture is about chromosome structure, very handy for the next colloquium!

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Chromosome structure

  1. 1. Genetics: Analysis and Principles By Robert J. Brooker CHAPTER 10 CHROMOSOME ORGANIZATION AND MOLECULAR STRUCTURE
  2. 2. In which form does DNA and RNA occur in a cell? <ul><li>Never naked! </li></ul><ul><li>Always associated with proteins </li></ul><ul><li>From small virus genome to big genome of a complex organisme. </li></ul><ul><li>Proteins associated with DNA play a significant role in regulation of gene expression/repression. </li></ul>
  3. 3. <ul><li>Viruses are small infectious particles containing nucleic acid surrounded by a capsid of proteins </li></ul><ul><li>For replication, viruses rely on their host cells </li></ul><ul><ul><li>ie., the cells they infect </li></ul></ul><ul><li>Most viruses exhibit a limited host range </li></ul><ul><ul><li>They typically infect only specific types of cells of one host species </li></ul></ul>VIRAL GENOMES
  4. 4. Animal virusses Lipid bilayer Picked up when virus leaves host cell
  5. 5. <ul><li>A viral genome is the genetic material of the virus </li></ul><ul><ul><li>Also termed the viral chromosome </li></ul></ul><ul><li>The genome can be </li></ul><ul><ul><li>DNA or RNA </li></ul></ul><ul><ul><li>Single-stranded or double-stranded </li></ul></ul><ul><ul><li>Circular or linear </li></ul></ul><ul><li>Viral genomes vary in size from a few thousand to more than a hundred thousand nucleotides </li></ul>Viral Genomes
  6. 7. Figure 10.1 General structure of viruses <ul><li>Bacteriophages may also contain a sheath, base plate and tail fibers </li></ul>Lipid bilayer Picked up when virus leaves host cell
  7. 8. <ul><li>During an infection process, mature viral particles need to be assembled </li></ul>Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 10-8 <ul><li>Viruses with a simple structure may self-assemble </li></ul><ul><ul><li>Genetic material and capsid proteins spontaneously bind to each other </li></ul></ul><ul><ul><li>Example: Tobacco mosaic virus </li></ul></ul>Figure 10.2 Capsid composed of 2,130 identical protein subunits
  8. 9. <ul><li>Complex viruses, such as T2 bacteriophages, undergo a process called directed assembly </li></ul><ul><ul><li>Virus assembly requires proteins that are not part of the mature virus itself; Helper proteins / “chaperone proteins” </li></ul></ul><ul><li>The noncapsid proteins usually have two main functions </li></ul><ul><ul><li>1. Carry out the assembly process </li></ul></ul><ul><ul><ul><li>Scaffolding proteins that are not part of the mature virus </li></ul></ul></ul><ul><ul><li>2. Act as proteases that cleave viral capsid proteins </li></ul></ul><ul><ul><ul><li>This yields smaller capsid proteins that assemble correctly </li></ul></ul></ul>Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
  9. 10. <ul><li>The bacterial chromosome is found in a region called the nucleoid </li></ul><ul><li>The nucleoid is not membrane-bounded </li></ul><ul><ul><ul><ul><ul><li>So the DNA is in direct contact with the cytoplasm </li></ul></ul></ul></ul></ul>BACTERIAL CHROMOSOMES
  10. 11. <ul><li>DNA supercoiling is a second important way to compact the bacterial chromosome </li></ul><ul><li>Figure 10.7 provides a schematic illustration of DNA supercoiling </li></ul>Supercoiling within loops creates a more compact DNA Figure 10.6
  11. 12. Terms and concepts to know: Compaction Coiling Supercoiling Gyrase topoisomerase
  12. 13. Plates preventing DNA ends from rotating freely Fewer turns More turns Both overwinding and underwinding can induce supercoiling Figure 10.7 These three DNA conformations are topoisomers of each other These two DNA conformations do not occur in living cells
  13. 14. Increasing of ‘coiling’ of the double helix in eukaryotes also occur: - DNA replication - transcription, RNA synthesis from a double stranded DNA
  14. 15. Figure 10.8 It makes transcription and translation easier, because the chains melt easier. negative supercoiling Does not only lead to a more compacted nucleoid
  15. 16. <ul><ul><li>1. DNA gyrase (also termed DNA topoisomerase II ) </li></ul></ul><ul><ul><ul><li>Introduces negative supercoils using energy from ATP </li></ul></ul></ul><ul><ul><ul><li>It can also relax positive supercoils when they occur </li></ul></ul></ul><ul><ul><li>2. DNA topoisomerase I </li></ul></ul><ul><ul><ul><li>Relaxes negative supercoils </li></ul></ul></ul>Supercoiling is regulated by two types of enzymes:
  16. 17. <ul><li>Eukaryotic species contain one or more sets of chromosomes </li></ul><ul><ul><li>Each set is composed of several different linear chromosomes </li></ul></ul><ul><li>The total amount of DNA in eukaryotic species is typically greater than that in bacterial cells </li></ul><ul><li>Chromosomes in eukaryotes are located in the nucleus </li></ul><ul><ul><li>To fit in there, they must be highly compacted </li></ul></ul><ul><ul><ul><li>This is accomplished by the binding of many proteins </li></ul></ul></ul><ul><ul><ul><li>The DNA-protein complex is termed chromatin </li></ul></ul></ul>EUKARYOTIC CHROMOSOMES
  17. 18. Has a genome that is more than twice as large as that of Genome size is very various, especially because of the presence of Repetitive DNA
  18. 19. <ul><li>A eukaryotic chromosome contains a long, linear DNA molecule </li></ul><ul><ul><li>Refer to Figure 10.11 </li></ul></ul><ul><li>Three types of DNA sequences are required for chromosomal replication and segregation </li></ul><ul><ul><li>Origins of replication </li></ul></ul><ul><ul><li>Centromeres </li></ul></ul><ul><ul><li>Telomeres </li></ul></ul>Organization of Eukaryotic Chromosomes
  19. 20. Prevent chromosome sticky ends and shortening Required for proper segregation during mitosis and meiosis Eukaryotic chromosomes contain many origins of replication approximately 100,000 bp apart Figure 10.11
  20. 21. <ul><li>Genes are located between the centromeric and telomeric regions along the entire chromosome </li></ul><ul><ul><li>A single chromosome usually has a few hundred to several thousand genes </li></ul></ul><ul><li>In lower eukaryotes (such as yeast) </li></ul><ul><ul><li>Genes are relatively small </li></ul></ul><ul><ul><ul><li>They contain primarily the sequences encoding the polypeptides </li></ul></ul></ul><ul><ul><ul><li>ie: Very few introns are present </li></ul></ul></ul><ul><li>In higher eukaryotes (such as mammals) </li></ul><ul><ul><li>Genes are long </li></ul></ul><ul><ul><ul><li>They tend to have many introns </li></ul></ul></ul><ul><ul><ul><li>intron lengths from less than 100 to more than 10,000 bp </li></ul></ul></ul>General features of eukaryotic chromosomes
  21. 22. <ul><li>Sequence complexity refers to the number of times a particular base sequence appears in the genome </li></ul><ul><li>There are three main types of repetitive sequences </li></ul><ul><ul><li>Unique or non-repetitive </li></ul></ul><ul><ul><li>Moderately repetitive </li></ul></ul><ul><ul><li>Highly repetitive </li></ul></ul>Repetitive Sequences
  22. 23. <ul><li>Unique or non-repetitive sequences </li></ul><ul><ul><li>Found once or a few times in the genome </li></ul></ul><ul><ul><li>Includes structural genes as well as intergenic areas </li></ul></ul><ul><li>Moderately repetitive </li></ul><ul><ul><li>Found a few hundred to a few thousand times </li></ul></ul><ul><ul><li>Includes </li></ul></ul><ul><ul><ul><li>Genes for rRNA and histones </li></ul></ul></ul><ul><ul><ul><li>Origins of replication </li></ul></ul></ul><ul><ul><ul><li>Transposable elements </li></ul></ul></ul><ul><li>Highly repetitive </li></ul><ul><ul><li>Found tens of thousands to millions of times </li></ul></ul><ul><ul><li>Each copy is relatively short (a few nucleotides to several hundred in length) </li></ul></ul>Repetitive Sequences
  23. 24. Eukaryotic Chromatin Compaction <ul><li>If stretched end to end, a doploid set of human chromosomes will be over 2 meter long! </li></ul><ul><ul><li>Yet the cell’s nucleus is only 2 to 4  m in diameter </li></ul></ul><ul><ul><ul><li>Therefore, the DNA must be tightly compacted to fit </li></ul></ul></ul><ul><li>The compaction of linear DNA in eukaryotic chromosomes involves interactions between DNA and various proteins </li></ul><ul><ul><li>Proteins bound to DNA are subject to change during the life of the cell </li></ul></ul><ul><ul><ul><li>These changes affect the degree of chromatin compaction </li></ul></ul></ul>
  24. 25. Eukaryotic Chromatin Compaction `````` Samenstelling relatieve hoeveelheid Histon eiwitten 115 Non-histon eiwitten 33 RNA 1 100 DNA
  25. 26. <ul><li>Histone proteins are basic </li></ul><ul><ul><li>They contain many positively-charged amino acids </li></ul></ul><ul><ul><ul><li>Lysine and arginine </li></ul></ul></ul><ul><ul><li>These bind with the phosphates along the DNA backbone </li></ul></ul><ul><ul><li>Histone proteins have a globular domain and a flexible, charged amino terminus or ‘tail’ </li></ul></ul><ul><li>There are five types of histones </li></ul><ul><ul><li>H2A, H2B, H3 and H4 are the core histones </li></ul></ul><ul><ul><ul><li>Two of each make up the octamer </li></ul></ul></ul><ul><ul><li>H1 is the linker histone </li></ul></ul><ul><ul><ul><li>Binds to linker DNA </li></ul></ul></ul><ul><ul><ul><li>Also binds to nucleosomes </li></ul></ul></ul><ul><ul><ul><ul><li>But not as tightly as are the core histones </li></ul></ul></ul></ul><ul><ul><li>Refer to Figure 10.13 </li></ul></ul>
  26. 27. <ul><li>Overall structure of connected nucleosomes resembles “beads on a string” </li></ul><ul><ul><li>This structure shortens the DNA length about seven-fold </li></ul></ul>Vary in length between 20 to 100 bp, depending on species and cell type Diameter of the nucleosome Figure 10.13
  27. 28. Play a role in the organization and compaction of the chromosome Figure 10.13
  28. 29. Regular, spiral configuration containing six nucleosomes per turn Irregular configuration where nucleosomes have little face-to-face contact Figure 10.16
  29. 30. <ul><li>The model of nucleosome structure was proposed in 1974 by Roger Kornberg </li></ul><ul><li>Kornberg based his proposal on various observations about chromatin </li></ul><ul><ul><li>Biochemical experiments </li></ul></ul><ul><ul><li>X-ray diffraction studies </li></ul></ul><ul><ul><li>Electron microscopy images </li></ul></ul>Experiment I: Nucleosome Structure Revealed Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
  30. 31. <ul><li>Markus Noll decided to test Kornberg’s model </li></ul><ul><li>He did this via the following procedure </li></ul><ul><ul><li>Digest DNA with the enzyme DNase I </li></ul></ul><ul><ul><li>Accurately measure the molecular weight of the resulting DNA fragments </li></ul></ul><ul><ul><li>The rationale is that the linker DNA is more accessible than the “core DNA” to the DNase I </li></ul></ul><ul><ul><ul><li>Thus, the cuts made by DNase I should occur in the linker DNA </li></ul></ul></ul>Experiment II: Nucleosome Structure Revealed Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
  31. 32. The Hypothesis <ul><ul><li>The experiment tests the beads-on-a-string model of chromatin structure </li></ul></ul><ul><ul><ul><li>It the model is correct, DNase I should cut in the linker region </li></ul></ul></ul><ul><ul><ul><ul><li>Thereby producing DNA pieces that are about 200 bp long </li></ul></ul></ul></ul>Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display
  32. 33. Figure 10.14
  33. 34. The Data Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 30 units ml-1
  34. 35. Interpreting the Data Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display All chromosomal DNA digested into fragments that are ~ 200 bp in length These longer pieces were all in multiples of 200 bp At low concentrations, DNase I did not cut at all the linker DNA This fragment contains two nucleosomes And this, three 30 units ml-1
  35. 36. Figure 10.15a ‘ BEADS ON A STRING’
  36. 37. Figure 10.15b ‘ BEADS ON A STRING’ + linker histone H1
  37. 38. Nucleosomes Join to Form a 30 nm Fiber Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display <ul><li>Nucleosomes associate with each other to form a more compact structure termed the 30 nm fiber </li></ul><ul><li>Histone H1 plays a role in this compaction </li></ul><ul><ul><li>At moderate salt concentrations, H1 is removed </li></ul></ul><ul><ul><ul><li>The result is the classic beads-on-a-string morphology </li></ul></ul></ul><ul><ul><li>At low salt concentrations, H1 remains bound </li></ul></ul><ul><ul><ul><li>Beads associate together into a more compact morphology </li></ul></ul></ul>
  38. 39. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 10-52 Figure 10.17 <ul><li>The third mechanism of DNA compaction involves the formation of radial loop domains </li></ul>Matrix-attachment regions MARs are anchored to the nuclear matrix, thus creating radial loops 25,000 to 200,000 bp Scaffold-attachment regions ( SARs ) or
  39. 40. The levels of compaction leading to a metaphase chromosome
  40. 41. The levels of compaction leading to a metaphase chromosome Figure 10.21
  41. 42. Compaction level in euchromatin Compaction level in heterochromatin During interphase most chromosomal regions are euchromatic Figure 10.21
  42. 43. Heterochromatin vs Euchromatin <ul><li>The compaction level of interphase chromosomes is not completely uniform </li></ul><ul><ul><li>Euchromatin </li></ul></ul><ul><ul><ul><li>Less condensed regions of chromosomes </li></ul></ul></ul><ul><ul><ul><li>Transcriptionally active </li></ul></ul></ul><ul><ul><ul><li>Regions where 30 nm fiber forms radial loop domains </li></ul></ul></ul><ul><ul><li>Heterochromatin </li></ul></ul><ul><ul><ul><li>Tightly compacted regions of chromosomes </li></ul></ul></ul><ul><ul><ul><li>Transcriptionally inactive (in general) </li></ul></ul></ul><ul><ul><ul><li>Radial loop domains compacted even further </li></ul></ul></ul>
  43. 44. <ul><li>There are two types of heterochromatin </li></ul><ul><ul><li>Constitutive heterochromatin </li></ul></ul><ul><ul><ul><li>Regions that are always heterochromatic </li></ul></ul></ul><ul><ul><ul><li>Permanently inactive with regard to transcription </li></ul></ul></ul><ul><ul><li>Facultative heterochromatin </li></ul></ul><ul><ul><ul><li>Regions that can interconvert between euchromatin and heterochromatin </li></ul></ul></ul><ul><ul><ul><li>Example: Barr body </li></ul></ul></ul>Figure 10.19
  44. 45. Histone Code Controls Compaction <ul><li>The compaction level of even euchromatin is too high for transcription factors and RNA polymerase to easily access and transcribe genes </li></ul><ul><ul><li>Chromatin remodeling changes chromatin structure </li></ul></ul><ul><ul><ul><li>regulates ability of transcription factors to access genes </li></ul></ul></ul><ul><ul><li>Histone core protein tails are modified </li></ul></ul><ul><ul><ul><li>over 50 different enzymes identified which modify tails </li></ul></ul></ul><ul><ul><ul><li>modifications include acetylation, methylation and phosphorylation-all covalent changes </li></ul></ul></ul><ul><ul><ul><li>refer to figure 10.20 </li></ul></ul></ul><ul><ul><li>Histone code hypothesis is that the pattern of modification is a code specifying alterations </li></ul></ul>
  45. 46. Figure 10.20 The histon-code 1. Lysines may be acetylated 2. Serines may be phoshorylated 3. arginines may be methylated
  46. 47. Metaphase Chromosomes <ul><li>As cells enter M phase, the level of compaction changes dramatically </li></ul><ul><ul><li>By the end of prophase, sister chromatids are entirely heterochromatic </li></ul></ul><ul><ul><li>Two parallel chromatids have an overall diameter of 1,400 nm </li></ul></ul><ul><li>These highly condensed metaphase chromosomes undergo little gene transcription </li></ul>
  47. 48. Eukaryotic Chromosome
  48. 49. Metaphase Chromosomes <ul><li>In metaphase chromosomes the radial loops are highly compacted and stay anchored to a scaffold </li></ul><ul><ul><li>The scaffold is formed from the nuclear matrix </li></ul></ul><ul><li>Histones are needed for the compaction of radial loops </li></ul><ul><li>Refer to Figure 10.22 </li></ul>
  49. 50. Metaphase Chromosomes Figure 10.22 (The scaffold)
  50. 51. <ul><li>Two multiprotein complexes help to form and organize metaphase chromosomes </li></ul><ul><ul><li>Condensin </li></ul></ul><ul><ul><ul><li>Plays a critical role in chromosome condensation </li></ul></ul></ul><ul><ul><li>Cohesin </li></ul></ul><ul><ul><ul><li>Plays a critical role in sister chromatid alignment </li></ul></ul></ul><ul><li>Both contain a category of proteins called SMC proteins </li></ul><ul><ul><li>Acronym = S tructural m aintenance of c hromosomes </li></ul></ul><ul><ul><li>SMC proteins use energy from ATP and catalyze changes in chromosome structure </li></ul></ul>
  51. 52. Cohesins along chromosome arms are released The alignment of sister chromatids via cohesin
  52. 53. The number of loops has not changed However, the diameter of each loop is smaller Condesin travels into the nucleus Condesin binds to chromosomes and compacts the radial loops During interphase, condensin is in the cytoplasm The condensation of a metaphase chromosome by condensin Model !
  53. 54. ‘ Chromosome territories’ chromosomen nemen een bepaalde ruimte in in de nucleus: Geen spaghetti Chromosome of a chicken Nucleus where each chromosome is colored differently
  54. 55. <ul><li>Viral Genomes </li></ul><ul><ul><li>- Viral genomes are relatively small and are composed of DNA or RNA </li></ul></ul><ul><ul><li>- Viral genomes are packaged into the capsid in an assembly process </li></ul></ul><ul><li>Bacterial Chromosomes </li></ul><ul><ul><li>- Bacterial chromosomes contain a few thousand gene sequences that are interspersed with other functionally important sequences </li></ul></ul><ul><ul><li>- The formation of chromosomal loops helps make the bacterial chromosome more compact </li></ul></ul><ul><ul><li>- DNA supercoiling further compacts the bacterial chromosome </li></ul></ul><ul><ul><li>- Chromosome function is influenced by DNA supercoiling </li></ul></ul><ul><li>Eukaryotic Chromosomes </li></ul><ul><ul><li>- The sizes of eukaryotic genomes vary substantially </li></ul></ul><ul><ul><li>- Eukaryotic chromosomes have many functionally important sequences including genes, origins of replication, centromeres, and telomeres </li></ul></ul><ul><ul><li>- The genomes of eukaryotes contains sequences that are unique, moderately repetitive, or highly repetitive </li></ul></ul><ul><ul><li>- Sequence complexity can be evaluated in a renaturation experiment </li></ul></ul><ul><ul><li>- Eukaryotic chromatin must be compacted to fit within the cell </li></ul></ul><ul><ul><li>- Linear DNA wraps around histone proteins to form nucleosomes, the repeating structural unit of chromatin </li></ul></ul><ul><ul><li>- The repeating nucleosome structure is revealed by digestion of the linker region </li></ul></ul><ul><ul><li>- Nucleosomes become closely associated to form a 30 nm fiber </li></ul></ul><ul><ul><li>- Chromosomes are further compacted by anchoring the 30 nm fiber into radial loop domains along the nuclear matrix </li></ul></ul><ul><ul><li>- The histone code controls chromatin compaction </li></ul></ul><ul><ul><li>- Condensin and cohesin promote the formation of metaphase chromosomes </li></ul></ul>Summary / study outline