IB 139 Lec 13 Guest Lecturer, Epigenetics, DNA and such

  1. What is the central dogma of biology?
    DNA -> Transcription -> RNA -> Translation -> Protein
  2. What is the enzyme involved in the transcription of DNA?
    RNA polymerase
  3. What is involved in the translation of RNA?
  4. How many chromosomes do humans have?
  5. Which parent do chromosomes come from?
    • Half mom
    • Half dad
  6. About how many base pairs are in the human genome?
    Just over 3 billion
  7. What are the general physical dimensions of DNA that's packed into the nucleus of human cells?
    • 2 meterrs long
    • 6 micrometers in diameter
  8. Almost half of our DNA consists of what?
    Lazy viruses
  9. What is the largest component of the human genome?
    Introns (26%)
  10. About how much of DNA has protein coding actually coded?
  11. About how many human genes are unclassified?
    ~4000 (23.6%)
  12. (T/F) Every cell in your body contains the same DNA.
  13. Where do all the different cell types come from if every cell in our body contains the same DNA?
    Errrr.. well?
  14. What are some examples of the different cell types?
    • Brain cells
    • Fat cells
    • Heart muscle cells
    • Red blood cells
    • Nerve cells
    • Etc.
  15. What is used as the filter between genotype and phenotype?
  16. What kinds of factors and processes affect epigenetic mechanisms?
    • Development (in utero, childhood)
    • Environmental chemicals
    • Drugs/Pharmaceuticals
    • Aging
    • Diet
  17. What is DNA methylation?
    Methyl group (an epigenetic factor found in some dietary sources) can tag DNA and activate or repress genes
  18. What are histones?
    Proteins around which DNA can wind for compactionand gene regulation
  19. What is histone modification?
    The binding of epigenetic factors to histone "tails" alters the extent to which DNA is wrapped around histones and the availability of genes in the DNA to be activated
  20. What are some health endpoints of faulty epigenetic mechanisms?
    • Cancer
    • Autoimmune disease
    • Mental disorders
    • Diabetes
  21. What determines DNA accessibility?
    Chromatin landscape
  22. How does chromatin landscape determine DNA accessibility?
    • There are certain sites that are hypersensitive to DNAase 1
    • Can lead to transcription
  23. What are the 3 DNase 1 hypersensitive sites?
    • Nucleosome-free enhancer region
    • Nucleosome-free promoter region
    • Nucleosome reposition region
  24. What is the purpose of injecting sequencing tags (like ATAC-seq) into DNA?
    • Can identify nucleosome deplete regions genome wide
    • Later, can find these places after fragmentation
  25. What was the old way of Assay for Transposase-Accessible Chromatin (ATAC)-sequencing?
    Dnase 1 - is an endonuclease that cleaves accessible DNA
  26. What are the drawbacks of the old way of ATAC-sequencing?
    • Digestion time variability
    • Sequence preference
    • Library prep
  27. What is the new way of Assay for Transposase-Accessible Chromatin (ATAC)-sequencing?
    TN5 - is a transposase that will insert sequencing tags into accessible DNA
  28. What are the advantages of the new way of ATAC-sequencing?
    • Fewer cells required
    • Easier library prep
    • Less sequence bias
  29. What is the old process of ATAC-seq?
    • Millions of cells
    • DNase 1
    • Cleavage of sensitive sites
    • Long nucleosome DNA fragments
    • Sequence ends of fragments and map back to genome
    • Infer locations of sensitive sites and nucleosomes
    • TF footprint?
  30. What is the new process of ATAC-seq?
    • 500-500,000 cells
    • TN5 transposase
    • Cleavage of sensitive sites
    • Short DNA fragments from sensitive region
    • Sequence ends of fragments and map back to genome
    • Infer locations of sensitive sites and nucleosomes
    • TF footprint?
  31. What are 3 cis-regulatory modules?
    • Promoters
    • Enhancers
    • Insulators
  32. What are promotors?
    Region for the assembly of the transcription machinery
  33. How do promotors regulate DNA transcription?
    Region for the assembly of the transcription machinery must be accessible for gene expression
  34. How do enhancers regulate DNA transcription?
    Modulates the levels of transcription activity of one or more genes
  35. How do insulators regulate DNA transcription?
    Bookend areas of activation or restriction
  36. What kind of regions do histone modifications mark?
    Regions of activity and repression
  37. What process can identify regions of histone modifications genome wide?
    Chromatin Immunoprecipitation (ChIP-seq)
  38. What does ChIP-seq do?
    • Identifies regions of histone modifications genome-wide
    • Can locate activity of epigenetic factors
  39. What are general transcription factors?
    Associated with actively transcribed genes
  40. What do sequence-specific transcription factors do?
    • Bind to cis-regulatory modules
    • Enhance or silence transcription
  41. What is CTCF?
    • The only known human insulator
    • Thought to be important in forming chromatin loops
  42. Give an overview of ChIP-seq.
    • Essentially, use antibodies to identify proteins and to sequence DNA
    • Have DNA with certain proteins on it
    • Cross-link: stick protein to the DNA
    • Shear: break it up into billions of little DNA pieces
    • Immunoprecipitation: use antibody to find protein of interest
    • Purify:
    • Get DNA sequencing:
    • Map: to reference the genome
    • Tag distribution: Use as an address to go back and find out where proteins were bound
  43. What is solid-phase amplification?
    • Illumina/Solexa sequencing
    • Can produce 100-200 million spatially separted clusters, providing free ends to which a universal sequencing primer can be hybridized to initiate the NGS reaction
Card Set
IB 139 Lec 13 Guest Lecturer, Epigenetics, DNA and such
IB 139 Lec 13 Guest Lecturer, Epigenetics, DNA and such