1. BME 130 – Genomes
Lecture 2
Mapping Genomes

2. Genomics in the news
An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
Morten Rasmussen1,2,*, Xiaosen Guo2,3,*,
Yong Wang4,*, Kirk E. Lohmueller4,*, …Eske Willerslev1,2,†
DOI: /science

3. Studying DNA The toolkit
DNA polymerases – synthesize DNA, usually from a template
Nucleases – break DNA polymers by cleaving the phosphodiester bond
Ligases – join DNA molecules together
End-modifying enzymes – add labels and make compatible ends for further manipulation

4. DNA polymerases Synthesize 5’ to 3’ (require free 3’ –OH)
Some have exonuclease activity
(as shown)
Reverse transcriptase
(from retro-virus) is a useful
RNA-dependent DNA polymerase

5. Nucleases 5’ATGACGTAGGATCCCATTGCAG3’ 3’TACTGCATCCTAGGGTAACGTC5’
Many kinds, but we mainly care about
Type II DNA restriction endonucleases
5’ATGACGTAGGATCCCATTGCAG3’
3’TACTGCATCCTAGGGTAACGTC5’
BamHI
5’ATGACGTAG3’ 5’GATCCCATTGCAG3’
3’TACTGCATCCTAG5’ 3’GGTAACGTC5’

6. Restriction sites are often palindromes and restriction enzymes are often dimers. Coincidence?
EcoRI

7. DNA ligases

8. End-modification enzymes
Terminal deoxynucleotidyl transferase adds bases to end of DNA polymer
Alkaline phosphatase removes phosphates from the 5’ ends of a DNA polymer
T4 polynucleotide kinase adds phosphates to the 5’ ends of a DNA polymer

9. Cloning vectors Name Maximum Insert size (kb) Plasmid ~5 Fosmid ~40
BAC
~200

10. Polymerase
Chain
Reaction

11. Administrivia Website:
Assign groups
PubMed – your tax dollars at work:

12. Mapping genomes

15. Repeat content of human
RepeatMasker (rmsk) Summary Statistics
item count
5,298,130
item bases
1,465,724,774 (50.59%)
item total
1,467,396,988 (50.65%)
smallest item 6
average item
277
biggest item
160,602
smallest score 21
average score
1,417
biggest score
75,230

16. A map is useful for assembly, no matter how it’s done

17. Restriction fragment length polymorphisms

22. Single nucleotide polymorphisms

23. dbSNP growth
Currently (dbSNPv131): 32,017,159 human SNPs in dbSNP!

24. Various ways to type SNPs (genotype)

31. Genes as markers

32. Remember Mendel?

33. Example of dihybrid of unlinked traits. Review Mendellian logic
Example of dihybrid of unlinked traits. Review Mendellian logic. Deviation from these numbers means the traits are linked.

34. Establishing order of genes known to be linked – a genetic map
If we know 3 markers are linked, but who is closer to who?

35. No test crosses in humans, but…
Finished here

39. Generating a restriction map

43. FISH map (Fluorescence in situ hybridization)

45. Stopped here