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BME 130 – Genomes
Lecture 2
Mapping Genomes
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: 10.1126/science.1211177
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
http://www.neb.com/nebecomm/products/categories.asp
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
Nucleases
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’
Restriction sites are often
palindromes and restriction
enzymes are often dimers.
Coincidence?
EcoRI
DNA ligases
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
Cloning vectors
Name
Maximum
Insert size
(kb)
Plasmid
~5
Fosmid
~40
BAC
~200
Polymerase
Chain
Reaction
Administrivia
Website:
http://courses.soe.ucsc.edu/courses/bme130/Fall11/01
Assign groups
PubMed – your tax dollars at work:
http://www.ncbi.nlm.nih.gov/pubmed
Mapping genomes
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
smallest
score
160,602
21
average score
1,417
biggest score
75,230
A map is useful for assembly, no
matter how it’s done
Restriction fragment length
polymorphisms
http://www.dna.gov/dna-databases/codis
Single nucleotide polymorphisms
dbSNP growth
Currently (dbSNPv131): 32,017,159 human SNPs in dbSNP!
Various ways to type SNPs (genotype)
Genes as markers
Remember Mendel?
Establishing order of genes
known to be linked – a
genetic map
No test crosses in humans,
but…
Generating a restriction map
FISH map (Fluorescence in situ hybridization)