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 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’

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 160,602 smallest score 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?

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.

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

No test crosses in humans, but… Finished here

Generating a restriction map

FISH map (Fluorescence in situ hybridization)

Stopped here