An overview of genomics:

1. Lecture of Principles of gene engineering 2008. 4/28 An overview of genomics: From the basis of molecular cloning to the genome sequencing projects (Human Genome Project). Dr. Jin-Mei Lai bio2028@mails.fju.edu.tw

2. So far in this course you have learned how to clone and identify the gene of your interest. cDNA  PCR DNA polymerase (Taq) A A A A + A A A A ligation Amp+ plate (+ X-gal & IPTG) selection ampR White colony: recombinant Inserted DNA disrupts lac Z’ gene Blue colony: non-recombinant

3. How can I get the sequence of specific gene? • Design specific primers (search information from gene database) • PCR (using cDNA or cDNA library as template) • cloning into expression vector Nick translation * Make a cDNA library 3

4. Generate cDNA from tissues or cell lines. •  isolation of total RNA • purification the mRNA by oligo-dT column • reverse transcription • PCR amplification RT-PCR 4

5. Why we should use cDNA? 5

6. What is a gene ? + • An open reading frame Its transcriptional control elements (promoter and terminator) Fig. 1.22

7. The differences of gene expression in prokaryotes and eukaryotes.

8. How can we study the unknown genes? Fully understanding the genome we studied will improve to identify and investigate the unknown genes. * Genome sequencing projects! • Genomic mapping. • Genetic mapping. • Physical mapping. • Nucleotide or Genome sequencing. 8

9. Genomic mapping The chromosome content of an organism (itskaryotype) can be visualized using a microscope. ~ Different chromosomes are usually different sizes (ranging in the human from 279x106 bp for chromosome 1 to 45x106 bp for chromosome 21). ~ distinct chromosome banding patterns. (Giemsa stain) shorter arm longer arm Cytological map (low resolution)

10. Some chromosome abnormalities that cause inherited genetic diseases can be observed by karyotype analysis. e.g. Down’s Sydrome (trisomy 21) Klinefelter’s syndrome (47XXY) * Cystic fibrosis  chromosome 7q31; CFRT

11. * Fluorescence in situ hybridization (FISH) ~ a kind of in situ hybridization in situ: in place DNA probes: radioactively labeled fluorescence labeled (now) Low resolution: less than 3 Mbp Yellow: satellite DNA in centromere

12. Genetic mapping ~ is a representation of the distance between two DNA elements based upon the frequency at which recombination occurs between the two. * The first genetic map of a chromosome: ~ from Drosophila mating crosses data The information gained from the experimental crosses could be used to plot out the location of genes.  Tightly linked genes are physically located close to each other, while those that were only weakly linked are physically further apart.

13. A centimorgan (cM) is defined as the distance between two loci on a genetic map. A cM is a measure of genetic distance and not physical distance. Look closely at the diagram. If two loci are far apart, it is possible to miss that a double cross-over occurred. 13

14. * Major drawbacks for genetic mapping ~ The requirement for aphenotype for the gene that is being mapped and the number of crosses required to generate accurate mapping data. ~ A tacit assumption of mapping based on crosses is that the recombination frequency is equal for all part of the chromosome. Except recombinational hot-spots and cold-spots In human, relatively low number of genes have been identified, hence difficult to estimate map distances.

15. * An alternative to genetic mapping using phenotypes is to follow the inheritance of DNA sequence variations between individuals. Though more than 99% of human DNA sequences are the same across the population. ~ still a huge numbers of variations in DNA sequence between individuals. Several methods used to exploit the inheritance of the variations to map genomic location. • Ex. • Single-nucleotide polymorphisms. • Variable number tandem repeats (VNTRs). • Microsatellites.

16. Single-nucleotide polymorphisms (SNPs). ~ the most common types of sequence variation between individuals. ~ occur as frequently as about once every 100- 300 bp What kinds of genome variations are there? Genome variations includemutationsand polymorphisms. Technically, a polymorphism (a term that comes from the Greek words "poly," or "many," and "morphe," or "form") is a DNA variation in which each possible sequence is present in at least 1% of people. For example, a place in the genome where 93 percent of people have a T and the remaining 7 percent have an A is a polymorphism. If one of the possible sequences is present in less than 1 percent of people (99.9 percent of people have a G and 0.1 percent have a C), then the variation is called a mutation.

17. Informally, the term mutation is often used to refer to a harmful genome variation that is associated with a specific human disease, while the word polymorphism implies a variation that is neither harmful nor beneficial. However, scientists are now learning that many polymorphisms actually do affect a person's characteristics, though in more complex and sometimes unexpected ways.

18. About 90 percent of human genome variation comes in the form of single nucleotide polymorphisms, or SNPs (pronounced "snips"). As their name implies, these are variations that involve just one nucleotide, or base. ~ frequency: once every 100-300 bp ~ may be “disease causing mutations” occur in non-coding regions of DNA some alter the restriction enzyme recognition sites. Restriction fragment length polymorphisms (RFLPs) (detected by Southern blotting using a radioactive DNA probe)

19. * Restriction fragment length polymorphisms (RFLPs) Southern blotting

20. 20

21. RFLP (Restriction Fragment Length Polymorphisms)

22. Highly repeated DNA sequences. --- short, arranged in tandem. 1. Satellite DNAs ~ consist of short sequences that form very large clusters. ex. satellite DNA in centromere 2. Minisatellite DNAs ~ range from 12 to 100 base pairs in length and are found in clusters containing as many as 3000 repeats. * unstable, the copy number often changes from one generation to the next. (polymorphic  apply to DNA fingerprinting) 3. Microsatellite DNAs ~ shortest and are present in small clusters of about 10~40 bps in length

23. 2. VNTR stands for "variable number of tandem repeats" A tandem repeat is a short sequence of DNA that is repeated in a head-to-tail fashion at a specific chromosomal locus. Tandem repeats are interspersed throughout the human genome. Some sequences are found at only one site -- a single locus -- in the human genome. For many tandem repeats, the number of repeated units vary between individuals. Such loci are termed VNTRs.

24. Think … One VNTR in humans is a 17 bp sequence of DNA repeated between 70 and 450 times in the genome. The total number of base pairs at this locus could vary from 1190 to 7650. VNTRs are detected as RFLPs by Southern Hybridization. 24

25. Minisatellite sequences are used to identify individuals in criminal or paternity cases through the technique of DNA fingerprinting. criminal case: V: victim D: defendant 25

26. 3. Microsatellites. ~ are short, 2-6 bp, tandemly repeated sequences that occur in a random fraction distributed throughout the genome. ~ generated by polymerase “slippage” during replication. The most common type is 5’-AC-3’ 26

27. Physical mapping ~ the physical map of a genome is a map of genetic markers made by analyzing a genomic DNA sequence directly, rather than analysing recombination events. • Restriction maps • Radiation hybrid maps • STS maps Ex 1 . NotI recognition sequence (5’-GCGGCCGC-3’) NotI would be expected to occur, by chance, every 48=65536 bp however, it cleaves human DNA on average once every 10 Mbp Why? The DNA sequence within the genome is not random! restriction mapping does provide highly reliable fragment ordering and distance estimation

28. Radiation hybrids RH maps are constructed by typing a panel of hybrids with a set of human DNA markers Whole-genome radiation hybrids Only a PROPORTION of the pieces of the broken human chromosomes will integrate into rodent chromosomes

29. Ex 3. STS maps. ~ STSs (sequence tagged sites) are short DNA sequences (100-200 base pairs) that were generated by PCR using primers based on already known DNA sequences. ~ have been sequenced and assigned to a chromosomal location, define a unique site on the genome. * Aligning clones by STS mapping. STS:  To order inserts from individual human chromosomes in a YAC library.

30. * Resolution ranges encountered in genome mapping.

31. The different types of cytological, genetic and physical map of a chromosome. cM: centiMorgan Mbp: Megabase pairs 31

32. The sequencing projects are then used to determine the individual base sequence of each clone. Manual DNA sequencing DNA sequencing methodologies: ca. 1977! • Maxam-Gilbert • base modification by general and specific chemicals. • depurination or depyrimidination. • single-strand excision. • not amenable to automation • Sanger • DNA replication. • substitution of substrate with chain-terminator chemical. • more efficient • automation?? 32

33. DNA sequencing: Maxam & Gilbert sequencing ~ The method is reliable for sequencing up to ~100 nucleotides at a time. The technique requires that the target DNA is end-labeled (usually radioactively).

34. Either 4 or 5 separate chemical reactions are performed. The reactions are carried out in two stages:Stage 1: Specific chemical modification of bases in the DNA. Stage 2: Chemical cleavage of sugar-phosphate backbone at modification site. 5’3’ direction

35. DNA sequencing: Sanger’s method (“bio” based methods) ~ dideoxynucleotide ~ based upon the faithful replication of DNA using a DNA 35

36. Sanger method - Can lead to clean and unambiguous assignment of about 300 bases per reaction. * 7M urea gel * High power level  70oC Reduce secondary structure of DNA fragments. 36

37. Automated DNA sequencing ~ a set of dideoxynucleotides has been developed that are labelled with fluorescent dyes precisely. BigDyeTM terminator 37

38. Sophisticated base calling software is available to convert the fluorescent patterns obtained into a sequence of DNA bases.  speed, more reliable in sequence interpretation. ~as many as 1000 bases can be read automatically from a single reaction, although the sequence obtained from within 500 bp of the primer is generally more reliable.

39. Capillary electrophoresis ABI 377 envelope: 96 lanes

40. How to sequence the genome? How to reconstruct the original genome sequence based on the small fragments that are cloned into individual vectors? Strategies  Clone contigs  Whole genome shotgun  Hierarchical shotgun 40

41. Clone contigs ~ the simplest way to generate overlapping DNA sequence is to isolate and sequence one clone, from a library, then identify (by hybridization) a second clone, whose insert overlaps with the first. The second clone is then sequenced and the information used to identify a third clone, whose inset overlaps with the second clone, and so on.

42. * Contig:(the basis of chromosome walking) ~ contiguous sequence of DNA created by assembling overlapping sequenced fragments of a chromosome.

43. Chromosome walking ~ This method is used to move systematically along a chromosome from a known location and to clone overlapping genomic clones that represent progressively longer parts of a particular chromosome.

44. Whole genome shotgun (WGS) - was first used to sequence the genome of the bacterium Haemophilus influenzae. ~ the fragments of the genome, which have been randomly generated, are cloned into a vector and each insert is sequenced.  the sequence is then examined for overlaps and the genome is reconstructed by assembling the overlapping sequences together.

45. Identifying additional clones that contained sequences close to the gap-point. * Advantage: ~ no prior knowledge of the sequence of the genome is required. * Disadvantage: ~ may limited by the ability to identify overlapping sequences. ~Time-consuming (every sequence must be compared with every other sequence in order to identify the overlaps) ~ Repetitive DNA sequences in the genome may lead to the incorrect assignment of contigs.

46. Hierarchical shotgun -- preferred by the Human Genome Project In this approach, genomic DNA is cut into pieces of about 150 Mb and inserted into BAC vectors, transformed into E. coli where they are replicated and stored. Each BAC fragment is fragmented randomly into smaller pieces and each piece is cloned into a plasmid and sequenced on both strands. These sequences are aligned so that identical sequences are overlapping. 46

47. Two general strategies for sequencing a complete genome. 47

48. What was the Human Genome Project? • The Human Genome Project (HGP) was the international, collaborative research program whose goal was the complete mapping and understanding of all the genes of human beings. All our genes together are known as our "genome." • Goals of HGP: • Determine the DNA sequence of the entire human genome • Store this information in databases • Identify all of the genes in human DNA • Improve tools for data analysis

49. Brief review of genomics- regarding to HGP Human Genome Project (HGP) ~ started at late 1980 by 20 centers of six nations (coordinated by NIH/USA), led first by Watson and after 1992 by Collins. ~ The completed sequence of the human genome (3x109 bp) was published in April 2003 (efforts spanning 13 yrs). ~ Joining by Celera Co. (funded in 1997 by Venter) accelerated the process (two years ahead of schedule). James D. Watson 49

50. The Beginning of the Project Most the first 10 years of the project were spent improving the technology to sequence and analyze DNA. Scientists all around the world worked to make detailed maps of our chromosomes and sequence model organisms, like worm, fruit fly, and mouse. 50