20080110 Genome exploration in A-T G-C space: an introduction to DNA walking
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This document discusses using "DNA walking" to summarize and explore genomic sequences. DNA walking maps DNA sequences onto 2D walks in "A-T G-C space" to visualize patterns. The author tests using DNA walks to detect duplications in genomes and construct phylogenies without alignment. While walks can uncover relationships, accuracy is limited. Future work could involve 3D walks in tetrahedral mappings to better represent genomic structure.
20080110 Genome exploration in A-T G-C space: an introduction to DNA walking
- 1. Genome exploration in A-T G-C space an introduction to ‘ DNA walking’ Jonathan Blakes Submitted for the degree MSc Biotechnology and Computation Julie Newdoll Dawn of the Double Helix Oil/Mixed, 2002
- 2. Exponential growth of DNA sequences GenBank release notes December 2007 “ from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months.” 83,874,179,730 base pairs in 80,388,382 entries
- 3. Genome Browsers EnsEMBL EMBL-EBI Sanger Institute Wellcome Trust UCSC University of California at Santa Cruz
- 4. Can we understand this information a priori, summarise and preserve fine structure ?
- 6. GraphDNA – DNA Walker
- 9. Mapping
- 10. Mapping 4 rotations for each of the 3 previous mappings 2 reflections of each of those 24 possible combinations of cardinal vectors These are the 3 most parsimonious mappings of those 24
- 11. A-T G-C
- 12. A-G C-T
- 13. A-C G-T
- 14. A-T G-C
- 15. A-T G-C is consistently smallest A-T G-C walks contain more information in less space are simply easier to print
- 21. Human chromosome 1 250,000,000 bases
- 22. S. cerevisiae chromosome 1
- 25. Duplications small (~4 base) sequences occur several times in each larger sequence for each small sequence calculate line between occurrences if the angle and length of 2 or more lines are consistent then draw lines to reveal possible duplications Can detect duplications by eye or algorithmically :
- 27. Comparison with published data This is a 7 fold contiguous duplication in the male Y chromosome. Members of the TSPY (Testis-specific Y-encoded proteins) family identified by Skaletsky et al Nature 423 (2003) using a combination of a whole chromosome dotplot with a 2-kb window and a custom Perl script running BLAST alignments of all 5-kb sequence segments, in 2-kb steps, of the entire MSY (Male Specific Y). exons introns
- 28. Phylogenetics Phylogenetics is the reconstruction of evolutionary relatedness from primary sequence information: DNA or protein Traditional phylogenetic methods such as ClustalW and TCoffee all start from a multiple sequence alignment Hard to find optimal alignment for many long sequences Want to use simple measures such as Manhattan or Euclidean distance derived from DNA walks to produce phylogenies without alignment Are these comparable to alignment methods?
- 30. Phylogeny algorithms Published Distance Matrix from Gilfillan GD, et. al. Microbiology 144 (1998) 829-838 of 7 aligned 1798-nucleotide long small rRNA of Candida and Saccharomyces species neighbour joining UPGMA
- 31. UPGMA method
- 32. Tree construction Distance Matrix Output Newick format string representation of a tree: (Bovine:0.69395, (Gibbon:0.36079, (Orang:0.33636, (Gorilla:0.17147, (Chimp:0.19268, Human:0.11927) :0.08386):0.06124):0.15057):0.54939, Mouse:1.21460);
- 33. Phylogenies with each mapping
- 34. Can summing 3 mappings eliminate bias? No. Possible improvements: A more complex distance measure, perhaps a composite of small sequence distances Larger sequences – human / chimpanzee chromosome – where mapping bias may be informative rather than destructive
- 35. Conclusion DNA walks can summarise information about nucleotide content in DNA sequences visualise tandem repeats uncover more distant relationships such as duplications and retroviral genomes without expert knowledge or complex algorithms be overlaid with annotations from Ensembl walks to function as an alternative to linear genome browsers be used to construct phylogenetic relationships but are inaccurate A-T G-C is most useful mapping for viewing 2D walks
- 36. Future 3D walks mappings where one nucleotide opposes another result in information loss, which can be helpful, but we can’t know what we are missing use a tetrahedral mapping: each step starts from the centre and proceeds to a corner should produce 3D structure like proteins but much bigger can recover 2D walk by viewing orientation
- 37. Acknowledgments Biosciences Dr. Gary Robinson (supervisor Biosciences) Dr. J ü rgen Schmidt (course convenor) Dr. Anthony Baines (Bioinformatics lecturer) Computing Dr. Colin Johnson (supervisor Computing)
Editor's Notes
- #4: Using our knowledge of gene structure – start codons (ATG), stop codons (UAA, UAG, UGA) and , BLASTs (sequence alignments) of mRNA transcripts with DNA
- #5: An alphabet of 4 bases, with words millions and millions of letters long with no punctuation.
- #20: Do you know what is at the top of this mountain? It is the origin of replication of the B. burgdorferi chromosome that, incidentally, has just been experimentally mapped. As a consequence, when you are climbing the mountain you are reading the lagging strand for replication and when you are going down the mountain you are reading the leading strand for replication. What is usually found, but not always if you remember Synechocystis , is that the leading strand is enriched in keto (G or T) bases and that the lagging strand is enriched in amino (A or C) bases. Interestingly, these biases have been reported for both eubacteria and archaea, mitochondria, chloroplasts, viruses and plasmids, but not for eukaryotes up to now. In B. burgdorferi the biases are so important that they affect the amino acid content of proteins and you can guess if a protein was encoded on the leading or the lagging strand solely from its amino acid content. The term ‘chirochore’ was coined to describe fragments of the genome corresponding to a mountainside, that is a DNA fragment more or less homogeneous for the base composition biases. This is a purely descriptive term without reference to any mechanism, reminiscent of ‘isochore’ for the description of DNA fragments with a homogeneous G+C content in some vertebrate chromosomes. On the other hand, the term ‘replichore’ was introduced to designate the two oppositely replicated halves of the chromosome between the origin and the terminus in bacteria. The good thing is that chirochore and replichore boundaries are the same in bacteria: the origins of replication are found at the top of the mountains while the termini are found at the bottom of the lowlands. This strongly suggests that these kinds of genome landscapes have something to do with replication. l Genomic tectonics A simple model to explain the universality of the phenomenon is based on the spontaneous deamination of cytosines that induce C®T mutations. The rate of this deamination is highly increased in single-stranded DNA, probably because of greater accessibility to the solvent in this state than in the double-stranded state. During replication the lagging strand is continuously protected by the newly synthesized leading strand, but the leading strand has to maintain a transient singlestranded state while waiting for the next Okazaki fragment to be long enough to restore the doublestranded state (see Fig. 6). This fundamental asymmetry of replication may explain the universality of the observed systematic biases in base composition; these are at least compatible with the hypothesis. The protection against cytosine deamination may differ between species and explain the variability in intensity of biases. The cytosine deamination theory is nice but it is just a theory. The fundamental limit of bioinformatics is that without experimental data you can discuss in silico results endlessly and fruitlessly. I would be very curious to know the minimum inhibitory concentration (MIC) of chemicals such as bisulphite, which catalyses the deamination of cytosine, for bacteria in which compositional biases are important (for instance B. burgdorferi , Treponema pallidum , Neisseria meningitidis ). These compounds may not only inhibit replication but also transcription because during transcription a transient single-stranded DNA state is necessary too. It would also be interesting to determine toxicological information for eukaryotic cells.
- #31: Unweighted Pair Group Method with Arithmatic Mean (UPGMA)
- #32: Unweighted Pair Group Method with Arithmatic Mean (UPGMA) simplest method cluster pairs with least distance, calculating the new distance using the mean