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Genome Browsers

Genome Browsers. UCSC (Santa Cruz, California) and Ensembl (EBI, UK). http://genome.ucsc.edu/. http://www.ensembl.org/. Eukaryotic Genomes: Not only collections of genes. Protein coding genes RNA genes (rRNA, snRNA, snoRNA, miRNA, tRNA) Structural DNA (centromeres, telomeres)

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Genome Browsers

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  1. Genome Browsers UCSC (Santa Cruz, California) and Ensembl (EBI, UK) http://genome.ucsc.edu/ http://www.ensembl.org/

  2. Eukaryotic Genomes: Not only collections of genes • Protein coding genes • RNA genes (rRNA, snRNA, snoRNA, miRNA, tRNA) • Structural DNA (centromeres, telomeres) • Regulation-related sequences (promoters, enhancers, silencers, insulators) • Parasite sequences (transposons) • Pseudogenes (non-functional gene-like sequences) • Simple sequence repeats

  3. Eukaryotic Genomes: High fraction non-coding DNA • Blue: Prokaryotes • Black: Unicellular eukaryotes • Other colors: Multicellular eukaryotes (red = vertebrates) Bron: Mattick, NRG, 2004

  4. Human Genome • 3 billion basepairs (3Gb) • 22 chromosome pairs + X en Y chromosomes • Chromosome length varies from ~50Mb to ~250Mb • About 22000 protein-coding genes • compare with ~14000 for fruitfly en ~19000 for Nematode C. elegans

  5. Human genome Bron: Molecular Biology of the Cell (4th edition) (Alberts et al., 2002) • Only 1.2% codes for proteins, 3.5-5% is under selection • Long introns, short exons • Large spaces between genes • More than half exists of repetitive DNA

  6. Variation Along Genome sequence • Nucleotide usage varies along chromosomes • Protein coding regions tend to have high GC levels • Genes are not equally distributed across the chromosomes • Housekeeping generally in gene-dense areas • Gene-poor areas tend to have many tissue specific genes Bron: Ensembl

  7. Chromosome organisation Bron: Lodish (4th edition) • DNA packed in chromatin • Active genes in less dense chromatin (beads-on-a-string) • Non-active genes often in densely packed chromatine (30-nm fiber) • Gene regulation by changing chromatin density, methylation/acetylation of the histones • Limited availability of chromatin information in genome browsers (post transcriptional modifications are currently under investigation with ChIP-on-chip experiments

  8. Genome browsers UCSC NCBI Ensembl http://genome.ucsc.edu/ http://www.ensembl.org/

  9. With the UCSC Genome Browser Genome Browsing http://genome.ucsc.edu/

  10. UCSC Genome browser

  11. Choose a species, an assembly and a gene

  12. Gene search results

  13. Genome browser

  14. Genomic Datatypes (Tracks)

  15. Transcription data rather complicated

  16. Browser → Gene record

  17. Gene record

  18. Gene record (2)

  19. Gene record (3)

  20. Gene record (4) “best hit”

  21. Gene record (5)

  22. Genomic elements • Genome browsers can be used to examine other things • Genomic sequence conservation • Pseudogenes • Duplications en deletions of pieces chromosome (Copy Number Variations, CNVs)

  23. Genomic Sequence Conservation • Not only protein coding parts are conserved in evolution • Conserved non-coding genomic sequences can be involved in gene regulation (enhancers, silencers, insulators) • With the UCSC browser one can examine genomic conservation

  24. Genomic Conservation (UCSC)

  25. Pseudogenes • Pseudogenes “look” like (are homologous to) protein-coding genes, but are non-functional • Two types: • Unprocessed pseudogenes (loss of function) • Processed pseudogenes (mRNAs that are retrotranscribed onto the genome  they miss introns and sometimes have a polyA) • The UCSC contains various databases of pseudogenes: • Yale pseudogenes (both types pseudogenes) • Vega pseudogenes (both types pseudogenes) • Retroposed genes (only processed pseudogenes)

  26. Pseudogenes (UCSC)

  27. Copy Number Variation • People do not only vary at the nucleotide level (SNPs); short pieces genome can be present in varying number of copies (Copy Number Polymorphisms (CNPs) or Copy Number Variants (CNVs) • When there are genes in the CNV areas, this can lead to variations in the number of gene copies between individuals • With the UCSC browser CNVs can be examined

  28. Copy Number Variation (UCSC)

  29. Finding a sequence in the genome

  30. BLAT – Search page

  31. BLAT - Results

  32. BLAT – “Details”

  33. BLAT – “Browser”

  34. Genome browsers UCSC Ensembl http://genome.ucsc.edu/ http://www.ensembl.org/

  35. With the Ensembl Genome browser Genome Browsing http://www.ensembl.org/

  36. Ensembl Genome browser

  37. Het Human Genome

  38. MapView – Overview chromosome

  39. ContigView – Zooming in (compare UCSD)

  40. ContigView (2)

  41. GeneView – Gene record

  42. TransView - mRNA Transcript

  43. TransView - mRNA Transcript (2)

  44. Alternative Transcripts Bron: Wikipedia (http://www.wikipedia.org/)

  45. GeneView - Show Alternative Transcripts

  46. GeneSpliceView - Alternative Transcripts

  47. Single Nucleotide Polymorphisms (SNPs) • Sequence variations within a species • Similar to mutations, but are simultaneously present in the population, and generaly have little effect • Are being used as genetic markers (a genetic disease is e.g. associated with a SNP) • ENSEMBL offers a nice SNP view

  48. GeneView - Show SNPs

  49. GeneSNPView - SNPs

  50. GeneView - Show Protein

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