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Levels at which Eucaryote Genome Organization can be Studied

Levels at which Eucaryote Genome Organization can be Studied. Gene organization/ organization of ‘non-gene’ sequences. Banding Patterns/ Chromatin Structure. Linear Sequence. …ATAGC. Repetitive Gene Pseudo- Element gene. DNA Content of Haploid Genomes

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Levels at which Eucaryote Genome Organization can be Studied

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  1. Levels at which Eucaryote Genome Organization can be Studied Gene organization/ organization of ‘non-gene’ sequences Banding Patterns/ Chromatin Structure Linear Sequence …ATAGC... Repetitive Gene Pseudo- Element gene

  2. DNA Content of Haploid Genomes of a Range of Phyla Flowering plants Birds Mammals Reptiles Amphibians Bony fish Cartilaginous fish Echinoderms Crustaceans Insects Molluscs Worms Fungi Algae Bacteria Mycoplasmas Viruses (Plasmids) 103 105 10 7 109 1011 DNA content (bp)

  3. Eucaryote Chromosome Numbers Organism Common Diploid Chromosome Name Number _____________________________________________________ Myrmecia pilosula Ant 2 Felis catus Cat 38 Homo sapiens Human 46 Canis familiaris Dog 78 Ophioglossum reticulatum Fern 1260

  4. Human Chromosome Sizes Size (Mb) 50 100 150 200 250 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y Chromosome Number

  5. Eucaryote Genome Sizes • Eucaryote genome size 100-100000 times larger than bacterial chromosome • Why do eucaryotes have larger genomes? • Developmental and differentiation processes • Larger genome size  greater complexity (cf. bacteria) • Repetitive sequences

  6. Proportions of Repetitive and Nonrepetitive DNA in Example Genomes 1010 109 108 107 106 105 70 64 54 46 36 70 30 30 83 Genome size (bp) 17 100 E. coli (bacterium) D. melanogaster (fruit fly) X. laevis (toad) M. musculus (mouse) C. elegans (nematode worm) N. tabacum (tobacco) Nonrepetitive Repetitive DNA DNA

  7. Human Genome Organization HUMAN GENOME Nuclear genome 3000 Mb 30-40000 genes? Mitochondrial genome 16.6 kb 37 genes ~30% ~70% Genes and gene- related sequences Extragenic DNA Two rRNA genes 22 tRNA genes 13 polypeptide- encoding genes 80% 20% Unique or moderately repetitive ~10% ~90% Unique or low copy number Moderate to highly repetitive Coding DNA Noncoding DNA Pseudogenes Interspersed repeats Gene fragments Introns, untranslated sequences, etc. Tandemly repeated or clustered repeats

  8. How Many Genes in the Human Genome? • Current estimate is 30,000-40,000 • Drosophila (fruitfly) has ~13,000 genes • C. elegans (nematode worm) has ~20,000 genes • Mouse has ~30,000 genes • Human gene transcripts (mRNA) commonly undergo alternative splicing • More human genes are transcription factors which interact with larger number of control elements Exon DNA Transcription Intron pre-mRNA Splicing mRNA1 mRNA2 mRNA3 Translated into 3 proteins

  9. Types of Repetitive Sequence in the Human Genome • Tandem repeats: satellite DNA • Interspersed repeats • SINEs, e.g., Alu elements • Retroviral-like sequences. e.g., LINEs • Duplicated genes incl. pseudogenes

  10. Satellite DNA Main band [DNA] Satellite band Density • Tandem repeats 1-170 bp in length • Can total several Mb in length • Noncoding/nontranscribed • May have a structural role? • ~10-20% of human genome

  11. Satellite DNA Amplification Amplification Mutation New amplification unit Amplification

  12. Short Interspersed Repetitive Elements (SINEs): Alu Elements • Characteristics • Consensus: 281 nt • Consists of two related units • Considerable variation in length due to deletions, substitutions, or insertions • ~1,000,000 elements/haploid genome (~12%) • Distribution • Average spacing is 4-kb apart • Scattered but non-random? • Deleterious when inserted within a gene • Examples of insertions which assist in transcription regulation when inserted in control region of a gene • Selfish DNA? 1 GGCCGGGCGC GGTGGCTCAC GCCTGTAATC CCAGCACTTT 41 GGGAGGCCGA GGCGGGCGGA TCACGAGGTC AGGAGATCGA 81 GACCATCCCG GCTAAAACGG TGAAACCCCG TCTCTACTAA 121 AAATACAAAA AATTAGCCGG GCGTAGTGGC GGGCGCCTGT 161 AGTCCCAGCT ACTTGGGAGG CTGAGGCAGG AGAATGGCGT 201 GAACCCGGGA GGCGGAGCTT GCAGTGAGCC GAGATCCCGC 241 CACTGCACTC CAGCCTGGGC GACAGAGCGA GACTCCGTCT 281 C

  13. Long Interspersed Nuclear Elements (LINEs) • Characteristics • 60 bp - 7 kb • Considerable variation in length due to 5’ truncations, deletions, and rearrangements • ~500,000 elements/haploid genome (15-20%) • 3-4,000 are full-length • 1-2% capable of transposition, probably via an • RNA intermediate (as with retroviruses) • Distribution • Found in A-T rich regions 5’ 3’ A-T rich ORF2 ORF1

  14. Pseudogenes and Gene Fragments • Many eucaryotic genes exist as variants which, for example, may be expressed during different stages of development • Families of evolutionarily-diverged genes with related functions • Pseudogenes: • Nonfunctional gene copies or gene fragments which have arisen during gene family expansion • Contain insertions, deletions, nonsense mutations • Usually non-transcribed • May be associated with functional gene copy

  15. -globin Region on Human Chromosome 11  G A 2 1   10 kb Alurepeats LINEs

  16. Splicing Removes Introns from a Primary Transcript Exon DNA Intron Transcription pre-mRNA Splicing mRNA Translation Protein

  17. Intron Numbers in Selected Human Genes Gene Size (kb) Number of introns _______________________________________________ Thrombomodulin 3.7 0 -globin 1.4 2 Ovalbumin 7.7 7 BRCA1 100 22 von Willebrand factor 175 52 Dystrophin 2400* 79 *The size of a bacterial genome!

  18. Introns in Globin Gene Family Gene Size (bp) 1098 876 8659 677 1418 Plant globin Leghaemoglobin Myoglobin Human -globin Human -globin 50 100 150 Number of amino acids

  19. Summary • Eucaryotic genome sizes > bacterial genome sizes • Different chromosome numbers and genome sizes in eucaryotes, but not absolutely correlated with evolutionary position • ~3% of human genome is coding • Remainder is extragenic or noncoding (pseudogenes, introns, etc.) • Repetitive DNA constitutes a large part of human genome: •  Tandem repeats: satellite DNA •  Interspersed repeats: SINEs, LINEs •  Duplicated genes: pseudogenes • Introns

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