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Organisation of human genome

Nuclear genome (3.2 Gbp) 24 types of chromosomes Y- 51Mb and chr1 -279Mbp . Mitochondrial genome . Organisation of human genome. LA COMPLEJIDAD BIOLÓGICA CRECIENTE EXIGE CAMBIOS GENÓMICOS QUE INCREMENTEN LA CAPACIDAD INFORMACIONAL DEL SISTEMA.

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Organisation of human genome

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  1. Nuclear genome (3.2 Gbp) 24 types of chromosomes Y- 51Mb and chr1 -279Mbp Mitochondrial genome Organisation of human genome

  2. LA COMPLEJIDAD BIOLÓGICA CRECIENTE EXIGE CAMBIOS GENÓMICOS QUE INCREMENTEN LA CAPACIDAD INFORMACIONALDEL SISTEMA... ...PERO EL NÚMERO DE GENES EN LOS DISTINTOS GENOMAS SECUENCIADOS NO CONCUERDA CON LO ESPERADO (APARENTEMENTE)

  3. Amphimedon queenslandica 18693 Bos taurus >22790 Trichoplax adhaerens 11514 Nematostella vectensis 18000 Nassonia vitripennis 17279 Homo sapiens 21527 Mus musculus 22083

  4. Danio rerio 21413 Drosophila melanogaster 13781 Ciona intestinalis 16000 Takifugu rubripes 18500 Caenorhabditis elegans 20224 Strongylocentrotus purpuratus 23300 Anolis carolinensis 17000 Xenopus tropicalis 18000 Gallus gallus <17000

  5. Gorilla gorilla 21000 Arabidopsis thaliana 26000 Oryza sativa 50000 Pan troglodytes 21000 Populus trichocarpa 45550 Glycine max 75778

  6. Why (coding) gene number doesn’t matter? • More sophisticated regulation of expression? • Proteome vastly larger than genome? • Alternate splicing • RNA editing • Postranslational modifications • Cellular location …but, remember there are other genes

  7. Genes in the genome: • Protein-coding genes (mRNA): around 20500 (as of 10/2012) • Non-coding RNAs • Ribosomal RNA (rRNA) • Transfer RNA (tRNA) • Small nuclear RNA (SnRNA) • Small nucleolar RNA (SnoRNA) • microRNA (miRNA) • Other non-coding RNAs (Xist, 7SK, etc.) • Peudogenes

  8. Non polypeptide–coding: RNA encoding

  9. Statistics about the current Gencode freeze (version 13) *The statistics derive from the gtf files, which include only the main chromosomes of the human reference genome. Version 13 (March 2012 freeze, GRCh37) General stats Total No of Genes 55123 Protein-coding genes 20670 Long non-coding RNA genes 12393 Small non-coding RNA genes 9173 Pseudogenes 13123        Total No of Transcripts 182967 Protein-coding transcripts 77901   Long non-coding RNA loci transcripts 19835 Total No of distinct translations 78119 Genes that have more than one distinct translations 14235

  10. Protein-coding genes (mRNA):

  11. HUMAN genes and their homology to genes from other organisms

  12. Noncoding regions in coding genes CODING GENES • Regulatory regions • RNA polymerase binding site • Transcription factor binding sites • Polyadenylation [poly(A)] sites • Enhancers • 5’- and 3’-UTRs

  13. DNA as a series of ‘docking’ sites It is the relative location of these docking sites to one another that permits genes to be transcribed, spliced, and translated properly and in specific spatial and temporal patterns.

  14. …some more statistics • Gene density 1/100 kb (vary widely); • Averagely 9 exons per gene • 363 exons in titin gene • Many genes are intronsless • Largest intron is 800 kb (WWOX gene) • Smallest introns – 10 bp • Average 5’ UTR 0,2-0,3 kb • Average 3’ UTR 0,77 kb but underestimated… • Largest protein: titin: 38,138 aa • Largest gene: dystrophin

  15. Human genes vary enormously in size and exon content

  16. An example of complex human gene locus INK4a-ARF From: Prof. Gordon Peters website

  17. Genes within genes Neurofibromatosis gene (NF1) intron 26 encode : OGMP (oligodendrocyte myelin glycoprotein) EVI2A and EVO2B (homologues of ecotropic viral intergration sites in mouse)

  18. Why gene number doesn’t matter? • More sophisticated regulation of expression • Proteome vastly larger than genome • Alternate splicing • RNA editing… • Postranslational modifications • Cooption • GRN’s connectivity

  19. REDES DINÁMICAS

  20. Why gene number doesn’t matter? • More sophisticated regulation of expression • Proteome vastly larger than genome • Alternate splicing • RNA editing… • Postranslational modifications • Cooption • GRN’s connectivity

  21. UCSC

  22. Location of CpG islands in the gene CpG islands do NOT have a deficit of CpG dinucelotides

  23. How epigenetics works Promoter Region Gene CpG Island = CpG = methylated CpG

  24. Unmethylated CpGs relax chromatin Gene RNA = CpG Proteins = methylated CpG

  25. Methylated CpGs constrain chromatin Gene RNA = CpG Proteins = methylated CpG

  26. Chromatin Modification Chromatin Remodeling SNF/SWI Transcription Factor Modification Acetylation Phosphorylation Histone Substitution H2AZ H2Ax H3.3 Histone Modification Acetylation Ubiquitination Sumoylation Methylation Phosphorylation DNA Methylation CpG dinucleotides MeCP2

  27. Eukaryotic transcription regulationModular construction and combinatorial control • The regulatory sequence (cis element) on DNA consists of multiple motifs specific for transcription factors. • Multiple transcription factors can bind simultaneously to the regulatory sequences and act together on the transcription of the gene.

  28. Co-activator protein Transcriptional activators binding to promoter region General transcription factors TBP Gene X TATA -35 Regulated Transcription

  29. (TTR= transthyretin)

  30. Distant Cis-Acting Elements Locus Control Region Regulatory site required for optimal expression of adjacent group of genes Insulator Element Prevents activation/repression extending to an adjacent regulatory sequence

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