Genes, Genomes, and Genomics.ppt

Genes, Genomes, and Genomics Two. Again … What’s in a chromosome? Hierarchical vs. Whole Genome The value of genome sequences lies in their annotation Annotation – Characterizing genomic features using computational and experimental methods Genes: Four levels of annotation Gene Prediction – Where are genes? What do they look like? Domains – What do the proteins do? Role – What pathway(s) involved in? How many genes? Current consensus (in flux …) 15,000 known genes (similarity to previously isolated genes and expressed sequences from a large variety of different organisms) 17,000 predicted (GenScan, GeneFinder, GRAIL) Based on and limited to previous knowledge What are genes? - 1 Complete DNA segments responsible to make functional products Products Proteins Functional RNA molecules RNAi (interfering RNA) rRNA (ribosomal RNA) snRNA (small nuclear) snoRNA (small nucleolar) tRNA (transfer RNA) What are genes? - 2 Definition vs. dynamic concept Consider Prokaryotic vs. eukaryotic gene models Introns/exons Posttranscriptional modifications Alternative splicing Differential expression Genes-in-genes Genes-ad-genes Posttranslational modifications Multi-subunit proteins Prokaryotic gene model: ORF-genes “Small” genomes, high gene density Haemophilus influenza genome 85% genic Operons One transcript, many genes No introns. One gene, one protein Open reading frames One ORF per gene ORFs begin with start, end with stop codon (def.) Eukaryotic gene model: spliced genes Expansions and Clarifications ORFs Start – triplets – stop Prokaryotes: gene = ORF Eukaryotes: spliced genes or ORF genes Exons Remain after introns have been removed Flanking parts contain non-coding sequence (5’- and 3’-UTRs) Where do genes live? In genomes Example: human genome Ca. 3,200,000,000 base pairs 25 chromosomes : 1-22, X, Y, mt 28,000-45,000 genes (current estimate) 128 nucleotides (RNA gene) – 2,800 kb (DMD) Ca. 25% of genome are genes (introns, exons) Ca. 1% of genome codes for amino acids (CD