10-810 /02-710Computational GenomicsEric [email protected] 4127http://www.cs.cmu.edu/~epxing/Class/10810-07/Ziv [email protected] 4107Takis [email protected] BST3 (Pitt)Topics• Introduction (1 Week)• Genetics (3 weeks)• Sequence analysis and evolution (4 weeks)• Gene expression (3 weeks)• Systems biology (4 weeks)Grades• 4 Problem sets: 36%• Midterm: 24%• Projects: 30%• Class participation and reading: 10%Introduction to Molecular Biology• Genomes• Genes• Regulation• mRNAs• Proteins• SystemsThe Eukaryotic CellCells Type• Eukaryots: - Plants, animals, humans- DNA resides in the nucleus- Contain also other compartments• Prokaryots: - Bacteria- Do not contain compartmentsCentral dogmaProteinmRNADNAtranscriptiontranslationCCTGAGCCAACTATTGATGAAPEPTIDECCUGAGCCAACUAUUGAUGAAGenome• A genome is an organism’s complete set of DNA (including its genes).• However, in humans less than 3% of the genome actually encodes for genes.• A part of the rest of the genome serves as a control regions (though that’s also a small part).• The goal of the rest of the genome is unknown (a possible project …).Comparison of Different Organisms 18,4001*108Worm4,200.05*108E. coli25,0001.3*108Plant25,00030*108Human13,6001.8*108Fly6,000.15*108YeastNum. of genesGenome sizeAssigning function to genes / proteins• One of the main goals of molecular (and computational) biology.• There are 25000 human genes and the vast majority of their functions is still unknown• Several ways to determine function- Direct experiments (knockout, overexpression)- Interacting partners- 3D structures- Sequence homologyHardEasierFunction from sequence homology• We have a query gene: ACTGGTGTACCGAT• Given a database with genes with a known function, our goal is to find another gene with similar sequence (possibly in another organism)• When we find such gene we predict the function of the query gene to be similar to the resulting database gene• Problems- How do we determine similarity?Sequence analysis techniques• A major area of research within computational biology.• Initially, based on deterministic (dynamic programming) or heuristic (Blast) alignment methods• More recently, based on probabilistic inference methods (HMMs).GenesGenomic DNAPromoter Protein coding sequence TerminatorWhat is a gene?Example of a Gene: Gal4 DNAATGAAGCTACTGTCTTCTATCGAACAAGCATGCGATATTTGCCGACTTAAAAAGCTCAAG TGCTCCAAAGAAAAACCGAAGTGCGCCAAGTGTCTGAAGAACAACTGGGAGTGTCGCTAC TCTCCCAAAACCAAAAGGTCTCCGCTGACTAGGGCACATCTGACAGAAGTGGAATCAAGG CTAGAAAGACTGGAACAGCTATTTCTACTGATTTTTCCTCGAGAAGACCTTGACATGATT TTGAAAATGGATTCTTTACAGGATATAAAAGCATTGTTAACAGGATTATTTGTACAAGAT AATGTGAATAAAGATGCCGTCACAGATAGATTGGCTTCAGTGGAGACTGATATGCCTCTA ACATTGAGACAGCATAGAATAAGTGCGACATCATCATCGGAAGAGAGTAGTAACAAAGGT CAAAGACAGTTGACTGTATCGATTGACTCGGCAGCTCATCATGATAACTCCACAATTCCG TTGGATTTTATGCCCAGGGATGCTCTTCATGGATTTGATTGGTCTGAAGAGGATGACATG TCGGATGGCTTGCCCTTCCTGAAAACGGACCCCAACAATAATGGGTTCTTTGGCGACGGT TCTCTCTTATGTATTCTTCGATCTATTGGCTTTAAACCGGAAAATTACACGAACTCTAAC GTTAACAGGCTCCCGACCATGATTACGGATAGATACACGTTGGCTTCTAGATCCACAACA TCCCGTTTACTTCAAAGTTATCTCAATAATTTTCACCCCTACTGCCCTATCGTGCACTCA CCGACGCTAATGATGTTGTATAATAACCAGATTGAAATCGCGTCGAAGGATCAATGGCAA ATCCTTTTTAACTGCATATTAGCCATTGGAGCCTGGTGTATAGAGGGGGAATCTACTGAT ATAGATGTTTTTTACTATCAAAATGCTAAATCTCATTTGACGAGCAAGGTCTTCGAGTCAGenes Encode for ProteinsMKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESR LERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGLFVQDNVNKDAVTDRLASVETDMPL TLRQHRISATSSSEESSNKGQRQLTVSIDSAAHHDNSTIPLDFMPRDALHGFDWSEEDDM SDGLPFLKTDPNNNGFFGDGSLLCILRSIGFKPENYTNSNVNRLPTMITDRYTLASRSTT SRLLQSYLNNFHPYCPIVHSPTLMMLYNNQIEIASKDQWQILFNCILAIGAWCIEGESTD IDVFYYQNAKSHLTSKVFESGSIILVTALHLLSRYTQWRQKTNTSYNFHSFSIRMAISLG LNRDLPSSFSDSSILEQRRRIWWSVYSWEIQLSLLYGRSIQLSQNTISFPSSVDDVQRTT TGPTIYHGIIETARLLQVFTKIYELDKTVTAEKSPICAKKCLMICNEIEEVSRQAPKFLQ MDISTTALTNLLKEHPWLSFTRFELKWKQLSLIIYVLRDFFTNFTQKKSQLEQDQNDHQS YEVKRCSIMLSDAAQRTVMSVSSYMDNHNVTPYFAWNCSYYLFNAVLVPIKTLLSNSKSN AENNETAQLLQQINTVLMLLKKLATFKIQTCEKYIQVLEEVCAPFLLSQCAIPLPHISYN NSNGSAIKNIVGSATIAQYPTLPEENVNNISVKYVSPGSVGPSPVPLKSGASFSDLVKLL SNRPPSRNSPVTIPRSTPSHRSVTPFLGQQQQLQSLVPLTPSALFGGANFNQSGNIADSS Example of a Gene: Gal4 AANumber of Genes in Public DatabasesStructure of Genes in Mammalian Cells• Within coding DNA genes there can be un-translated regions (Introns) • Exons are segments of DNA that contain the gene’s information coding for a protein• Need to cut Introns out of RNA and splice together Exons before protein can be made • Alternative splicing increases the potential number of different proteins, allowing the generation of millions of proteins from a small number of genes.Identifying Genes in Sequence Data• Predicting the start and end of genes as well as the introns and exons in each gene is one of the basic problems in computational biology.• Gene prediction methods look for ORFs (Open Reading Frame).• These are (relatively long) DNA segments that start with the start codon, end with one of the end codons, and do not contain any other end codon in between.• Splice site prediction has received a lot of attention in the literature.Comparative genomicsRegulatory RegionsPromoterThe promoter is the place where RNA polymerase binds to start transcription. This is what determines which strand is the coding strand.DNA Binding Motifs• In order to recruit the transcriptional machinery, a transcription factor (TF) needs to bind the DNA in front of the gene. • TFs bind in to short segments which are known as DNA binding motifs.• Usually consists 6 – 8 letters, and in many cases these letters generate palindromes.Example of MotifsMessenger RNAs (mRNAs)RNAFour major types (one recently discovered regulatory RNA).• mRNA – messenger RNA• tRNA – Transfer RNA• rRNA – ribosomal RNA• RNAi, microRNA – RNA interferenceMessenger RNA• Basically, an intermediate product• Transcribed from the genome and translated into protein• Number of copies correlates well with number of proteins for the gene.• Unlike DNA, the amount of messenger RNA (as well as the number of proteins) differs between different cell types and under different conditions.Complementary base-pairingmRNAlabelhybridizationAUGCUACG• mRNA is transcribed from the DNA • mRNA (like DNA, but unlike proteins) binds to its complementActivatorsGeneRNAPIITFIIHTranscription apparatusmRNAHybridization and Scanning—Glass slide arrays- Prepare Cy3,