Functional Genomics Research Stream State of the Union... Research Meeting: February 16, 2010 Functional Genomics & Research Report III Concepts Genomics Molecular Biology Computational Biology
Genome Genome Simplest Definition: Complete set of all genes contained on a single (haploid) set of chromosomes. Secondary Definition: The canonical DNA sequence across contained on a single (haploid) set of chromosomes. Genome Viewer (SGD) SGD = Saccharomyces Genome Database Genome Viewer (SGD) SGD = Saccharomyces Genome Database Image: SGD Genome Browser Image: SGD Genome Browser > Chr 3 from 100843 to 121674 CTATGTTTTGCCTCAGAGTAGCACAAAGCATGAGAAAGAGGGGTTCCTTCGAAAGAAACA AAAAGACGAGCCCATTTGGGTTTCCCCTAGCAAAATTGACTTTGCTGATCTAAGTAGGAG AACTAAAGCATTGACGCCAGAGCGTAATACTGTTCCTTTGAAAAACAACGACAGTAGAAA ATACAAATATACTGGAGAGGGATCTATCGGTAATATGACAAATATGCTGTTAACTAAAGA TGCTTCGTACGCGTACTTAAAAGATTTTGTTGCGTTGAGTGACGATGAAGATGAAGATGG GAAACAGAACTGCGCTGTTGGTGGCCCAGAGAAACTGAAATTTTATTGAGTGTTTTATTG ATTTTTTTTTTCTTTTTAATTTAATGCAATGTATACATTTACATAAAATATGGACAAATA AGAAAAAGGGGGAAAAACCTCCCACTTAAGTAAAACTGAATATATTAGATACCTTTACCT ACTATCAAAGGTGAATGCTTTTGGATCAATAGGGGTTCCATCGGGGGCAATACCATTTTG GCCGAACTTTCTTTCCATATATAATAGTCTAGCCTTATCGAAATCTACATTATCGTTTTC CATAATTTGTTTAATCTCATTCTTGGAGACATCATCCAAACCACCTCTTACGTCGTTGCT ATTCTCCGAGATAATATCGAAATTCCTGGAATGGAGACCGTTTTCTAGGTCATCAGCAAA GGAATCATTTAAACGTATATGTCTATTAAAACGTAATTGTATTCTTGAACGCAGTGCACG AAATTTGTCGGCTATTACAGCTGTTAGTAATTTGATACGGTTTGCACTTTGCATTTTCAA ATGCTTAAATATACATACCAACTTTGGTTTTCCGGTGTGCCATAAGAAGGCATAAAGACA ATAGCACAACCCAGAGGAGCAATTTGAGATAGAACAAACTCTTCATACTCGTATTTGCAA TTTTTGGAAATTAATTGTGTAGCTTTTCTTCTCTTAATTGGTGGCAGTTTTTATATATTC AGTTTAGAATACCCTTTTTTTTTTTTTTTTTTTCTTCGCTTTTCGCATCTCATCGCTGGA AGTGGTGCTCTTTTACAGGGATTAAATAAGGTTATTCTTTTTGGTCAAAATGATAAATAT AACTATTAAAGTTATTTATAACCCGCCCGCTTCCTTATTATTTATACGTTATCATAAAGT ACACAGGTCATGGTTCGGTTGGTGCTTAGGAATTAATCACGTCTAGCATAAGAGATCTGT AAACTACAACCACCATAATTATAATTATTTAATTTTTGAATACAAAAATCTGCATCTACT AAATTTTCATATTCTACAACAGCAACACCAGTTGGTTGACCATTTTCCTGTGGTTTCAAT TCCGCGTTATTGATTTTGCCGATAGGCCCAAACAAGTCGAATAAATCGCTTCTTGCTGTT GAGAATGGTAAATTACTACAATAAATGAAACAGTTTCTATCCCCTCCTGGATTGACACCT TCAGTAAATTTTGCTGCAGTTTC...
Genomics A Definition: The study of many possible DNA sequence properties in a specific genome or across related genomes. Evolutionary relationship of conserved regions DNA sequence (coding sequence) DNA sequence motifs (regulation) DNA nucleotide frequencies... many more... Functional Genomics? Image: UCSC Genome Browser Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects) to describe gene (and protein) functions and interactions. Unlike genomics and proteomics, functional genomics focuses on the dynamic aspects such as gene, translation, and protein-protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and protein products. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional gene-by-gene approach. Wikipedia Transcription Factors Protein that binds specific DNA sequences controlling the activation or repression of. cis-regulatory sequence start stop
Transcription Factors Protein that binds specific DNA sequences controlling the activation or repression of. Transcription Factors Protein that binds specific DNA sequences controlling the activation or repression of. TF start stop TF start stop cis-regulatory sequence cis-regulatory sequence mrna produced AAAAAAAAAAAA One Gene Whole Genome (Saccharomyces cerevisiae has 16 chromosomes + mitochondrial DNA) 1000 200K TF start stop cis-regulatory sequence mrna produced AAAAAAAAAAAA TF start stop cis-regulatory sequence AAAAAAAAAAAA mrna produced
Whole Genome (Saccharomyces cerevisiae has 16 chromosomes + mitochondrial DNA) 1000 200,000 Whole Genome (Saccharomyces cerevisiae has 16 chromosomes + mitochondrial DNA) 1000 200,000 I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI M I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI M Simon et al. Serial regulation of al regulators in the yeast cell cycle. Cell (2001) vol. 106 (6) pp. 697-708 cellular nucleus: many regulatory processes
Future Lecture... Next-generation highthroughput sequencing methods and technologies by ABI SOLiD. High resolution measurement of gene expression and protein to DNA interactions. Bioinformatics aka Computational Biology Many Disciplines Encompassed: mathematics, statistics algorithmic, technique data mining, machine learning databases, information storage & retrieval solving biological problems Images: Dell, IBM Corporations High Resolution Imagery Data Modeling (networks, traversals) Data Analysis & Visualization Low Resolution High Resolution
Recommended Reading Yeast Background Spellman et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell (1998) vol. 9 (12) pp. 3273-97 Simon et al. Serial regulation of al regulators in the yeast cell cycle. Cell (2001) vol. 106 (6) pp. 697-708 Gasch et al. The genomics of yeast responses to environmental stress and starvation. Funct Integr Genomics (2002) vol. 2 (4-5) pp. 181-92 Research Progress Report III Harbison et al. Transcriptional regulatory code of a eukaryotic genome. Nature (2004) vol. 431 (7004) pp. 99-104 Hu et al. Genetic reconstruction of a functional al regulatory network. Nat. Genet. (2007) pp. RPR III Corrections constantly updated post on Results Central
III.A Reagent Production III.B Buffers & ph III.C Controlled Cellular Growth & Sample III.D Nucleic Acid Preparation... future lecture...
III.E Nucleic Acid Quantity & Quality Evaluation... future lecture... III.F Gel Electrophoresis... future lecture... III.G Polymerase Chain Reaction (PCR) III.H Results Central Progress Reports... future lecture...
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