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Introduction to genomes & genome browsers Content Introduction The human genome Human genetic variation SNPs CNVs Alternative splicing Browsing the human genome Celia van Gelder CMBI UMC Radboud December 2011 [email protected] Exponential Growth in Genomic Sequence Data # of genomes First 2 bacterial genomes complete Currently 1000+ completed genomes First eukaryote complete (yeast) First metazoan complete (flatworm) Exponential Growth in Genomic Sequence Data © Pevzner 2011 The cow genome Houston Chronicle Houston scientists milk cow genome for its secrets Weekly Times Now Bovine genome to revolutionise food production National Geographic Cow Genome Decoded -- Cheaper Beef for Everybody? BBC News Cow genome 'to transform farming The human genome • Genome: the entire sequence of DNA in a cell • 3 billion basepairs (3Gb) • 22 chromosome pairs + X en Y chromosomes • Chromosome length varies from ~50Mb to ~250Mb • About 22000 protein-coding genes • Human genome is 99.9% identical among individuals Eukaryotic Genomes: more than collections of genes • Genes & regulatory sequences make up 5% of the genome Protein coding genes RNA genes (rRNA, snRNA, snoRNA, miRNA, tRNA) Structural DNA (centromeres, telomeres) Regulation-related sequences (promoters, enhancers, silencers, insulators) – Parasite sequences (transposons) – Pseudogenes (non-functional gene-like sequences) – Simple sequence repeats – – – – The human genome cntnd • Only 1.2% codes for proteins • Long introns, short exons • Large spaces between genes • More than half consists of repetitive DNA Alu repeat ~300 bp > million copies From: Molecular Biology of the Cell (4th edition) (Alberts et al., 2002) Variation along genome sequence • Nucleotide usage varies along chromosomes – Protein coding regions tend to have high GC levels • Genes are not equally distributed across the chromosomes – Housekeeping generally in genedense areas – Gene-poor areas tend to have many tissue specific genes From: Ensembl Chromosome organisation (1) Genes that are ON Genes that are OFF Chromosome organisation (2) • DNA packed in chromatin Genes that are OFF • Non-active genes often in densely packed chromatin (30-nm fiber) Genes that are ON • Active genes in less dense chromatin (beads-on-a-string) • Gene regulation by changing chromatin density, methylation/acetylation of the histones From: Lodish (4th edition) Introduction to genomes & genome browsers Content Introduction The human genome Human genetic variation CNVs SNPs Alternative splicing Browsing the human genome Human Genetic Variation • Every human has essentially the same set of genes, but there are different forms of each gene -- known as alleles • Genetic variation explains some of the differences among people, such as: – Blood group – Eye color – Skin color – Hair color – Higher or lower risk for getting particular diseases • • • • • Cystic fibrosis, Sickle cell disease, Diabetes, Cancer, Arthritis, Asthma Stroke, Heart disease Alzheimer's disease, Parkinson's disease Depression, Alcoholism Variations in the Genome Common Sequence Variations Polymorphism Deletions Insertions Chromosome Translocations Today’s focus 1. Single Nucleotide Polymorphisms (SNPs) 2. Copy number variations (CNV) 3. Alternative transcripts Single Nucleotide Polymorphisms (SNPs) • SNPs are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered. • For a variation to be considered a SNP, it must occur in at least 1% of the population. • SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome. SNPs & medicine • Although more than 99% of human DNA sequences are the same, variations in DNA sequence can have a major impact on how humans respond to: – disease; – environmental factors such as bacteria, viruses, toxins, and chemicals; – and drugs (& side-effects). • This makes SNPs valuable for biomedical research and for developing pharmaceutical products or medical diagnostics. SNP & disease, Alzheimer Alzheimer's disease (AD) & apolipoprotein E • • • The APOE gene encodes the protein apolipoprotein E, a cholesterol carrier that is found in the brain and other organs. Its exact role in the development of AD is unclear. Several studies have indicated a role in amyloid beta aggregation and clearance, influencing the onset of amyloid beta deposition. SNP & disease, Alzheimer (2) Two SNPs - three APOE variants • APOE contains 2 SNPs that result in 3 possible alleles: E2, E3, E4. • Variant E2 E3 E4 • rs429358 T T C + + + rs7412 T C C A person who inherits at least one E4 allele will have a greater chance of developing AD. Today’s focus 1. Single Nucleotide Polymorphisms (SNPs) 2. Copy number variations (CNV) 3. Alternative transcripts Copy Number Variation • People do not only vary at the nucleotide level (SNPs) • Copy Number Variations (CNVs): gains and losses of large chunks of DNA sequence consisting of between ten thousand and five million letters • When there are genes in the CNV areas, this can lead to variations in the number of gene copies between individuals • CNVs contribute to our uniqueness. CNVs can also influence the susceptibility to disease. • CNVs may either be inherited or caused by de novo mutation Copy Number Variation Normal cell CN=2 deletion CN=0 amplification CN=1 CN=3 CN=4 CNVs and their possible effects on gene expression. Cabianca D S , Gabellini D J Cell Biol 2010;191:1049-1060 © 2010 Cabianca and Gabellini CNVs & disease • Many inherited genetic diseases result from CNVs; – – – – – Gene copy number can be elevated in cancer cells Autism Schizophrenia (dept. human genetics) Mental retardation (dept. human genetics) Parkinsons disease • There are CNVs that protect against HIV infection and malaria. • The contribution of CNV to the common, complex diseases, such as diabetes and heart disease, is currently less well understood Today’s focus 1. Copy number variations (CNV) 2. Single Nucleotide Polymorphisms (SNPs) 3. Alternative transcripts Alternative splicing Alternative splicing • Defects of the machinery of alternative splicing have been implicated in many diseases, including: – neuropathological conditions such as Alzheimer disease – cystic fibrosis, those involving growth and developmental defects – many human cancers, e.g. BRCA1 in breast cancer – Beta-globin in Beta-thalassemia Introduction to genomes & genome browsers Content Introduction The human genome Human genetic variation CNVs SNPs Alternative splicing Browsing the human genome Annotating the genome • A genome sequence is of limited use without functional annotation. • Genome annotation is the process of attaching biological information to sequences. It consists of two main steps: • identifying elements on the genome • attaching biological information to these elements. • Annotating the genome – Bioinformatics! • The genome browser is a tool for visualizing genome annotation. why present the whole genome? • Browsers provide context to understand genomic regions of interest • See features in and around a specific gene • Explore larger chromosome regions • Search & retrieve information on a gene- and genomescale • Investigate genome organization • Compare genomes Basic Genome Annotation • Genomic location • Gene features • • • Exons Introns UTRs • Transcript(s) • • Pseudogenes Non-coding RNA • Protein(s) • Links to other sources of information Advanced Genome Annotation • • • • • • • • Cytogenetic bands Polymorphic markers Genetic variation Repetitive sequences Expressed Sequence Tags (ESTs) cDNAs or mRNAs from related species Regions of sequence homology Genomic sequence variation Possible research questions P. Schattner, Genomics 93 (2009):187-195 [Human] Genome Browsers Not limited to only human data EBI Ensembl NCBI Map Viewer UCSC Genome Browser Other Ensembl Installations http://www.ensemblgenomes.org/ Organized Data Based on Chromosome Location Gene X tracks genes & predictions variations & repeats cross-species comparative data & many more types of data from expression & regulation to mRNA and ESTs… Description Transcript data Structure Gene Ontology Pathway Data Homologous Genes Expression Data Etc…. Ensembl Genes – biological basis • All Ensembl transcripts are based on proteins and mRNAs in: – UniProt/Swiss-Prot (manually curated) – UniProt/TrEMBL – NCBI RefSeq (manually curated) 36 ↔ Ensembl Homepage 37 HGNC • HGNC – a unique name and symbol for every gene in human http://www.genenames.org/ Names in Ensembl • • • • • ENSG### Ensembl Gene ID ENST### Ensembl Transcript ID ENSP### Ensembl Peptide ID ENSE### Ensembl Exon ID For other species than human a suffix is added: – MUS (Mus musculus) for mouse: ENSMUSG### – DAR (Danio rerio) for zebrafish: ENSDARG###, etc. Tabs in Ensembl • Location Tab • Transcript Tab • Gene summary Tab 42 tracks tracks Ensembl: An Example Click for more details Gene Structure in Ensembl Synopsis- What can I do with Ensembl? • View, examine & explore annotated information for any chromosomal region: – Genes, – ESTs, mRNAs, alternative transcripts – Proteins – SNPs, and SNPs across strains (rat, mouse), populations (human), or even breeds (dog) – homologues and phylogenetic trees across more than 40 species – whole genome alignments – conserved regions across species – gene expression profiles • Upload your own data and use BLAST/BLATagainst any Ensembl genome • Export sequence, or create a table of gene information • Extra slides follow now 53/37 ©CMBI 2009 Chromosome organisation (1) From: Lodish (4th edition) titel Alternative Transcripts Ensembl: Many Additional Tools best scoring match BLAST/BLAT BioMart data retrieval and download Copyright OpenHelix. 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