1. 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 2013 c.vangelder@cmbi.ru.nl

2. Exponential Growth in Genomic Sequence Data # of genomes Currently 1000+ completed genomes First 2 bacterial genomes complete First eukaryote complete (yeast) First metazoan complete (flatworm)

3. ©CMBI 2013 Genome projects http://www.genomesonline.org/

4. The pig genome

5. 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 20000 protein-coding genes ( average gene length 3000 bases, but largest known gene is 2.4 Mb (dystrophin)) Human genome is 99.9% identical among individuals This means that every 2 persons differ in 3 million nts!!

6. 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

7. The human genome cntnd From: Molecular Biology of the Cell (4 th edition) (Alberts et al., 2002) 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

8. Chromosome organisation (1) Genes that are OFF Genes that are ON

9. Chromosome organisation From: Lodish (4 th edition) DNA packed in chromatin Non-active genes often in densely packed chromatin (30-nm fiber) Active genes in less dense chromatin (beads-on-a-string) Gene regulation by changing chromatin density, methylation/acetylation of the histones Genes that are OFF Genes that are ON

10. Introduction to genomes & genome browsers Content  Introduction  The human genome  Human genetic variation CNVs SNPs Alternative splicing  Browsing the human genome

11. 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

12. Variations in the Genome Common Sequence Variations Polymorphism Deletions Translocations Insertions Chromosome

13. Today’s focus 1.Single Nucleotide Polymorphisms (SNPs) 2.Copy number variations (CNV) 3.Alternative transcripts

14. 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 make up about 90% of all human genetic variation and occur every 100 to 300 bases. SNPs can occur in coding (gene) and non coding regions of the genome; <1% alter the protein sequence

15. SNPs determine properties like eye color, hair (curly or straight), or if you can taste bitter or not. are used for identification and forensics are used for estimating predisposition to disease can cause drug side–effects and/or non responsiveness for the drug have impact on how humans respond to environmental factors like bacteria, viruses, toxins and chemicals are used to predict specific genetic traits are used for classifying patients in clinical trials are used for mapping and genome-wide association studies of complex diseases

16. SNP - Bitter tasting, TAS2R38

17. SNP & disease, Alzheimer Alzheimer's disease (AD) & apolipoprotein E (APOE) Apolipoprotein E is a cholesterol carrier that is found in the brain and other organs. APOE is suspected to be involved in amyloid beta aggregation and clearance, influencing the onset of amyloid beta deposition. APOE contains 2 SNPs that result in 3 possible alleles: E2, E3, E4. Variant rs429358 rs7412 E2 T + T E3T + C E4C + C A person who inherits at least one E4 allele will have a greater chance of developing AD.

18. Today’s focus 1.Single Nucleotide Polymorphisms (SNPs) 2.Copy number variations (CNV) 3.Alternative transcripts

19. Copy Number Variation Copy Number Variations (CNVs): gains and losses of large chunks of DNA sequence (10kB – 5Mb) 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

20. Copy Number Variation Normal cell deletion amplification CN=0 CN=1 CN=3 CN=4 CN=2

21. CNVs and their possible effects on gene expression. Cabianca D S, Gabellini D J Cell Biol 2010;191:1049-1060 © 2010 Cabianca and Gabellini

22. 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

23. Today’s focus 1.Copy number variations (CNV) 2.Single Nucleotide Polymorphisms (SNPs) 3.Alternative transcripts

24. Alternative splicing

25. Defects in 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 – Parkinsons Disease

26. Introduction to genomes & genome browsers Content  Introduction  The human genome  Human genetic variation CNVs SNPs Alternative splicing  Browsing the human genome

27. Annotating the genome Annotation: attaching biological information to sequences. Two main steps: identifying elements on the genome attaching biological information to these elements.

28. Basic & Advanced Genome Annotation Basic: – Genomic location – Gene features: Exons, Introns, UTRs – Transcript(s) – Pseudogenes, Non-coding RNA – Protein(s) – Links to other sources of information Advanced – Cytogenetic bands – Polymorphic markers – Genetic variation, including SNPs & CNVs – Repetitive sequences – cDNAs or mRNAs from related species – Genomic sequence variation – Regulation sequences (enhancers, silencers, insulators)

29. [Human] Genome Browsers EBI Ensembl NCBI Map Viewer UCSC Genome Browser Not limited to only human data

30. Ensembl ©EMBL-EBI

31. Other Ensembl Installations ©EMBL-EBI

32. genes & predictions variations & repeats cross-species comparative data & many more types of data from expression & regulation to mRNA and ESTs… Gene X Description Transcript data Structure Gene Ontology Pathway Data Homologous Genes Expression Data Etc…. Organized Data Based on Chromosome Location tracks

34. HGNC – a unique name and symbol for every gene in human http://www.genenames.org/ ENSG### Ensembl Gene ID ENST### Ensembl Transcript ID ENSP### Ensembl Peptide ID ENSE### Ensembl Exon ID

35. Ensembl: An Example Click for more details tracks

36. Direction of transcription Above blue line: forward strand Below blue line: reverse strand

37. Ensembl Transcripts ©EMBL-EBI

40. 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