Genome Browsers UCSC (Santa Cruz, California) and Ensembl (EBI, UK)

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 Eukaryotic Genomes: Not only collections of genes

Blue: Prokaryotes Black: Unicellular eukaryotes Other colors: Multicellular eukaryotes (red = vertebrates) Eukaryotic Genomes: High fraction non-coding DNA Bron: Mattick, NRG, 2004

3 billion basepairs (3Gb) 22 chromosome pairs + X en Y chromosomes Chromosome length varies from ~50Mb to ~250Mb About protein-coding genes –compare with ~14000 for fruitfly en ~19000 for Nematode C. elegans Human Genome

Human genome Bron: Molecular Biology of the Cell (4 th edition) (Alberts et al., 2002) Only 1.2% codes for proteins, 3.5-5% is under selection Long introns, short exons Large spaces between genes More than half exists of repetitive DNA

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 gene-dense areas –Gene-poor areas tend to have many tissue specific genes Bron: Ensembl

Chromosome organisation Bron: Lodish (4 th edition) DNA packed in chromatin Active genes in less dense chromatin (beads-on-a-string) Non-active genes often in densely packed chromatine (30-nm fiber) Gene regulation by changing chromatin density, methylation/acetylation of the histones Limited availability of chromatin information in genome browsers (post transcriptional modifications are currently under investigation with ChIP-on- chip experiments

Genome browsers UCSC NCBI Ensembl

Genome Browsing With the UCSC Genome Browser

UCSC Genome browser

Choose a species, an assembly and a gene

Gene search results

Genome browser

Genomic Datatypes (Tracks)

Transcription data rather complicated

Browser → Gene record

Gene record

Gene record (2)

Gene record (3)

Gene record (4) “best hit”

Gene record (5)

Genomic elements Genome browsers can be used to examine other things –Genomic sequence conservation –Pseudogenes –Duplications en deletions of pieces chromosome (Copy Number Variations, CNVs)

Genomic Sequence Conservation Not only protein coding parts are conserved in evolution Conserved non-coding genomic sequences can be involved in gene regulation (enhancers, silencers, insulators) With the UCSC browser one can examine genomic conservation

Genomic Conservation (UCSC)

Pseudogenes Pseudogenes “look” like (are homologous to) protein- coding genes, but are non-functional Two types: –Unprocessed pseudogenes (loss of function) –Processed pseudogenes (mRNAs that are retrotranscribed onto the genome  they miss introns and sometimes have a polyA) The UCSC contains various databases of pseudogenes: –Yale pseudogenes (both types pseudogenes) –Vega pseudogenes (both types pseudogenes) –Retroposed genes (only processed pseudogenes)

Pseudogenes (UCSC)

Copy Number Variation People do not only vary at the nucleotide level (SNPs); short pieces genome can be present in varying number of copies (Copy Number Polymorphisms (CNPs) or Copy Number Variants (CNVs) When there are genes in the CNV areas, this can lead to variations in the number of gene copies between individuals With the UCSC browser CNVs can be examined

Copy Number Variation (UCSC)

Finding a sequence in the genome

BLAT – Search page

BLAT - Results

BLAT – “Details”

BLAT – “Browser”

Genome browsers UCSC Ensembl

Genome Browsing With the Ensembl Genome browser

Ensembl Genome browser

Het Human Genome

MapView – Overview chromosome

ContigView – Zooming in (compare UCSD)

ContigView (2)

GeneView – Gene record

TransView - mRNA Transcript

TransView - mRNA Transcript (2)

Alternative Transcripts Bron: Wikipedia (

GeneView - Show Alternative Transcripts

GeneSpliceView - Alternative Transcripts

Single Nucleotide Polymorphisms (SNPs) Sequence variations within a species Similar to mutations, but are simultaneously present in the population, and generaly have little effect Are being used as genetic markers (a genetic disease is e.g. associated with a SNP) ENSEMBL offers a nice SNP view

GeneView - Show SNPs

GeneSNPView - SNPs

GeneView - Show Protein

ProtView - Protein

ProtView - Protein Sequence

ProtView – Search proteins with the same domains

DomainView – Proteins with a certain domain (Interpro = SMART + PFAM + others)

ProtView - Find Proteins In the Same Protein Family

FamilyView – Alignments of homologous proteins

Finding Human Genes

Finding a human gene (2)

Blast

Blast (2)

UCSC vs Ensembl: Which is better ? They more or less contain the same information UCSC is a bit easier in use Ensembl gives more detailed information and more flexible data export Other small differences in data (e.g. UCSC has more extensive genomic conservation data) Whatever your are familiar with !!