Genome Browsers

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

http://www.ensembl.org/http://genome.ucsc.edu/

• 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 22000 protein-coding genes– compare with ~14000 for fruitfly en ~19000 for

Nematode C. elegans

Human Genome

Human genome

Bron: Molecular Biology of the Cell (4th 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 (4th 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 browsersUCSC

NCBI

Ensembl

http://www.ensembl.org/

http://genome.ucsc.edu/

Genome Browsing

With the UCSC Genome Browser

http://genome.ucsc.edu/

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 browsersUCSC

Ensembl

http://www.ensembl.org/

http://genome.ucsc.edu/

Genome Browsing

With the Ensembl Genome browser

http://www.ensembl.org/

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 (http://www.wikipedia.org/)

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 !!