Download The human genome

Introduction to genomes & genome browsers
Content
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The human genome
Human genetic variation
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SNPs
CNVs
Alternative splicing
Browsing the human genome
Celia van Gelder
CMBI
UMC Radboud
June 2010
[email protected]
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
• 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
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)
From: Lodish (4th edition)
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


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
– blue vs. brown eyes
– genetic diseases such as cystic fibrosis or Huntington’s disease are
caused by dysfunctional alleles
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.
TA
AT
CG
G
TA
GC
TA
TA
AT
C G
(SNP)
G
TA
AGTC
TA
CG
AT
CG
AT
GC
T A
GC
T A
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, example
Alzheimer's disease & apolipoprotein E
• ApoE contains two SNPs that result in three possible alleles for this
gene: E2, E3, and E4.
• Each allele differs by one DNA base, and the protein product of
each gene differs by one amino acid.
• Each individual inherits one maternal copy of ApoE and one
paternal copy of ApoE.
• Research has shown that a person who inherits at least one E4
allele will have a greater chance of developing Alzheimer's disease.
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):
duplications and deletions of pieces of chromosome
• When there are genes in the CNV areas, this can lead to variations
in the number of gene copies between individuals
• 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
• CNVs are common in cancer and other diseases.
• CNVs are also common in normal individuals and contribute to our
uniqueness. These changes can also influence the susceptibility to
disease.
• Since CNVs often encompass genes, they can have important roles
both in characterizing human disease and discovering drug
response targets.
CNV & disease, examples
CNVs have been implicated in
• Gene copy number can be elevated in cancer cells
• Autism
• Schizophrenia (dept. human genetics)
• Mental retardation (dept. human genetics)
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
Introduction to genomes & genome browsers
Content


The human genome
Human genetic variation




CNVs
SNPs
Alternative splicing
Browsing the human genome
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)
Annotating the genome
• Genome annotation is the process of attaching biological
information to sequences.
It consists of two main steps:
1.
identifying elements on the genome, a process called Gene Finding,
and
2.
attaching biological information to these elements.
• Automatic annotation tools try to perform all this by computer
analysis, as opposed to manual annotation which involves human
expertise. Ideally, these approaches co-exist and complement each
other in the same annotation pipeline.
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)
34
↔
Ensembl Homepage
35
Ensembl and VEGA/Havana
• Automatic annotation pipeline:
Gene building all at once (whole genome)
Ensembl
• Manual curation:
case-by-case basis
VEGA/Havana: Vertebrate Genome Annotation
• Merged: (gold) Havana/Ensembl
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
41
tracks
tracks
Ensembl: An Example
Click for
more
details
Gene Structure in Ensembl
Synopsis- What can I do with Ensembl?
•
View genes along with other annotation along the chromosome
•
View alternative transcripts (including splice variants) for a gene
•
Explore homologues and phylogenetic trees across more than 40 species for any
gene
•
Compare whole genome alignments and conserved regions across species
•
View microarray sequences that match to Ensembl genes
•
View ESTs, clones, mRNA and proteins for any chromosomal region
•
Examine single nucleotide polymorphisms (SNPs) for a gene or chromosomal region
•
View SNPs across strains (rat, mouse), populations (human), or even breeds (dog)
•
View positions and sequence of mRNA and protein that align with an Ensembl gene
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©CMBI 2009
Alternative Transcripts
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BLAST/BLAT
BioMart
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