Translational Genomics - Summary
Lecture 1 Genome Architecture
The human cell consists of DNA in the nucleus and in the mitochondria. The nucleus has 22 pairs of
autosomes, 2 sex chromosomes (XX or XY). In total 23 chromosomes and it contains ~20.000 protein
coding genes and ~25.000 non-coding genes.
DNA base pairs Adenine -Thymine have 2 hydrogen bonds in between while Guanine – Cystine has
3 hydrogen bonds. This means that GC base pairs are attached much stronger. This can lead to
problems during DNA sequencing. Here, primers will attach stronger to GC sites in the sequence and
will not detach easily.
Components of the human genome
o SINEs
o LINEs
o Protein coding genes (1.5%)
o Introns
o Miscellaneous unique sequences
o Miscellaneous heterochromatin
o Segmental duplications
o Simple sequence repeats
o DNA transposons
o LTR retrotransposons
Functional DNA
1) Protein coding
Genes consists of:
Promoter, 5’ UTR (untranslated region), introns, exons (coding
sequence ORF), 3’ UTR
The promoter is a redundant sequence
The introns are spliced out
Intergenic: region between two genes
2) Non-coding genes
Long non coding RNAs (LncdRNAs)
Small non coding RNAs (siRNAs, miRNAs, piRNAs)
Deregulation of non-coding genes can lead to multiple diseases
Small ncRNA: mechanism of action
dsRNA or short hairpin RNA undergoes a dicer dependent processing,
resulting in siRNA fragments. piRNA precursors (ssRNA) undergo a dicer
independent processing. These fragments are then single stranded and bind to
Argonaut proteins (AGO) which is part of RISC (RNA-induced silencing
complex) in the cytoplasm. This siRNA/RISC complex goes to the
complementary RNA fragment and then degrade that mRNA. So you
have specific gene silencing.
These siRNA/RIS complexes:
o Inhibit translation initiation
o mRNA deadenylation (The poly A tail, this is namely taken up by the RISC
complex degradation)
, o Inhibition of translation elongation.
Example= Feingold syndrome 2: miR-17~92 deletion
Long non-coding RNA (lncdRNAs)
There are 3 types:
o intronic (between the protein coding regions, exons)
o intergenic (between genes)
o Natural antisense transcript (NAT)
LncRNAs can bind proteins, DNA, or RNA . it can bring proteins to other
genes etc., so it then functions as a scaffold.
NATs – Natural antisense transcript
Transcriptional interference: It hampers the transcription of the
complementary gene.
RNA masking: expression of antisense transcripts can dictate the way in
which the sense transcript is differentially spliced.
Double-stranded RNA (dsRNA)-dependent mechanisms
3) Regulatory
elements
Contain distal
regulatory elements
and a promoter
sequence (proximal
promoter elements
and core promoter).
Regulatory elements
can be anywhere in the gene.
Core promoter: first 1 kb where gene expression starts
Enhancer: increases expression
Silencer: decreases expression
Insulator: long-range regulatory element and contain protein
binding sites and mediate chromosomal interactions and
it can work as a enhancer or barrier. It protects a gene from
the regulatory effects of neighbouring genes.
TATA box: is where the transcription initiates, where the
transcription factor binds to.
Junk DNA
Transposable elements (TEs)
o ~45% of the human genome
o <0.05% active
o Most abundant: Alu elements (10% of the human genome)
TE classes
o Class I (42% of human genome)
Retrotransposons
- LINEs – L1/L2/L3 (21%)
- SINEs – Alu/tRNA (13%)
- LTR (8%)
o Class II (3% human genome)
, DNA transposons
De novo: mutations happen just after fertilization, your parents do not have these. Each individual
has ~80 de novo mutations.
Genomic imprinting
People inherit two copies of their genes—one from their mother and one from their father. Usually
both copies of each gene are active, or “turned on,” in cells. In some cases, however, only one of the
two copies is normally turned on. Which copy is active depends on the parent of origin: some genes
are normally active only when they are inherited from a person’s father; others are active only when
inherited from a person’s mother.
Q: What is the most extreme example of the effect of epigenetic modification on gene expression?
It's the X chromosome – X-inactivation
DNA methylation causes imprinting causes inactivation
Genomic imprinting is essential for normal development. However, deregulation results in complex
diseases.
The same deletion can cause two different diseases:
Angelman syndrome – Maternal deletion
o Intellectual disability
o Laugh a lot unexpectedly
o Ataxia (uncoordinated movement)
o No speech
o Epilepsy
o Typical face
o Friendly
Prader Willi syndrome – Paternal deletion
Neonatally
o Hypotonia
o Feeding problems
First decade of life
o Obesitas
o Small
, o Intellectual disability (mild)
o Hypogonadism
o Behavioural problem
Uniparental disomy (UPD) occurs when a person receives two copies of a chromosome, or part of a
chromosome, from one parent and no copies from the other parent. UPD can occur as a random event
during the formation of egg or sperm cells or may happen in early fetal development. Both
chromosomes of one cell/organism are derived from one parent.
Isodisomy: two identical chromosomes of one parent.
Heterodisomy: two different chromosomes of the same parent.
Lecture 2 Genome Variation: SNVs, CNVs, chromosomes
Genome variation
Variation: any deviation from the reference genome
Polymorphism: variation ≥1% of the alleles in a population
Mutation: variation <1% of the alleles in a population
Pathogenic: disease-causing mutation or polymorphism
CNV: deletion or duplication ≥1 kb
Rare variant: variant with a MAF <5%
Aneuploidy: abnormal chromosomal number e.g. trisomy
There are six different genomic variation in living individuals
o SNV - single nucleotide variant (base pair change)
o INDELS - insertion or deletion of < ~10 bp
o CNV – copy number variant deletion or duplication
bigger than 1kb
o Repeat expansion – 2 to >6000 base pairs
o Structural chromosomal abnormalities (translocations,
ring chromosomes, inversions)
o Aneuploidy (one chromosome extra)
SNV – Single nucleotide variation
o Substitution
- Synonymous: the amino acid is the name = silent
Lecture 1 Genome Architecture
The human cell consists of DNA in the nucleus and in the mitochondria. The nucleus has 22 pairs of
autosomes, 2 sex chromosomes (XX or XY). In total 23 chromosomes and it contains ~20.000 protein
coding genes and ~25.000 non-coding genes.
DNA base pairs Adenine -Thymine have 2 hydrogen bonds in between while Guanine – Cystine has
3 hydrogen bonds. This means that GC base pairs are attached much stronger. This can lead to
problems during DNA sequencing. Here, primers will attach stronger to GC sites in the sequence and
will not detach easily.
Components of the human genome
o SINEs
o LINEs
o Protein coding genes (1.5%)
o Introns
o Miscellaneous unique sequences
o Miscellaneous heterochromatin
o Segmental duplications
o Simple sequence repeats
o DNA transposons
o LTR retrotransposons
Functional DNA
1) Protein coding
Genes consists of:
Promoter, 5’ UTR (untranslated region), introns, exons (coding
sequence ORF), 3’ UTR
The promoter is a redundant sequence
The introns are spliced out
Intergenic: region between two genes
2) Non-coding genes
Long non coding RNAs (LncdRNAs)
Small non coding RNAs (siRNAs, miRNAs, piRNAs)
Deregulation of non-coding genes can lead to multiple diseases
Small ncRNA: mechanism of action
dsRNA or short hairpin RNA undergoes a dicer dependent processing,
resulting in siRNA fragments. piRNA precursors (ssRNA) undergo a dicer
independent processing. These fragments are then single stranded and bind to
Argonaut proteins (AGO) which is part of RISC (RNA-induced silencing
complex) in the cytoplasm. This siRNA/RISC complex goes to the
complementary RNA fragment and then degrade that mRNA. So you
have specific gene silencing.
These siRNA/RIS complexes:
o Inhibit translation initiation
o mRNA deadenylation (The poly A tail, this is namely taken up by the RISC
complex degradation)
, o Inhibition of translation elongation.
Example= Feingold syndrome 2: miR-17~92 deletion
Long non-coding RNA (lncdRNAs)
There are 3 types:
o intronic (between the protein coding regions, exons)
o intergenic (between genes)
o Natural antisense transcript (NAT)
LncRNAs can bind proteins, DNA, or RNA . it can bring proteins to other
genes etc., so it then functions as a scaffold.
NATs – Natural antisense transcript
Transcriptional interference: It hampers the transcription of the
complementary gene.
RNA masking: expression of antisense transcripts can dictate the way in
which the sense transcript is differentially spliced.
Double-stranded RNA (dsRNA)-dependent mechanisms
3) Regulatory
elements
Contain distal
regulatory elements
and a promoter
sequence (proximal
promoter elements
and core promoter).
Regulatory elements
can be anywhere in the gene.
Core promoter: first 1 kb where gene expression starts
Enhancer: increases expression
Silencer: decreases expression
Insulator: long-range regulatory element and contain protein
binding sites and mediate chromosomal interactions and
it can work as a enhancer or barrier. It protects a gene from
the regulatory effects of neighbouring genes.
TATA box: is where the transcription initiates, where the
transcription factor binds to.
Junk DNA
Transposable elements (TEs)
o ~45% of the human genome
o <0.05% active
o Most abundant: Alu elements (10% of the human genome)
TE classes
o Class I (42% of human genome)
Retrotransposons
- LINEs – L1/L2/L3 (21%)
- SINEs – Alu/tRNA (13%)
- LTR (8%)
o Class II (3% human genome)
, DNA transposons
De novo: mutations happen just after fertilization, your parents do not have these. Each individual
has ~80 de novo mutations.
Genomic imprinting
People inherit two copies of their genes—one from their mother and one from their father. Usually
both copies of each gene are active, or “turned on,” in cells. In some cases, however, only one of the
two copies is normally turned on. Which copy is active depends on the parent of origin: some genes
are normally active only when they are inherited from a person’s father; others are active only when
inherited from a person’s mother.
Q: What is the most extreme example of the effect of epigenetic modification on gene expression?
It's the X chromosome – X-inactivation
DNA methylation causes imprinting causes inactivation
Genomic imprinting is essential for normal development. However, deregulation results in complex
diseases.
The same deletion can cause two different diseases:
Angelman syndrome – Maternal deletion
o Intellectual disability
o Laugh a lot unexpectedly
o Ataxia (uncoordinated movement)
o No speech
o Epilepsy
o Typical face
o Friendly
Prader Willi syndrome – Paternal deletion
Neonatally
o Hypotonia
o Feeding problems
First decade of life
o Obesitas
o Small
, o Intellectual disability (mild)
o Hypogonadism
o Behavioural problem
Uniparental disomy (UPD) occurs when a person receives two copies of a chromosome, or part of a
chromosome, from one parent and no copies from the other parent. UPD can occur as a random event
during the formation of egg or sperm cells or may happen in early fetal development. Both
chromosomes of one cell/organism are derived from one parent.
Isodisomy: two identical chromosomes of one parent.
Heterodisomy: two different chromosomes of the same parent.
Lecture 2 Genome Variation: SNVs, CNVs, chromosomes
Genome variation
Variation: any deviation from the reference genome
Polymorphism: variation ≥1% of the alleles in a population
Mutation: variation <1% of the alleles in a population
Pathogenic: disease-causing mutation or polymorphism
CNV: deletion or duplication ≥1 kb
Rare variant: variant with a MAF <5%
Aneuploidy: abnormal chromosomal number e.g. trisomy
There are six different genomic variation in living individuals
o SNV - single nucleotide variant (base pair change)
o INDELS - insertion or deletion of < ~10 bp
o CNV – copy number variant deletion or duplication
bigger than 1kb
o Repeat expansion – 2 to >6000 base pairs
o Structural chromosomal abnormalities (translocations,
ring chromosomes, inversions)
o Aneuploidy (one chromosome extra)
SNV – Single nucleotide variation
o Substitution
- Synonymous: the amino acid is the name = silent
