Translational genomics - lectures
Lecture 1 – Genome architecture - 9-09-2021
The human genome→ it has cells. There is DNA in the nucleus and DNA in the mitochondria. There
are 22 pair of autosomes, there are 2 sex chromosomes, there are 20000 coding (protein) genes and
25000 non-coding genes (they code for RNA, but not for a protein).
- A mouse has 19 pair of autosomes and 2 sex chromosomes
These are the basepairs. Purines
are the adenine and guanine.
Pyrimidines are thymine and
Cytosine.
There are two hydrogen bonds
between A-T, and three
between G and C.
In the beginning of an exon
there are lots of G’s and C’s.
then comes the ATG, which is
the start codon, and then all
nucleotides will appear.
These are the components of the
human genome. The important one
are the protein-coding genes, however
this is only 1.5%.
The functional parts are protein-coding
genes, Intron, miscellaneous unique
sequences, miscellaneous
heterochromatin, and segmental
duplications. The rest are ‘junk’.
Functional DNA consists out of:
- Protein coding genes
- Non-coding genes
- Regulatory elements
Protein coding genes:
This is what a gene looks like, starting from
5’UTR till 3’UTR, so the promotor region is not
included. 5’UTR is the place where the
ribozyme binds (this is G-C rich). The coding
sequence is the red sequence in this picture.
The yellow/orange parts are the untranslated regions (UTR).
,When there are different tissues, there are also different isoforms.
Non-coding genes:
At the ssRNA you do not have to do
anything, just that the strangs are
between 24 and 31 nucleotide long. At
the hairpin-RNA that is ds so you have to
remove all that information, therefore
diver-dependent processing.
Then the mature small RNA’s are seen by
proteins (argonaute family). All these
proteins recognize the RNA’s, so then you
get the RNA-protein complex and they
will look for genes. They recognize the
genes (coding genes, transposons and
exogenous genes) via the miRNA.
Mechanism of action for the miRNA → it can inhibit the translation initiation, it can inhibit the
translation elongation or it causes mRNA deadenylation (here it removes the poly-A-tale, and then
the RNA get degraded really fast).
Feingold syndrome 2: a disease where there is a deletion of miRNA group. The fingers and toes are
really short and it looks like that the thumb is almost gone. Furthermore they have syndactyly
(fingers/toes are fused together)
➔ mRNAs result in diseases
Long non-coding RNAs (lnc); sometimes you have a intronic lncRNA, or you can have a intergenic
lncRNA (in between genes) and you sometimes have a natural antisense transcript (NAT). lncRNAs
always have introns, while shortRNAs do not have introns.
- lncRNAs can bind to a protein, like a guide. For example a protein that is not available
anymore they can store it. Further they can bind to DNA and RNA.
NATs; mechanism of action → you got for instance RNA pol II, the
first strand there is transcription of your gene. But the lower gene
can not be translated, because RNA pol II is on the upper gene. So
mechanism of action of NAT is hindering the transcription of the
other gene.
,Another action of NAT is at the pre-mRNA, certain exons are not
spliced so if it binds to exon 3 you only get exon 1 + 2.
Third mechanism is that it can bind to RNA and do RNA editing. There
they do nuclear retention (so an A will transform into T). And they do
chromatin modification, so they break down into siRNAs. What happens
is that there is inhibition of gene expression after these actions.
Regulatory elements: proximal promotor elements and the core promotor are regulators in gene
expression. There are also distal regulatory elements that regulate gene expressions, these are
enhancers, silencers, insulators and locus control region.
Junk DNA: Transposable elements (TEs) are moving through the genome, they did this during
evolution but now they do not move anymore. They are 45% of the human genome, only 0.05% is
active. The most abundant elements are the Alu elements (10% of the human genome, alu elements
are only found in primates (humans/monkeys)).
TE consists out of 2 classes, Class I (42 % of human genome) and Class II (3% of human genome).
Class I are retrotransposons:
- LINEs (21%)
- SINEs (Alu) (13%)
- LTR (8%)
Class II are DNA transposons.
TE diseases → Insertion of Alu in DMD
The epigenome:
What is the most extreme example of the effect of epigenetic modification on gene expression, what
is present at birth? → inactivation of the X-chromosome.
Genetic imprinting→ DNA methylation. The C’s can be
methylated (CH3), only C’s from GC islands. The
methylation is present at birth, so it is always there. The
methylation causes inactivation.
Genomic imprinting → in the gametes already
one locus/gene got an imprint. At
spermatogenesis the old imprint will be removed
and there will be a new one. Also present for
oogenesis. It does not alter the genetic sequence.
, Genomic imprinting: Essential for normal development. Deregulation results in complex genetic
diseases. About 100 imprinted genetic loci.
- Prader-Willi syndrome / Angelman
syndrome → normally you have one
imprinted allele from the mother and
one from the father. Deletion in
mothers allele results in Angelman
syndrome. Deletion in fathers allele
results in Prader-Willi syndrome.
- Angelman syndrome: intellectual
disability, laugh a lot unexpectedly,
ataxia, no speech, epilepsy, typical
face, friendly.
- Prader-Willi: hypotonia (decreased
muscle tone), feeding problems,
obesities, small, intellectual disability (mild), hypogonadism, behavioural problems.
Lecture – genome variation – 10-09-21
Throughout the world people are using the same
reference genome (1 individual), same golden
standard. About 70% of the genome consists out of
the RPCI-11.
3 billion base pairs are in the UCSC, genome browser.
Terminology:
- 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.
Variation:
Repeat expansion: the repeat is GCG and this will
be expanded multiple times.
Lecture 1 – Genome architecture - 9-09-2021
The human genome→ it has cells. There is DNA in the nucleus and DNA in the mitochondria. There
are 22 pair of autosomes, there are 2 sex chromosomes, there are 20000 coding (protein) genes and
25000 non-coding genes (they code for RNA, but not for a protein).
- A mouse has 19 pair of autosomes and 2 sex chromosomes
These are the basepairs. Purines
are the adenine and guanine.
Pyrimidines are thymine and
Cytosine.
There are two hydrogen bonds
between A-T, and three
between G and C.
In the beginning of an exon
there are lots of G’s and C’s.
then comes the ATG, which is
the start codon, and then all
nucleotides will appear.
These are the components of the
human genome. The important one
are the protein-coding genes, however
this is only 1.5%.
The functional parts are protein-coding
genes, Intron, miscellaneous unique
sequences, miscellaneous
heterochromatin, and segmental
duplications. The rest are ‘junk’.
Functional DNA consists out of:
- Protein coding genes
- Non-coding genes
- Regulatory elements
Protein coding genes:
This is what a gene looks like, starting from
5’UTR till 3’UTR, so the promotor region is not
included. 5’UTR is the place where the
ribozyme binds (this is G-C rich). The coding
sequence is the red sequence in this picture.
The yellow/orange parts are the untranslated regions (UTR).
,When there are different tissues, there are also different isoforms.
Non-coding genes:
At the ssRNA you do not have to do
anything, just that the strangs are
between 24 and 31 nucleotide long. At
the hairpin-RNA that is ds so you have to
remove all that information, therefore
diver-dependent processing.
Then the mature small RNA’s are seen by
proteins (argonaute family). All these
proteins recognize the RNA’s, so then you
get the RNA-protein complex and they
will look for genes. They recognize the
genes (coding genes, transposons and
exogenous genes) via the miRNA.
Mechanism of action for the miRNA → it can inhibit the translation initiation, it can inhibit the
translation elongation or it causes mRNA deadenylation (here it removes the poly-A-tale, and then
the RNA get degraded really fast).
Feingold syndrome 2: a disease where there is a deletion of miRNA group. The fingers and toes are
really short and it looks like that the thumb is almost gone. Furthermore they have syndactyly
(fingers/toes are fused together)
➔ mRNAs result in diseases
Long non-coding RNAs (lnc); sometimes you have a intronic lncRNA, or you can have a intergenic
lncRNA (in between genes) and you sometimes have a natural antisense transcript (NAT). lncRNAs
always have introns, while shortRNAs do not have introns.
- lncRNAs can bind to a protein, like a guide. For example a protein that is not available
anymore they can store it. Further they can bind to DNA and RNA.
NATs; mechanism of action → you got for instance RNA pol II, the
first strand there is transcription of your gene. But the lower gene
can not be translated, because RNA pol II is on the upper gene. So
mechanism of action of NAT is hindering the transcription of the
other gene.
,Another action of NAT is at the pre-mRNA, certain exons are not
spliced so if it binds to exon 3 you only get exon 1 + 2.
Third mechanism is that it can bind to RNA and do RNA editing. There
they do nuclear retention (so an A will transform into T). And they do
chromatin modification, so they break down into siRNAs. What happens
is that there is inhibition of gene expression after these actions.
Regulatory elements: proximal promotor elements and the core promotor are regulators in gene
expression. There are also distal regulatory elements that regulate gene expressions, these are
enhancers, silencers, insulators and locus control region.
Junk DNA: Transposable elements (TEs) are moving through the genome, they did this during
evolution but now they do not move anymore. They are 45% of the human genome, only 0.05% is
active. The most abundant elements are the Alu elements (10% of the human genome, alu elements
are only found in primates (humans/monkeys)).
TE consists out of 2 classes, Class I (42 % of human genome) and Class II (3% of human genome).
Class I are retrotransposons:
- LINEs (21%)
- SINEs (Alu) (13%)
- LTR (8%)
Class II are DNA transposons.
TE diseases → Insertion of Alu in DMD
The epigenome:
What is the most extreme example of the effect of epigenetic modification on gene expression, what
is present at birth? → inactivation of the X-chromosome.
Genetic imprinting→ DNA methylation. The C’s can be
methylated (CH3), only C’s from GC islands. The
methylation is present at birth, so it is always there. The
methylation causes inactivation.
Genomic imprinting → in the gametes already
one locus/gene got an imprint. At
spermatogenesis the old imprint will be removed
and there will be a new one. Also present for
oogenesis. It does not alter the genetic sequence.
, Genomic imprinting: Essential for normal development. Deregulation results in complex genetic
diseases. About 100 imprinted genetic loci.
- Prader-Willi syndrome / Angelman
syndrome → normally you have one
imprinted allele from the mother and
one from the father. Deletion in
mothers allele results in Angelman
syndrome. Deletion in fathers allele
results in Prader-Willi syndrome.
- Angelman syndrome: intellectual
disability, laugh a lot unexpectedly,
ataxia, no speech, epilepsy, typical
face, friendly.
- Prader-Willi: hypotonia (decreased
muscle tone), feeding problems,
obesities, small, intellectual disability (mild), hypogonadism, behavioural problems.
Lecture – genome variation – 10-09-21
Throughout the world people are using the same
reference genome (1 individual), same golden
standard. About 70% of the genome consists out of
the RPCI-11.
3 billion base pairs are in the UCSC, genome browser.
Terminology:
- 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.
Variation:
Repeat expansion: the repeat is GCG and this will
be expanded multiple times.
