KB L1-3 Flashcards
What three transcriptional regulators make cells specific?
Epigenetics
Trans- acting elements
Nc-RNA
Drosophila is advantageous to study development because? (6)
Small Short generation time (9 days) Lots of mutant Phenotypes Fate maps available for certain areas Only around 13,000 genes Complete genome sequence available
What other model systems are there (than dros?)
Nematode worm - simplest organism with a nervous system
Zebra fish - embryo is visible during development
Mouse - common mammal due to sequencing o
General structure of a transacting domains
DNA binding domain with ATTA binding motif
Transregulatory domain, interacts with other components of the transcription machinery to help regulate gene expression
Stages of drosophila development
Day 0 - fertilisation Embryonal development Day 1 hatching Larva - 3x larval stages with Sep motifs Day 5 pupation Pupa Metamorphosis Day 9 adult
What time frames are transcription factors influencing developmental decisions?
Integration of long and short signals through the action range of the transcription factors
Order of drosophila segmentation
Egg-polarity genes (bicoid) - head and tail are defined, maternal effect genes
Gap genes - Kruppel and Hunchback - expressed in larger overlapping domains
Pair-rule (Evo and ftz) - define seven segments each so get 14 segments
Segment polarity genes (engrailed) - anterior and posterior of each segment, expressed in each of the 14 segments
Hox genes - tells segment what they are going to become. Defining the areas of the organism ie thorax and abdomen
If you delete drosophila segment genes what happens
The are where the genes were expressed will be missing and the expression of genes down stream of the mutation will be affected showing a hierarchy of gene expression
What does Evo stand for?
Even-skipped
What results in evo being turned on?
Several types of signalling. Pathway in a cluster of mesodermal cells
What tissue develops cells expressing evo and what does it go on to make?
Muscle develops cells expressing evo and goes on to make heart and body wall muscle
what is evo regulated by in mesoderm?
An enhancer, and within the enhanced there are sites that bind regulatory factors that are at the end of receptor tyrosine kinase signalling pathways and regions that bind to factors from wingless and decapentapleigic signalling systems plus a binding site for twist (specific to undifferentiated mesoderm) and tinman (marker for dorsal mesoderm cells)
What did halfon et al show about binding sites in the evo enhancer?
By mutating the binding sites halfon shows that they are all needed to achieve proper expression of evo. The signalling and receptors is like a code deciphered by the enhancer
There is homology between genes that control organ formation in humans and flies what does this mean?
That we can study flies as model organisms for organ development
What mutant phenotype led to the formation of hox genes?
Antennapedia
What do all bilateral animals possess?
A common genetic mechanism for patterning the A/P axis involving the hox cluster
Properties of the homeodomain
183bp, Very basic protein domain 30% K and R Secondary structure is HTH motif Hox TF bind ATTA One of the helices sits in the major groove making contact with the bases
Structure of a typical homeodomain
Variable region Homopeptide (highly conserved) Intron Homeodomain Acidic tail
In hox LOF transformations mutants what happens?
Affected body structures resemble of anterior ones.
What are gof mutant hox Phenotypes due to?
ectopic expression of more posterior hox genes which are capable of cancelling out the function of more anterior ones
What is an example of posterior prevalence?
Abd-A is the posterior most region of the fly embryo. When under control of a heat shock promoter all head and thoracic segments attain a more posterior like identity
What occurs on hoxc8 -/- mutant
= attachment of the 8th pair of ribs to the sternum and appearance of a 14th pair of ribs on the first lumbar vertebra
What is ubx protein
Ultrabithorax identified by mutations that transform halteres (balancing organs in flies) into an extra pair of wings
What does ftz activate?
Ubx and antp
What does ubx protein activate/repress?
Activated ubx and represses antp
If you use a heat shock promoter to express antp in the drosophila germline what happens?
Antenna to leg Homeric transformation
How are homeodomain containing TFs specific - 2 ways?
By dimerisation to cofactors (however this is not enough to explain the specificity of hox genes and enhancers are also important I increasing specificity)
What is the role of the cofactor exd in flies and what is its homologue in mammals?
Exd - extra dentide, loss = loss of most segmental differentiation with no apparent change in hox expression
Pbx is the homologue in mammals
How many hox clusters are there in drosophila?
2 clusters
The antennapedia complex and the bit borax complex
How is animal patterning ie, dorsal/ventral patterning genetically conserved?
By TGFβ family members dpp in dros and BMP4 in vertebrates
And their interacting ligands sog and chordin.
What is co-linearity?
Where the position of the gene in the genome corresponds to where the gene is expressed in the embryo
How many classes of homeobox genes are there
20
Hox is one class
Similarity in homeodomains between vertebrates and invertebrates?
A homeodomain in frog has 1 as different to that in a fly and the path of divergence between these organisms occurred around 500million years ago
What chromosome is hox a
Hox b
Hox C
And hox d on?
A- c7
B - c17
C - c12
D - c2
How do similar genes align in hox clusters?
In paralogous groups ie A4 is more similar to B4 and D4 than A3 and A5
How many duplications of hox clusters in mammals?
2 to give 4 clusters
What happens if you swap paralogous hox coding regions?
What happens on swapping non coding regions and what does this suggest?
Swapping b4 for a4 etc there is little effect on development
Non coding regions are moved this disrupts development, suggesting that whist the genes are similar they are expressed differently spatiotemporally and this involves non coding regions
What hox rearrangements cause leukaemias?
MLL/AL1/HRX
Action of trxG and pcg on hox genes?
They repress/activate hox genes on A/P body axis
In a mouse hox genes are expressed in the abdomen what happens on trxG and pcg mutants?
TrxG: diminished hox gene products
Pcg: hox genes expressed in abdomen, thorax and head
What is the role of krox20 in mouse hindbrain development?
A transcription factor that activates hoxB2 in the hindbrain of the developing mouse. It is expressed in odd number rhombomeres 3&5
What is krox20 in mammals and what happens on KO
Egr2
KO
R3 looks like r2 and r5 looks like r6
What is a good system for showing colinearity?
The hindbrain of the mouse and hoxb2-b5 expression
Can you drop a hox gene randomly into the genome and expect correct expression?
No, there are complex local and distal control elements
What dros genes are there no equivalent of?
The gap and the pair-rule genes
What do chromatin modifiers do to hox genes in ESC?
Repress them (pcg and ncRNAs)
Describe hox gene expression in development
Initially in development hox genes are switched off (global silencing) they become progressively activated during development following a temporal sequence that correlates with the genes position in the cluster in a 3’-5’ direction - temporal colinearity
How is hox gene expression switched on and maintained?
By PcG and trxG systems
Why is the temp rial nature of colinearity important?
Because even if the end product is maintained, but the temporal expression is incorrect there are phenotypic changes
In ESCs how are hox genes labelled and what happens on expression of hox?
They are bivalently labelled.
Down reg of H3K27me3
Up reg of H3K4me3
What removes H3K27me3 marks?
Kdm6 and Kdm6a
How are hox genes moved physically into an activated domain?
Shunted into active domain one at a time. Genes are segregated into a separated domain as they are activated but they maintain interactions with the cluster - linear sliding.
This 3D nature suggests that the location within the nucleus may also affect hox gene expression
What does cis- regulation of hox genes do?
Control their transcriptional patterns and are a major determinant of hox gene spatial expression
What is cis-regulatory activity independent of?
Hox genes being located in a hox cluster.
What is spatial control of hox gene expression seem mostly independent of?
Genomic arrangement. In organisms where hox genes are not clustered hox expression still maintains spatially colinear gene expression.
Example of where hox genes are not clustered and still maintains co- linear gene expression.
And is this generally the case?
D. Buzzatti has two distinct splits in hox genes compared with D. Melanigaster but changes don not seem to lead to any significant differences in hox gene expression arguing that integrity of gene compels is not an absolute requirement for establishment of hox expression patterns
However, many links between colinear activation being linked to clusters which may in part be due to compact structure of the hox loci.
What is the relationship of hoxD11 and 12 with PRC2?
Seem to be involved in homing PRC2 to the hoxD cluster. But removal from mouse genome does not appear to have any deleterious effects on development or on hoxD expression in mouse embryo
What does retanoic acid do to methylation patterns and cell state?
Decrease in H3K27me3 and increase in H3K4me3
Causes undifferentiated to differentiated and 24/36 hox genes to be expressed in differentiated cells
How does Ret acid affect spatiotemporal expression of hox genes?
Timing 3’ first 5’ last
Sensitivity 3’: most sensitive to RA 10-8
5’: least sensitive 10-5
so 3’ End genes can switch on at the lowest concentrations
What factors affect hox expression like RA?
Wnt, FGF and gdf11
What would the gradient if RA explain
Co-linearity
Ectopic expression of hoxa7
Hoxa4
Hoxd4 in mice
Hoxa7 - craniofacial abnormalities and homeotic transformations of vertebrae axis and atlas switch
Hoxa4 - mega colon, innervation in colon prevented, cannot express faeces
Hoxd4 - homeotic transformations of skull bones
Knockout by homologous recombination of hoxa3, hoxc8
Hoxa3 - severe head and throat abnormalities
Hoxc8 - homeotic transformation of vertebrate
When does a double hox knockout give a more sever phenotype?
Hoxa11 or hoxd11- regional bone abnormalities
Hoxa11 AND hoxd11 - radius and ulna missing homeotic transformations of vertebrae and sever kidney defects
Paralogues seem to have some sort of functional redundancy built in
Naturally occurring hoxd13 mutation?
Human: synpolydactyly (6 fingers) co segregated with a 15 residue polyalanine stretch in exon 1 of hoxd13 gene. Gain if function mutations Increase in penetrance and severity with increase in expansion size
Semidominant mutation Aa mild phenotype AA severe phenotype
What do 2 different hoxd13 deletions do?
Result in premature stop codons and have been assoc with some synpolydactyly phenotype and foot malformation. Such truncations would eliminate function of hoxd13 protein suggesting the SPD phenotypic variant was due to haploinsufficiency for the hoxd13 gene
Hoxa13 natural mutation:
Human: hand-foot-genital syndrome, dominant nonsense mutation in homodomain generate a truncated protein unable to bind DNA. Haploinsufficiency leading to phenotype
Hoxa13 deletion in mice leads to?
Hyopolydactyly - deformed paws. Suggests paralogues are important for hand/foot development and affect other genes required for hand/foot development.
Role of the lncRNA HOTAIR in hox gene expression
HOTAIR is transcribed between hoxc11 and hoxc12 and blocks genes in the posterior hoxD cluster. HOTAIR targets PRC2 and LSD1 to specific areas of hoxD
HOTAIR conservation between mice and humans is low, removal in mice has no negative effect on embryonic development or h3k27me3 pattern changes
Hoxa9 in cancer?
AML t(7;11) NUP98 fusion with hoxa9 - temperospatial deregulation and hoxa9 over expression
Hoxa5 in breast cancer
Hoxa5 regulates p53
Hoxa5 promoter is hyper methylated leads to p53 decreased expression and also RARβ normally triggers apoptosis through caspases 2&8 so leads RARβ means less apoptosis
Hoxb13 over expression is associated with what in cancer?
Is associated with tamoxifen reaistance in ER+ primary tumours
Pax genes were found in dros: characteristics?
Contains 128 amino acid paired box, found in other proteins. DNA binding domain
Dros: paired gene
Mammalian homologue : PAX
4 groups based on structural similarities and patterns of expression
Non clustered
With or without a homeodomain and an octapeptide
How does the paired domain bind DNA?
It has two subdomains that interact with the DNA sequence GTTCC PD And HD are transcriptional regulators
What are THDs?
Impacted homeodomains that are shorter than traditional HDs
Is there functional redundancy in pax?
No only 9 pax genes and four subgroups
Why is pax important in CNS development?
Cross regulatory feedback loops are thought to maintain and stabilise developing regions of the brain and spinal cord so that aberrant pax expression overturns neuronal fate
What is the general role of pax?
Maintenance of progenitor cells - prevent differentiation
Group I pax 1 mutations
Mouse undulated tail - kinked tail no human equivalent
Abnormalities of vertebrae
GrI PAX 9 abnormalities
Implicated in oesophageal cancer - good prognosis
Mutation leads to oligodontia - missense mutation (in mice, lots of muts including no teeth)
GrII PAX2 mutations
Renal-coloboma syndrome (human)
Optic nerve tumours, kidney and ear defects
Group II PAX 8 defects
Follicular thyroid tumours (somatic pax8 mutations)
t(2;3) produces pax8:PPARγ fusion protein (activated oncoprotein)
PPARγ is usually what?
A growth retarding protein the translocation to fusion protein may inhibit this and prevent apoptosis the PAX8:PPARγ fusion is overtly invasive compared to those cancers without
Group II pax5 mutations
Implicated in B cell development
Large cell lymphomas in humans t(9;14) puts pax5 next to IgH gene a strong promoter - up reg of pax5
When are the group 2 of genes required?
In very early brain development and segmentation but are transcriptionally down regulated before birth
How do pax genes carry out developmental transitions of progenitor cells
By acting in regulatory networks often controlling the balance of prolif and diff of progenitors
Germline pax3 mutations
Pax 3 is essential for neural crest development
Pax3 muts get splotch mutant in mice abnormalities of pigmentation and neural tube defects
Pax3 muts in humans
Waardenburg syndrome, pigmentation defects, deafness, eye defects, germline mutation gives inherited defects analogous to splotch in ferret
Pax7 upregulates?
Snail, foxd3 and sox genes downstream neural crest specifier cells
In splotch mice what do neural crest cells fail to undergo?
Proliferative expansion prior to migration due to defects intrinsic to the neural crest
Somatic pax3 mutations
- alveolar rhabdosarcoma and aggressive childhood muscle tumour where cells resemble alveoli
t(2;13) translocation gives pax3-fkhr fusion and 100 fold gof effect on pax3 downstream targets and a dominant negative effect on WT pax expression
Somatic Mutations in pax7
t(1;13) gives similar pax7-fkhr fusion
Similar diseases.
Tinman human homologue
Effect of KO in dros and human expression
HH: Nkx2.5/csx
KO tinman in fly: dead larvae, missing dorsal vessel and other dorsal mesoderm derivatives
Nkx2.5 : expressed in fetal heart primordia. Mutation leads to embryonic lethality and embryonic heart development is arrested at initial stage of heart looping
It would seem the underlying genetic mechanism for blood pumping organ is well conserved
Pax6 mutation in mouse:
Small eye mutant
Pax6 mutant in humans and dros analogue
Aniridia, WAGR syndrome
Dros - eyeless
How widely conserved is pax6?
Present in triphoblastic animals ie flatworms / nematodes
Deep conservation as photoreceptor proteins are used by all animals even if eye organisation has changed
What is pax6 promoter subject to?
Methylation in some human tumours perhaps silencing prevents tumour suppression and contributes to tumourigenesis
Where were zinc fingers discovered
In a frog transcription factor
Characteristics of zinc fingers:
DNA/ RNA binding domain with a cys+his or a cys+cys bindin a zn2+. These coordinate zinc in a tetrahedral fashion.
Zn finger helices interact with the major groove of the DNA. You can predict Zn finger binding due to the amino acid side chains. Multiple Zn fingers gives DNA binding specificity
What are the four types of Zn finger gene subclasses and the Zn coordinating amino acids?
TFIIA - CC/HH
nuclear hormone receptors CC/CC
retroviral GAG products CC/CH
yeast transcriptional factors 6xC coordinate 2 Zn ions
Developmental gene example of a zinc finger
Kruppel
Drosophila is a gap gene that regulates pair-rule genes.
Mutations in Kruppul lead to developmental problems
What is Gli3?
A zinc finger gene at the end of sonic hedgehog signalling pathway which is important in development
Mouse: extra toes mutant
Human: Grieg syndrome - skeletal malformations of hands feet and cranium (fuses early preventing proper brain dev)
Wt1 as a zinc finger gene
Deletion in WAGR syndrome.
Human: WAGR and drash
Wt1 is important in genutounrinary tract development
Pou genes are:
Regulators of development expressed in early embryogenesis and during forebrain development.
Critical transactivators POU genes are expressed in distinct spatiotemporal patterns in the forebrain an area that does not express classic HD genes
3 POU genes and organism of discovery
Pit1 - rat
Oct1/2 - human
Unc86 - nematode
All POU genes have what?
A POU homeodomain (60aas) and a POU specific domain (DNA binding domain 74-82aas) separated by a spacer of 15-27aas
How does POU domains interact with DNA?
Can be both positive and negative regulators of transcription and have alt splice variants. Specific domain and HD give DNA binding specificity and bund DNA as 2 separate domains. Helix 3 binds to the DNA often at A/T rich regions and octomer sequences (8 bases). The POU specific domain is thought to be involved in protein-protein interactions so probably binds to DNA dimers.
PIT1 gene disease and expression
In humans: CPHD
Mouse: dwarfism
Expressed in the pituitary glands
Pit1 is required for specification of 3/5 cell types in the anterior pituitary gland
Expression of SKN1A
Skin
Disease of BRN4 and place of expression
Dfn3 deafness - X linked
Expression in the neural tube
Brn3c disease and expression
DFNA15 deafness autosomal expressed in the auditory system
Oct4 expression
ES cells and oocytes
RPF1 disease and expression
Wilms tumour - rare germline mutations
Expressed in various places
PIT1 stimulants what hormones in the pituitary gland and what happens on loss?
Prolactin and thyroid stimulatory hormone
Without development does not occur properly
Describe transition from a pre-implantation embryo to differentiation in terms of hox/oct expression
Pre implant embryo: oct4++, hoxa5-
Differentiation: oct4-, hoxa5 ++
How does oct4 affect hoxa5
Direct regulation by binding an octomer sequence in hoxa5.
Oct4 is important in maintaining pleuripotentcy and is expressed in the female germline until gastrulation And is restricted to primordial germ cells by E8.5. High levels of oct4 seems to prevent differentiation into any cell type
What are sox genes?
High mobility group. This superfamily bind DNA specifically wth TCF and MATA
Developmental gene example of a zinc finger
Kruppel
Drosophila is a gap gene that regulates pair-rule genes.
Mutations in Kruppul lead to developmental problems
What is Gli3?
A zinc finger gene at the end of sonic hedgehog signalling pathway which is important in development
Mouse: extra toes mutant
Human: Grieg syndrome - skeletal malformations of hands feet and cranium (fuses early preventing proper brain dev)
Wt1 as a zinc finger gene
Deletion in WAGR syndrome.
Human: WAGR and drash
Wt1 is important in genutounrinary tract development
Pou genes are:
Regulators of development expressed in early embryogenesis and during forebrain development.
Critical transactivators POU genes are expressed in distinct spatiotemporal patterns in the forebrain an area that does not express classic HD genes
3 POU genes and organism of discovery
Pit1 - rat
Oct1/2 - human
Unc86 - nematode
All POU genes have what?
A POU homeodomain (60aas) and a POU specific domain (DNA binding domain 74-82aas) separated by a spacer of 15-27aas
How does POU domains interact with DNA?
Can be both positive and negative regulators of transcription and have alt splice variants. Specific domain and HD give DNA binding specificity and bund DNA as 2 separate domains. Helix 3 binds to the DNA often at A/T rich regions and octomer sequences (8 bases). The POU specific domain is thought to be involved in protein-protein interactions so probably binds to DNA dimers.
PIT1 gene disease and expression
In humans: CPHD
Mouse: dwarfism
Expressed in the pituitary glands
Pit1 is required for specification of 3/5 cell types in the anterior pituitary gland
Expression of SKN1A
Skin
Disease of BRN4 and place of expression
Dfn3 deafness - X linked
Expression in the neural tube
Brn3c disease and expression
DFNA15 deafness autosomal expressed in the auditory system
Oct4 expression
ES cells and oocytes
RPF1 disease and expression
Wilms tumour - rare germline mutations
Expressed in various places
PIT1 stimulants what hormones in the pituitary gland and what happens on loss?
Prolactin and thyroid stimulatory hormone
Without development does not occur properly
Describe transition from a pre-implantation embryo to differentiation in terms of hox/oct expression
Pre implant embryo: oct4++, hoxa5-
Differentiation: oct4-, hoxa5 ++
How does oct4 affect hoxa5
Direct regulation by binding an octomer sequence in hoxa5.
Oct4 is important in maintaining pleuripotentcy and is expressed in the female germline until gastrulation And is restricted to primordial germ cells by E8.5. High levels of oct4 seems to prevent differentiation into any cell type
What are sox genes?
High mobility group. This superfamily bind DNA specifically wth TCF and MATA
What do all sox genes contain?
A SRY box which is a 79aa DNA binding domain and induces a bend in the DNA. They do this to open the DNA so other TFs can access it.
Characteristics of sox genes?
Highly conserved
SRY box encoded by a single exon
Non clustered
DNA binding to AT rich regions.
Sox genes bind to the minor groove in the DNA and bend it at an angleZ
SoxA-H are activators excluding SoxB2 which is a repressor and soxD subgroup which lacks a transactivation domain (interrupted by retrovirus insertion)
What three things do sox genes interact with?
Interact with: DNA binding proteins to stabilise DNA binding and activate/repress transcription. And adaptor proteins to regulate sox activity (increase specificity to target gene). And nuclear import proteins
How does sox proteins make contact with other TFs?
Via an HMG domain which can also bind DNA
What do sox2 and pax6 do together?
Activate δ crystalline expression during lens induction
Where is SRY expressed?
Sertoli cells in developing tested
How was SRY the first sox end identified?
Cloning by identifying Y sequences in XX males - in gametogenesis translocation of Y material onto X chromosome
SRY is on the Y chromosome of all males.
What mice is SRY absent in and what is the result?
In Tdy mice, get XY females
What does exctopic expression of sox9 induce?
Testes development
What reduces Sry expression in mice?
Mice lacking the +KTS form of WT1 suggesting that sry expression is perhaps due to +KTS being invoked in RNA metabolism
In transgenic sry females you get?
XX males although not with 100% efficiency
What is sry relationship with sox9?
Sry activates sox9. Sox9 is maintained by fgf9 in XX gonad primordia. Wnt4 ensures ovary development by suppressing fgf9. Mice lacking fgf9 experience XY sex reversal. In XY cells it would seem sry upregulates sox9 establishing an inductive loop between sox9 and fgf9 locking in the male determination pathway
What do all sox genes contain?
A SRY box which is a 79aa DNA binding domain and induces a bend in the DNA. They do this to open the DNA so other TFs can access it.
Characteristics of sox genes?
Highly conserved
SRY box encoded by a single exon
Non clustered
DNA binding to AT rich regions.
Sox genes bind to the minor groove in the DNA and bend it at an angleZ
SoxA-H are activators excluding SoxB2 which is a repressor and soxD subgroup which lacks a transactivation domain (interrupted by retrovirus insertion)
What three things do sox genes interact with?
Interact with: DNA binding proteins to stabilise DNA binding and activate/repress transcription. And adaptor proteins to regulate sox activity (increase specificity to target gene). And nuclear import proteins
How does sox proteins make contact with other TFs?
Via an HMG domain which can also bind DNA
What do sox2 and pax6 do together?
Activate δ crystalline expression during lens induction
Where is SRY expressed?
Sertoli cells in developing tested
How was SRY the first sox end identified?
Cloning by identifying Y sequences in XX males - in gametogenesis translocation of Y material onto X chromosome
SRY is on the Y chromosome of all males.
What mice is SRY absent in and what is the result?
In Tdy mice, get XY females
What does exctopic expression of sox9 induce?
Testes development
What reduces Sry expression in mice?
Mice lacking the +KTS form of WT1 suggesting that sry expression is perhaps due to +KTS being invoked in RNA metabolism
In transgenic sry females you get?
XX males although not with 100% efficiency
What is sry relationship with sox9?
Sry activates sox9. Sox9 is maintained by fgf9 in XX gonad primordia. Wnt4 ensures ovary development by suppressing fgf9. Mice lacking fgf9 experience XY sex reversal. In XY cells it would seem sry upregulates sox9 establishing an inductive loop between sox9 and fgf9 locking in the male determination pathway
In sry transgene in XX mice how efficient is maleness?
30%
What are the two types of chromosomal abnormality?
Numerical - euploidy, aneuploidy
Structural - translocations, chromosome rearrangements, deletions, duplications etc
What is diandry and digyny
Diandry is triploidy due to dispermy or diploid sperm so extra set of paternal chromosome
Diagyry is triploidy due to diploid ovum or non-expulsion of polar body so extra set of material chromosomes
What is a pre implantation lethal aneuploidy?
Nullisomy (2n-2)
What trisomies survive?
13,18,21
How is trisomy 21 detected and diagnosed?
Detected cytogenetically and diagnosed by chorionic villus samples or by detecting fetal blood in maternal circulation
What does monosomy or trisomy arise from?
Non disjunction in meiosis I or meiosis II
Tetrasomy and pentasomy arise from?
Nondisjunction during meiosis I and meiosis II
What effect does maternal age have on trisomy rate?
Frequency of trisomies increases exponentially as maternal age increases
Learn table on page 19
About incidence of aneuploidy
What effect does maternal age have on trisomy rate?
Frequency of trisomies increases exponentially as maternal age increases. However this involves chronically ageing and not biological ageing
What is a strategy for trisomy correction?
Down’s syndrome patient fibroblast. Trisomy 21 iPSC + Zinc finger targeting vector and xist with an inducible promoter
+ doxycyclin which activates xist on extra C21 to create a C21 Barr body
What is a Barr body?
Heterochromatin covering a chromosome
Anuploidy live born and syndrome:
XO - Turners, short, webbing around neck, cardio and renal problems
XXY/XXYY - Kleinfelters, infertile and mental retardation
XYY (XXX) - Jacobs most subtle abnormalities
In cri-du-chat syndrome what is the most important gene that is lost?
TERT on C5 involved in telomere length maintenance
What does deletion of sonic hedgehog on chromosome 7q lead to?
Holoprosenceohaly
What are the main unbalanced chromosome rearrangements
Micro deletions, Duplications, Dicentric chromosome (two centromeres) Ring chromosomes (telomere loss) Paracentric and peri centric rearrangements
Paracentric chromosome rearrangement is
Pericentric chromosome rearrangement is
Para: In one arm of the chromosome, doesn’t involved the centromere
Peri: involves centromere so rearrangement in each arm
If the rearrangement is in frame it is unlikely to affect the carrier. More likely to affect children during crossing over
What is trisomy 21?
Down’s syndrome - 15 fold increase In Leukaemia
What is patau syndrome
Trisomy 13
What is Edwards syndrome?
Trisomy 18
What is a strategy for trisomy correction shown by Jiang et al 2013
Down’s syndrome patient fibroblast. Trisomy 21 iPSC + Zinc finger nuclease targeting vector and xist with an inducible promoter to the DYRK1A Locus with a transgene carrying dox control component rtTA into the AAVS1 gene on chr19
+ doxycyclin which activates xist on extra C21 to create a C21 Barr body the edited C21 was enriched in all HC marks examined including H3K27me3, UBH2A and H4K20me.
Xist induction on C21 showed repression of the APP gene.
In vitro when more than one copy of c21 carried xist there was lack/loss of xist localisation after 20days showing there is selection and epigenetic adaption to circumvent a functional monosomy or nulisomy.
What is a Barr body?
Heterochromatin covering a chromosome
Anuploidy live born and syndrome:
XO - Turners, short, webbing around neck, cardio and renal problems
XXY/XXYY - Kleinfelters, infertile and mental retardation
XYY (XXX) - Jacobs most subtle abnormalities
In cri-du-chat syndrome what is the most important gene that is lost?
TERT on C5 involved in telomere length maintenance
What does deletion of sonic hedgehog on chromosome 7q lead to?
Holoprosenceohaly
What are the main unbalanced chromosome rearrangements
Micro deletions, Duplications, Dicentric chromosome (two centromeres) Ring chromosomes (telomere loss) Paracentric and peri centric rearrangements
How in paracentric rearrangement crossing over what causes gametes to be unviable?
Two centromeres or no centromeres the loss/ gain of genes does not make the chromosome unviable
Pericentric rearrangements causes what in crossing over?
Loss of certain genes and duplication of another
What is a common pericentric inversion?
Inv(3)(p25q21)
Leads to facial abnormalities, cleft palate and mental retardation. Often need to look at parents to see how imbalance arises
Two types of translocation?
Robertsonian and reciprocal
How can reciprocal translocations be viewed?
FISH
How often is UPD observed with chromosomal abnormalities?
30%
What can complete chromosome UPD arise from?
Gamete complementation, triatomic rescue, monosomic rescue, mitotic error in connection with robersonian translocation, isochromosome formation, deletion and duplication
What can segmental UPD arise from?
Post zygote X somatic recombination between maternal and paternal homologue a or in connection with numeric and or structural chromosomal aberrations
What is heterodisomy?
Inheriting both chromosomes from 1 parental pair. On fusion with sperm - trisomy so loss of paternal chromosome. Due to error in meiosis I
What is isodisomy?
Inheriting
Pathogenic UPD includes:
Recessive diseases where parent is a carrier ie UPD7 - cystic fibrosis and UPD15 Bloom syndrome
Maternal or paternal UPD of chromosome 15 gives prader willi syndrome or angleman syndrome (imprinting syndromes)
UPD11p15.5 BWS
UPD can have what type of karyotypes? (5)
- Have proven/suggested normal karyotype
- Abnormal balanced karyotype
- Abnormal unbalanced karyotype (with small supernumerary chromosomes or no sSMC)
- Cases with segmental UPD
- Often due to Robertsonian translocation
What is sSMC?
A 47th extra little chromosome - can be a ring chromosome or a double minute
Can be a marker
Only really makes a difference in isodisomy
Pathogenic UPD includes:
Recessive diseases where parent is a carrier ie UPD7 - cystic fibrosis and UPD15 Bloom syndrome
Maternal or paternal UPD of chromosome 15 gives prader willi syndrome or angleman syndrome (imprinting syndromes)
UPD11p15.5 BWS
UPD can have what type of karyotypes? (5)
- Have proven/suggested normal karyotype
- Abnormal balanced karyotype
- Abnormal unbalanced karyotype (with small supernumerary chromosomes or no sSMC)
- Cases with segmental UPD
- Often due to Robertsonian translocation
What is sSMC?
A 47th extra little chromosome - can be a ring chromosome or a double minute
Can be a marker
Only really makes a difference in isodisomy
On silencing of C21 what pathology is reversed?
Deficits in proliferation and neural rosette formation are rapidly reversed
Difference in time between male and female meiosis
In Male meiosis begins with puberty and cells in the male testis progress from metaphase I to metaphase II without delay. Each cell that enters meiosis produces 4 sperm
In the female. All oocytes initiated meiosis during fetal development but after homologous chromosomes undergo synopsis and initiate recombination. The oocyte enters a period of mitotic arrest. Resumption of meiosis and completion of the first division occurs years later in the ovary of a sexually mature woman just before ovulation. After completion of MI the oocyte arrests at metaphase of MII and normally the second division is completed only after fertilisation. Each cell that enters meiosis gives one egg and ⅔ polar bodies
How many fertilised human eggs have the wrong number of chromes and how does this differ from mice?
10-30% majority being monsomy or trisomy and with anueploidy accounting for ⅓ of spont abortions
In mice does not exceed 1-2%
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
Three types of non disjunction
1 true non disjunction (homologues travel together to the same pole)
2 achiasmate non disjunction (where homologues fail to pair and independently travel to the same pole)
3 premature separation of sister chromatids
What trisomies do paternal errors account for?
50% of 47, XXYs and trisomy 2 but only 5-10% of most other trisomies
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
What associations other than maternal age are associated with trisomies?
None, many have been implicated but they have not been verified
What genetics is there contrasting evidence over link to Down syndrome? This is a long answer
MTHFR point mutation 677C>T. Protein involved in Folate metabolism and cellular methylation reactions.
James et al suggested that the point mutation leads to abberant methylation and may increase likelihood of meiotic non-disjunction.
Also
MTRR polymorphisms protein involved in folate pathway and liked to increase in spins bifida.
James et al 1999 showed that mothers with Down syndrome children had a higher proportion of heterozygous (MTHFR) and mutant homozygotes (both).
However this is only in relation to trisomy 21 folate metabolism doesn’t affect non disjunction in any other chromosome trisomy. And the evidence for 21 is disputed as Peterson et al were unable to demonstrate any increase in MTHFR mutations compared with controls. Since this data was published 15 years on there has been lots of conflicting reports but the evidence is that folate metabolism has only a weak independent maternal risk for having a child with DS. There is arguments that due to MI beginning in embryogenesis he maternal grandmothers folate intake may provide risk.
