Module 1: Developmental genetics

meiosis generally in males

• diploid spermatocyte duplicates DNA, then splits, then DNA does not replicate, and those cells split, creasing haploid cells that mature into sperm

• meiosis starts during puberty, continues through rest of life

meiosis generally in females

• Unequal division of cytoplasm in Meiosis I, leading to creation of polar bodies at end of Meiosis II that will not mature into oocytes

• first meiotic division of oocyte occurs when female is in mothers womb, then arrests in Meiosis I until menstruation

zygote

fertilized oocyte (union of oocyte and sperm)

process of oocyte maturity

oocyte → zygote → 2-cell stage → 4-cell stage → 8-cell uncompacted morella → 8-cell compacted morulla → early blasocyst → late-stage blastocyst → implementation of blastocyst

cleavage of morulla

leads to genetically identical twins, each of with their own placenta and amniotic sac

cleavage of blastocyst

leads to genetically identical twins with a shared placenta and their own amniotic sac

cleavage of implanted blastocyst

leads to twins with shared placenta and shared amniotic sac

cleavage of formed embryonic disc

leads to conjoined twins

anterior-posterior axis

determined by entry position of sperm, and later determined by HOX genes

dorsal-ventral axis

determined by sonic hedgehog genes

left-right axis

needed for cardiac development and position of viscera (internal organs)

homeobox gene system (HOX)

system that encodes transcription factors to homeodomain, humans have 39 HOX genes; resulted from duplication and divergence from primordial HOX

homeodomain

conserved DNA sequence that regulates large-scale anatomical features in early development

HOX gene expression by position

3’ end of cluster are expressed towards head and are expressed earlier in development, 5’ end of cluster are expressed towards tail and expressed later in development

HOX determination by type

A and B clusters determine head-tail, C and D clusters determine position in developing limbs

HOX gene structure

2 exons and an intron, homeobox is in exon 2

why are HOX genes special?

genomic organization in clusters correlates with function during development

HOXA13 mutation

hand-foot-gentical syndrome

HOXD13 mutation

synpolydactyl digit fusion

birth defect

structural defect or chromosomal abnormality that is present at birth but not necessarily diagnosed at birth

malformation

structural defect resulting from intrinsic abnormality in greater than 1 genetic programs operating in development

Gli3

DNA-binding TF that is a mediator of sonic hedgehog (represses or activates depending on length), helps to determine limb digit number and identity

greig cephalopolysyndactyly

caused by mutations or copy number variation in Gli3 gene, causes webbed fingers, prominent forehead, potential intellectual disabilities

causes of malformations

• chromosomal imbalance (ex. trisomies)

• copy number variations

• single gene defects

• multifactorial

• teratogens

deformation

structural birth defect caused by extrinsic factors impinging physically on the fetus during development

arthrogrypopsis multiplex congenita (AMC)

lack of room caused congenital joint contractures, leading to shortened tendons, reduced movement

disruptions

birth defect that results from destruction of irreplaceable normal fetal tissue after plasticity period has ended, can be caused by trauma, teratogens, and vascular insufficiency

amnion disruption

strands separate from amniotic sac, strands then float and can wrap around appendages, then strings may restrict movement (ex. amniotic band syndrome)

pleiotropy

birth defect from a single causative agent that causes abnormalities in >1 organ system or multiple structures

syndrome

type of pleiotropy where one cause has multiple effects

waardenburg syndrome

example of syndrome, four different types; WS1 causes wide nasal bridge, WS2 causes congenital deafness, WS3 upper limb deformation and fusion of joints/fingers/bones, WS4 absence of certain ganglia, accumulation of feces w/n colon and failure to thrive

sequence

type of pleiotropy where one cause leads to a change in something where that change has downstream effects

isolated pierre robin syndrome

example of sequence, genetic changes cause facial abnormalities to head and face, which causes problems with breathing, which causes a failure to thrive

neural tube defects

failure to close neural tube; spina bifida (failure to close spine during development), anencephaly → absent forebrain, meninges, neonatal death, multifactorial with genetic and environmental components, folic acid plays a role

nondisjunction

chromosome imbalance from incorrect chromosome separation during meiosis I or II

why is arresting in meiosis I a risk for nondisjunction?

decrease in cohesion ability = decrease in ability chromatids to bind

effect of maternal age on birth defects

increased risk of aneuploidy in females (incorrect # of chromosomes) due to decreased cohesion, increased epigenetic alterations and increased ROS exposure and damage

effect of paternal age on birth defects

increase in germ-line mutations, higher risk of cancer, autism, schizophrenia, and de novo unbalanced structural chromosomal offspring

aneuploidy

presence of abnormal # chromosomes in a cell (measured as a multiple of a haploid set)

trisomy 21

down syndrome, results in hypotonia (softer muscles), dysmorphic facial features, short stature, intellectual disability, and variable symptoms

down syndrome from robertsonian translocation

chromosome 14 and 21 both break and rejoin the long arms, leading to a fragment of the short arms that is usually lost; leading to variability in offspring viability

partial trisomy 21

duplication of a limited segment of chromosome 21, usually part of 21q and typically gene empty or gene poor, can sometimes lead to down syndrome

trisomy 13

patau syndrome, 3 copies of chrom. 13 or robertsonian translocation of 13q:14q, symptoms include severe intellectual disability, heart defects, etc.; increased incidence with older mothers and inheritable with stable translocations of 13q:14q

trisomy 18

edwards syndrome, 3 copies of chr. 18 or partial trisomy, symptoms include severe intellectual disability, heart defects, low birth rate, nondisjunction of chr. 18 is not heritable, partial trisomy 18 can be through non-symptomatic carriers

uniparental disomy

results from chromosome disjunction with both copies of the chromosome derived from the same parent, mostly chromosomes with imprinted regions, clinically relevant for recessive disorders where only 1 parent is carrier

genomic rearrangements

mutational changes in genome that are different from base pair mutations, including duplications, deletions, inversions, and translocations; can be neutral or change phenotype by changing copy number of dosage sensitive genes, disrupting genes, or create fusion genes

non-allelic homologous recombination

homologous recombination occurring between lengths of DNA that have high sequence similarity but are not alleles; more common in low copy repeat sequences (LCRS), can cause deletions or duplications

genomic rearrangements

stretch of unique sequence, flanked by large, highly homologous segmental duplications, often associated with cognitive disease

idiopathic chromosomal abnormalities

chromosomal abnormality that does not occur in a genomic hotspot, occurs in highly variable chromosomal locations

Chromosome 1p36

small deletion in part of the terminal 10 Mb of chr 1p, leads to severe intellectual disability, structural brain abnormalities, seizures, hypotonia, etc., typically de novo deletions, some inherited from parent with balanced translocation

reciprocal translocation

two non-homologous chromosomes are exchanged without the loss or net gain of genetic material

robertsonian translocation

long arms of the chromosomes break off and fuse, leaving the smaller arts to fuse, which is typically lose, happens in chromosomes 13, 14, 15, 21, 22

inversion

segment breaks off and reattaches, but in the opposite orientation, inversion ring is formed, where crossing over occurs

ring chromosomes

structural abnormality where broken parts of chromosome fuse, resulting in a ring, which can result in loss of genetic material

mosaicism

the property or state of being composed of cells of two genetically different types that originally derived from a single zygote; due to mutations occurring after conception but early in development

germline mosaicism

when the mutation occurs after gamete formation, present in some but not all gametes and will determine if the offspring will be affected

segmental mosaicism

occurs during embryonic development, manifests as segmental or patchy depending on developmental stage of mutation, often somatic, if occurs before separation of germline cells, it could affect gametes and become heritable

segmental neurofibromatosis mosaicism

genetic defect in cells derived from neural crest, causes cafe-au-late spots and benign tumors of nerve sheath; caused by post-zygotic mutation of NF1 in chrom 17q

sonic hedgehog (SHH)

gene that is important for front to back axis, differing concentrations of SHH associated with development of different structures (closer to neural cord, higher the concentration)

SHH mutations

autosomal dominant, loss of function of 1 allele causes birth defects, can cause holoprosencephaly (failure of midface and forebrain to develop), cleft palate, eyes close together, or absence of forebrain structures

SHH for limb development

regulates TFs for limb development, cells that are more exposed to SHH form pink, ring, and middle finger, cells that are not exposed for thumb and pointer

Gli3

gene needed for number and identity of digits, full Gli3 needed for normal development

RET gene

encodes RET proto-oncogene, plays a crucial rols in neural crest development, regulates cell death and survival balance positional information, needed for normal intestine organogenesis and enteric nervous system, promotes formation of peyer’s patch-like structures

Hirschprung disease

typically caused by RET mutations (missense or stop codon) that leads to decreased RET activity, absence of enteric nerves in intestines and no normal gastrointestinal motility

copy number variations

gains or losses of DNA of areas greater than 1000 bps, inherited and common, larger CNVs more often cause disease and are associated with regulatory regions and dosage-dependent gene

teratogens

an agent or factor which causes malformation of an embryo, interfere with intrinsic molecules mediating gene action, effects depend on type of teratogen, dose, time of exposure, and length of exposure

isotretinoin

3-ris retinoic acid, related to vitamin A, relatively safe for adults; causes severe birth defects in babies, hearing and visual impairment, missing or malformed earlopes, facial dysmorphism, mental retardation

thalidomide syndrome

causes phocomelia (seal limbs) in newborns as a result of pregnant mother ingestion of thalidomide

thalidomide mechanism

not recognized by ATP binding cassette proteins as toxic, so remains intracellular, causes oxidative stress through ROX production, leading to apoptosis in apical ectodermal ridge and zone of polarizing activity

fetal alcohol syndrome

caused by moderate to excessive maternal alcohol exposure in pregnancy, leads to brain abnormalities, CNS dysfunction, neurocognitive problems, and behavioral problems

Zika infections

can cause microcephaly, brain defects, deafness, limb malformation, and growth restriction in newborns

zika and RA

zika virus introduces extra stretches of RARE (RA-response elements) consensus sequence repeats in genome of developing brain, leading to a disruption of RA signaling and the genes involved in neural tube development, causing disruptions in proper brain development

steps for male sex determination

fertilization, which establishes chromosomal sex, then initiation of gonadal sex, which is guided by SRY gene on Y chromosome, then sex-specific differentiation of internal and external sexual organs, then secondary sexual characteristics obtained at puberty

chromosome Y

relatively gene poor, gene function restricted to gonadal and genital development

SRY

sex-determining region on chromosome Y, encoded testis-determining factor, contains no introns, expressed briefly early in development

testis-determining factor (TDF)

dna-binding protein that promotes DNA bending, leads to increased SOX9 and testes differentiation

microdeletions of chromosome Y

common in oligospermia and azoospermia, Yq cluster of azoospermia factors (AZF) genes involved, de novo Yq mutations account for significant proportion of infertility in males

chromosome X

contains 1000 genes, not all inactivated, genes on Xp more prone to escaping inactivation; 1 X chromosome is inactivated early in development by epigenetic mechanisms (methylation

sex chromosome abnormalities

most common genetic disorder, can be numerical or structural, present in all cells or mosaic; can result in a delay in onset of puberty, infertility, or ambiguous genitalia

klinefelter syndrome

47, XXY resulting from nondisjunction of either parent. infertile, no germ-line cell development; diagnosis is typically in adulthood, can lead to slightly decreased IQ but still normal behavior

turner syndrome

45, X or 46 XX with a structurally abnormal second X of mosaicism; caused by nondisjunction during meiosis or loss of chromosome from zygote/early embryo, oocytes degenerate with atrophied ovaries, other affected organs probably involve X-linked genes that are not inactivated in females

unbalanced X autosome translocation

similar to autosomal translocation, offspring only normal when the chromosome that is activated results in a net inclusion of normal chromosomes (balanced translocation)

XY gonadal dysgenesis

progressive loss of germ cells, leading to underdeveloped and dysfunctional gonads, no development of mature secondary characteristics; 46 XX DSD-males, 46 XY CGD-female

46, XX

testicular DSD in males, male external genitalia with female chromosomal sex, diagnosed at puberty, caused by translocation of SRY on X chromosome because of aberrant recombination

46, XY females

androgen insensitivity, X-linked disorder, cause testes in abdomen or in inguinal canal, AR mutations in androgen binding or DNA binding domain change the ORF of gene.

46, XX with ambiguous/male genitalia

normal uterus and ovaries, defects in enzymes of adrenal cortes for cortisol biosynthesis, most often in 21-hydroxylase deficiency

prenatal diagnosis

goal is to inform prospective parents about the risk for birth defects or genetic disorders to provide them with informed choices on how to manage that risk; methods are amniocentesis and chorionic villus sampling

prenatal screening

goal is to identify pregnancies for prenatal diagnosis, methods are ultrasound and positive screening test

chorionic villus sampling

perorformed at 10-13 weeks gestation, biopsy of chorion examined, increased risk of miscarriage, rare risk of injury to fetus, infection, and leakage of amniotic fluid

amniocentesis

performed at 16-20 weeks gestation, amniotic fluid examined for genetic testing and protein testing, increased risk of miscarriage

pre-implantation diagnostics (pre-IVF)

choosing fertilized eggs based on if they are affected or unaffected

maternal blood screening

screens for alpha-feto protein using levels in the maternal serum, appropriate levels fall between the threshold for down syndrome and the threshold for spinal bifida

postnatal heel prick

performed on blood spot testing 48-72 hours after birth involving metabolites, immune tests, or hormones, or other genes, tests for PKU, cystic fibrosis, hypothyroidism, congenital adrenal hyperplasia, etc.