Genetics Chapter 5 Spring 2020

Example of disomy

2 copies of the dads chromosome 15 and 1 copy of the moms There is an aneuploidy rescue mechanism to get rid of the extra and produce a normal If you are lucky the extra dads will get disgusted but if you are not lucky the moms will get digested and then you will have AS The biological significance of genomic imprinting is still a matter of specu

The Igf-2 gene encodes a growth hormone called insulin-like growth factor 2

A functional Igf-2 gene is necessary for a normal size Imprinting results in the expression of the paternal but not the maternal allele The paternal allele is transcribed into RNA The maternal allele is not transcribed Igf-2m or Igf-2- is a mutant allele that yields a defective protein This may cause a mouse to be dwarf depending on whether it inherits the mutant allele from its father or mother Cross: Homozygous normal male (Igf-2 Igf-2) X homozygous mutant female (Igf-2- Igf-2-) Offspring are heterozygous (Igf-2 Igf-2-) They have inherited an Igf-2 allele from their father Reciprocal cross: Homozygous mutant male (Igf-2- Igf-2-) X homozygous normal female (Igf-2 Igf-2) Offspring are heterozygous (Igf-2 Igf-2-) They have inherited an Igf-2- allele from their father

Endosymbiosis theory

A theory that mitochondria and chloroplasts originated from bacteria that took up residence within a primordial eukaryotic cell. Primordial eukaryotic cell and the mitochondria tries to disguise itself so it is engulfed by the primordial cell and then it started to depend on the nuclear dna to divide Chloroplast and mitochondria did this in the plant cell Nucleus never transfers genes to the mitochondria and the chloroplast Gene transfer can occur Between two mitochondria, two chloroplasts or a mitochondrion and a chloroplast Certain mitochondrial mutations sometimes don't manifest in offspring because the nucleus can override mutations from mitochondria and chloroplasts

Interpreting the Data for lyon

All nine clones expressed one of the two types of G-6-PD enzyme, not both Clones 2,3,5,6,9 and 10 only the slow type Clones 4,7, and 8 expressed only the fast type Because of lyonization you don't see that people who have abnormal numbers of X chromosomes die due to barr body formation Due to facultative heterochromatin formation In the embryonic stage there is also an impact on the growing cells **Reasons we see abnormalities but no death

The Lyon Hypothesis Tested

Analyzed the expression of a human X-linked gene Selected a female who is heterozygous for G6PD → has the fast moving and the slow moving forms - The gene encodes glucose-6-phosphate dehydrogenase (G-6-PD), an enzyme used in sugar metabolism Fast form → fewer functional amino acids Slow form --> more amino acids Based on how quickly they migrate when they are run through gel electrophoresis Biochemists had found that individuals vary with regards to the G-6-PD enzyme This variation can be detected when the enzyme is subjected to agarose gel electrophoresis fast vs slow The mobility of G-6-PD proteins from various individuals Thus heterozygous adult females produce both types of enzymes Hemizygous males produce either the fast or the slow type

Imprinting in Action

Angleman (chromosome 15) Paternal (maternally expressed) Disomy: 2 copies of the dad (uniparental disomy) Terrible symptoms of angelman syndrome Prader Willi (next to on chromosome 15) SNRPN, NDN Maternal (paternally expressed) Disomy: 2 copies of the mom (Uni Maternal disomy)

The process of X inactivation can be divided into three stages

Both X chromosomes are working until initiation Initiation (at the gastrula stage) One of the X chromosomes is targeted to be inactive Spreading The chosen X chromosome is inactivated Maintenance The inactivated X chromosome is maintained as such during future cell divisions It will continue to remain silenced in all of the cells

Gastrula stage

Cells start migrating a different rates and during this time the bud of organs form In this stage the cell will randomly inactivate either the dominant or recessive allele and converted to a barr body = Initiation *** Transcription is common but whether or not it translates determines if it is coding or noncoding RNA Noncoding RNA is produced after initiation from the inactivated and it will spread to the end of the chromosome and begin compacting it Then it becomes a barr body because it can not transcribe or translate Barr body = compacted X chromosome

Imprinted genes follow a non-Mendelian pattern of inheritance

Depending on how the genes are "marked", the offspring expresses either the maternally-inherited or the paternally-inherited allele Not both This is termed mono-allelic expression Good gene from mom and bad gene from dad and if gene from mom is silenced then you're dead

Dosage compensation in different species

Depending on the species, dosage compensation occurs via different mechanisms marsupials always silence the other X Drosophila melanogaster → insects upregulated by 2 fold Females can have either XAXA bright apricot or XAXa pale apricot However males can only have XAY they are bright apricot ***Leaking of gene products to give you the bright apricot Upregulation and overcompensation for only having one X Caenorhabidits elegans → Earthworms are interesting because they are hermaphrodites The female part there is downregulation 25%+25% = 50% for 2 Xs The male part there is one X that is = 50% which equals 100% total In birds, the sex chromosomes are the Z, a large chromosome containing many genes W, a micro-chromosome containing few genes Males are ZZ; females are ZW Z chromosome in males does not undergo condensation like one of the X chromosomes in female mammals dosage compensation may occur if either/or Genes on the Z chromosome in male are down-regulated 50% Corresponding genes in the female could be up-regulated twofold

X Inactivation Depends on Xic, Xist, TsiX and Xce

During Gastrula stage 2 Xic (one for each chromosome) = inactivation center = 2 genes → 1 is active and 1 is inactive The genetic control of inactivation - not entirely understood at the molecular level a short region on the X chromosome termed the X-inactivation center (Xic) plays a critical role For inactivation to occur, each X chromosome must have a Xic region The Xic region contains a gene named Xist (for X-inactive specific transcript) The Xist gene is only expressed on the inactive X chromosome It does not encode a protein A gene designated TsiX also plays a role in chromosome choice It is located in the Xic region It is expressed only during early embryonic development It encodes an RNA complementary to Xist RNA Termed antisense RNA (where Xist RNA is the sense RNA) Tsix antisense RNA is believed to bind to Xist sense RNA and inhibit its function In other words, TsiX RNA prevents X chromosome inactivation A second region termed the X chromosome controlling element (Xce) affects the choice of the X chromosome to be inactivated A female heterozygous for different Xce alleles will have a skewed X-inactivation The X chromosome that carries a strong Xce allele is more likely to remain active than one with a weak Xce allele

At the cellular level, imprinting is an epigenetic process that can be divided into three stages

Establishment of the imprint during gametogenesis Maintenance of the imprint during embryogenesis and in the adult somatic cells Erasure and reestablishment of the imprint in the germ cells You erase and establish This is where it becomes sex specfic Epigenetic changes are not inherited → the live and die with the individual Spermatogenesis Marking during spermatogenesis and make it in the individual Adding methyl groups The child form has the marking of the dad and then you have a normal child Erasure and re establishment Oogenesis Only erasure

Water snail Lymnaea peregra

Example of maternal effect gene In this species, the shell and internal organs can be arranged in one of two directions Right-handed (dextral) Left-handed (sinistral) The snail's body plan curvature depends on the cleavage pattern of the egg immediately after fertilization Heterozygous female Dd (2n)→ D (n) and d(n) The mother is making gene products around the sinstral gene (d) containing egg The sperm also brings a d The genotype is dd but the phenotype is dextral → due to the maternal gene effect The F1 mothers are Dd → the dominant allele D caused ALL the F2 offspring to be dextral F2 mothers include 3 types DD or Dd mothers produce dextral offspring dd mothers produce sinistral offspring The phenotype of the progeny is determined by the mother's genotype NOT phenotype

Vegetative mutants

Have mutations in genes located in the mitochondrial genome Show a non-Mendelian pattern of inheritance two types Neutral Supressive

Segregational mutants

Have mutations in genes located in the nucleus Segregate in a Mendelian manner in meiosis Haploid dominant mutants/ nuclear mutants Equal concentrations of normal or mutant phenotypes

Human Mitochondrial Diseases

Human mtDNA is transmitted from mother to offspring via the cytoplasm of the egg the transmission of human mitochondrial diseases follows a strict maternal inheritance pattern Several human mitochondrial diseases have been discovered chronic ****degenerative disorders affecting the brain, heart, muscles, kidneys and endocrine glands Hearing, muscular, seeing defects → come from the mother's mitochondrial genes Example: Leber's hereditary optic neuropathy (LHON) Affects the optic nerve - degeneration - retinal ganglion cells and their axons May lead to progressive loss of vision in one or both eyes LHON is caused by one of several mutations in different mitochondrial genes (1-3)

AS is characterized by

Hyperactivity Unusual seizures Repetitive symmetrical muscle movements Mental deficiencies

The discovery of the barr body

In 1949, Murray Barr and Ewart Bertram identified a highly condensed structure in the interphase nuclei of somatic cells in female cats but not in male cats = Barr body Ohno - suggested Barr Body could be a condensed X chromosome The mechanism of X inactivation = the Lyon hypothesis (XCI) Wanted to explain the condensed X chromosome a white and black variegated coat color found in certain strains of mice a white and black variegated coat color found in certain strains of mice A female mouse has inherited two X chromosomes One from its mother that carries an allele conferring white coat color (Xb) One from its father that carries an allele conferring black coat color (XB) The epithelial cells derived from this embryonic cell (lower case b) will produce a patch of white fur The cells derived from B will produce a patch of black fur

Heterodisomy

In meiosis 1 there is nondisjunction and the homologs don't separate Therefore after meiosis 2 the chromosomes have a copy of the maternal and paternal homologs when they should only have 1

Patterns of inheritance that deviate from a Mendelian pattern

Maternal effect Epigenetic inheritance Involve genes in the nucleus Extranuclear inheritance Involves genes in organelles other than the nucleus Mitochondria Chloroplasts

Oogenesis in females

Maturing animal oocytes are surrounded by maternal cells that provide them with nutrients These nurse cells are diploid, whereas the oocyte becomes haploid

Imprinting vs haploinsuffiency

Monoallelic is normal for imprinted genes BUT for haploinsufficiency you need another copy of the functional gene

The Petite Trait in Yeast

Mutations that yield defective mitochondria are expected to make cells grow much more slowly Saccharomyces cerevisiae mutants - petites they formed small colonies on agar plates Wild-type strains formed larger colonies Two mutants Segregational Vegetative

Isodisomy

Nondisjunction in meiosis 2 so the sister chromatids don't separate

Heteroplasmy

Presence of both normal and mutated mtDNA, resulting in variable expression in mitochondrial inherited disease The offspring can be green, white or green and white patches Based on the pattern of segregation of the chloroplasts in the G2 phase of mitosis happens randomly A fertilized egg inherited two types of chloroplast Green and white As the plant grows, the chloroplasts are irregularly distributed to daughter cells

PWS is characterized by

Reduced motor function Obesity Mental deficiencies

facultative heterochromatin

Regions that can interconvert between euchromatin and heterochromatin

Why H19 is paternally imprinted

Sequence: Differentially methylated region → IGF2 → imprinting control region → H19 → enhancer sequence Enhancers = given to DNA sequences that bind to activator proteins Proteins binding to the enhancer will upregulate transcription DMR = one of the regions involved in imprinting mechanisms ICR = one of the regions involved in imprinting mechanisms In either ICR or DMR You will have huge sequences of cytosine and thymine bonded by phosphodiester bonds Protein that binds to these sites = CTC binding factor 2 CTC binding factors on DMR and ICR → when you have two it will cause your DNA to turn and loop MOTHER The loop causes igf2 to be hidden and then no methylated region → so the activator can not induce transcription of igf2 There is no methylated factors which means that any protein that binds to the enhancer will induce transcription and translation of h19 will occur H19 = a tumor suppressor gene → we don't have a phenotype associated with it so we call it → the mother does not have the igf2 FATHER Dad is methylated but still not expressing igf2 (because it doesn't always express) 5th carbons of the CTC binding in DMR and ICR are methylated If there is methylation CTC binding factor can not bind When you compact the euchromatic regions they become heterochromatic NO CTC Binding factor is binding BUT the methylation on the DMR and ICR and is going to induce compaction of h19 Because h19 cant be activated because it is compacted so the enhancer gene is going to activate igf2 transcription instead This means that h19 is the actual gene that is PATERNALLY IMPRINTED = because it is silenced in the father which is the definition of imprinting

IGF-2

The imprint mechanism is methylation! Works only from the dads chromosome Normal from the dad x Mutated from the mom = Carrier which produces the normal phenotype Mutant from the dad x normal from the mom = mutated because of the sex specfic gene First step is removing the methylation in spermatogenesis Female mouse: The dad's Igf2 has methylation from the dad and her mom has given her the one that is not methylated Male mouse: The dad's Igf2 has methylation from the dad and her mom has given her the one that is not methylated Erasure no reestablishment Next generation: Half of the pups will have the normal size and half will have the abnormal size → because the dad's igf2 is passing it on

Chlorplasts in extranuclear inheritance

The main function of chloroplasts is photosynthesis The genetic material in chloroplasts is referred to as cpDNA ***It is typically about 10 times larger than the mitochondrial genome of animal cells The cpDNA of tobacco plant consists of 156,000 bp It carries between 110 and 120 different genes rRNA and tRNA genes Many genes that are required for photosynthesis Many chloroplast proteins are encoded by genes in the nucleus These proteins contain chloroplast-targeting signals that direct them from the cytoplasm into the chloroplast Genes designated ORF open reading frame → encode polypeptides with unknown functions

Mitochandria in nuclear inheritance

The main function of mitochondria is oxidative phosphorylation A process used to generate ATP (adenosine triphosphate) ATP is used as an energy source to drive cellular reactions Central Dogma: the mom is going to pass on her mitochondria If you are comparing circular DNA of mitochondria and chloroplasts Mitochondria has a smaller genome than the chloroplasts The genetic material in mitochondria is referred to as mtDNA The human mtDNA consists of only 17,000 bp It carries relatively few genes rRNA and tRNA genes 13 genes that function in oxidative phosphorylation Note: Most mitochondrial proteins are encoded by genes in the nucleus These proteins are made in the cytoplasm, then transported into the mitochondria Only 3% of mitochondrial DNA is noncoding → very efficient compared to the rest of the sequences of our DNA

Paternal leakage

The paternal parent provides mitochondria through the sperm When the sperm is injecting its nucleus for fertilization mitochondria from the dad In the mouse, for example, 1-4 paternal mitochondria are inherited for every 100,000 maternal mitochondria per generation of offspring

Some genes on inactivated X are expressed in somatic cells of females

These genes escape the effects of X inactivation They include Xist Pseudoautosomal genes

The Pattern of Inheritance of Organelles

Varies among different species Heterogamous species Produce two kinds of gametes Female gamete → Large Provides most of the cytoplasm of the zygote Doesn't really move Male gamete Small Provides little more than a nucleus Very motile In these species, organelles are typically inherited from the mother Isogamous → algae and fungi because they can only have one type of gamete

Disomy

a condition where you inherit two copies of a chromosome from one parent

Genomic imprinting

a phenomenon in which expression of a gene depends on whether it is inherited from the male or the female parent Comes under epigenetic pattern of inheritance Imprinting = silencing!! "marking process with memory" → sex specific marking Starts during gametogenesis

which chromosome is AS and PWS involved with

a small deletion in chromosome 15 If it is inherited from the mother, it leads to AS If it is inherited from the father, it leads to PWS

The Lyon Hypothesis

an adult female who is heterozygous for the fast and slow G-6-PD alleles should express only one of the two alleles in any particular somatic cell and its descendants, but not both Take 0.1 microliters in a loop and you get a very thin concentration of starter cells Harvest the cells and run the gel electrophoresis You will get one or the other forms instead of both → DUE to random inactivation of one of the X's This kind of inheritance pattern is due to DOSAGE COMPENSATION

Morphogen

determines fate and phenotype of a group of cells through a concentration gradient across the developing region Compounds produced by certain genes that are going to change the phenotype and fate of the developing cells due to a concentration gradient in the embryonic development stage They follow maternal pattern of inheritance

Maternal effect genes...

encode RNA and proteins that play important roles in the early steps of embryogenesis For example Cell division → metaphase plate Cleavage pattern → meiosis different amounts in each haploid Body axis orientation → flies with different body types defective alleles in maternal gene effects tend to have a dramatic effect on the phenotype of the individual

Dosage compensation

females have two copies of X while males have just one In order to compensate for the singular copy of X we are going to convert one of our X chromosomes into an inactive form

Evalina the calico cat

gene modifer effect White color is due to another gene called the piebald because the piebald SS is dominant over black and orange S gene is super dominant = white If you have Ss and XOXO (orange) or XOXo(orange and black) or XoXo (black) you will get the other colors and white If you have ss and XOXO (orange) or XOXo(orange and black) or XoXo (black) then you will only get black or orange depending on the genotype The only time that male cats can be black and orange is if they have a disease --> an extra x chromosome

Imprinting and DNA Methylation

genomic imprinting is permanent in the somatic cells of an animal --the marking of alleles can be altered from generation to generation Methylation could enhance the binding of proteins that inhibit transcription AND OR INhibit the binding of proteins that enhance transcription

Maternal inheritance

inheriting an organelle from the mother and the genes of that organelle from the mother In plants they inherit the mitochondria and chloroplasts from the mother

Neutral mutation

it has no effect When wild type is crossed with = all wild type offspring Most of the genes are missing in the neutral so the whole becomes dominant

Maternal inheritance in the four-o'clock plant

pigmentation in Mirabilis jalapa (the four o'clock plant) shows a non-Mendelian pattern of inheritance Leaves could be green, white or variegated (with both green and white sectors) Incomplete dominance is the pattern of inheritance here the pigmentation of the offspring depended solely on the maternal parent and not at all on the paternal parent

Epigenetic Inheritance

refers to a pattern in which a modification occurs to a nuclear gene or chromosome that alters gene expression Epigenetic changes are caused by DNA and chromosomal modifications oogenesis, spermatogenesis or early embryonic development Example: dosage compensation and genomic imprinting

Maternal effect

refers to an inheritance pattern for certain nuclear genes in which the genotype of the mother directly determines the phenotype of her offspring The genotype of the father and offspring themselves do not affect the phenotype of the offspring This phenomenon is due to the accumulation of gene products that the mother provides to her developing eggs

extranuclear inheritance

refers to inheritance patterns involving genetic material outside the nucleus Mitochondria and chloroplasts In our cells we have hundreds to thousands of mitochondria and each have DNA regions These organelles are found in the cytoplasm cytoplasmic inheritance The genetic material of mitochondria and chloroplasts is located in a region called the nucleoid The genome is composed of a single circular chromosome containing double-stranded DNA Chloroplasts tend to have more nucleoids per organelle than mitochondria

Angelman Syndrome cause

results from lack of expression of a single gene UBE3A Ubiquitin protein ligase 3A (UBE3A)→ tags proteins and brings them to get degraded The gene is paternally imprinted (silenced) (uniparental disomy)

Praderwilli Syndrome cayse

results most likely from the lack of expression of a gene designated SNRNP and NDN (necdin) SNRNP encodes a small nuclear ribonucleoprotein polypeptide N which is a complex that controls gene splicing Splicing → complexes that are involved in removing the introns from the exon Necdin - growth suppressor of neurons in the brain THe gene is maternally imprinted (silenced (unimaternall disomy)

Suppressive mutation

suppresses the wild type When crossed with the wild type = all petite Small genome is easier to keep petite It has most of the DNA with a few missing spots so it is harder to suppress and then the petite becomes more prevalent

Barr bodies in X chromosome inactivation

the DNA becomes highly compacted They have to unwind and code for different things because there are certain genes that both X and Y which means that they are both making 50-50% The parts of the X chromosome that is compacted need to be unwound to express the genes → we have some genes that are common to X and Y that follow the pseudoautosomal pattern of inheritance