Non-Mendelian Inheritance Notes

Non-Mendelian Inheritance

Introduction

• Genes with a Mendelian inheritance pattern follow four rules:
  1. Offspring traits are directly influenced by gene expression.
  2. Genes are passed unchanged across generations (except for rare mutations).
  3. Genes follow Mendel’s law of segregation.
  4. With multiple genes, they follow Mendel’s law of independent assortment.

Deviations from Mendelian Patterns

• This chapter covers inheritance patterns that do not follow Mendelian rules:
  • Maternal effect: breaks rule 1
    • Involves nuclear genes.
    • Offspring's genotype does not directly determine phenotype as predicted by Mendel.
  • Epigenetic inheritance: breaks rule 2
    • Involves nuclear genes.
    • Genes are modified (e.g., methylation) during:
      • Gametogenesis - genomic imprinting.
      • Early embryonic development - dosage compensation (X-chromosome inactivation).
  • Extranuclear inheritance: breaks rule 3
    • Involves genes in organelles other than the nucleus.
      • Mitochondria.
      • Chloroplasts.
  • Linkage (Chapter 6): breaks rule 4
    • Involves nuclear genes.
    • Two or more genes are close on the same chromosome.

5.1 Maternal Effect

• Maternal effect: inheritance pattern where the female parent's genotype directly determines the offspring's phenotype.
  • The genotypes of the male parent and the offspring do not affect the offspring's phenotype.
  • This is due to the accumulation of gene products provided by the female parent to developing eggs.

Discovery of Maternal Effect Genes

• The first example was discovered in the 1920s by A. E. Boycott, studying the water snail, Limnaea peregra.
  • The snail's shell and internal organs can be arranged in two directions:
    • Right-handed (dextral).
    • Left-handed (sinistral).
  • The dextral orientation is more common and dominant.

Experiment Showing the Inheritance Pattern of Snail Coiling

• In the F1 generation:
  • Reciprocal crosses produce offspring with the same genotype but different phenotype.
• In the F2 generation:
  • A 3:1 phenotypic ratio would be predicted by a Mendelian pattern of inheritance.
  • The 3:1 phenotypic ratio shows up in the F3 generation.
• The phenotype of the offspring depended solely on the genotype of the mother, NOT her phenotype
  • DD or Dd mothers produce dextral offspring
  • dd mothers produce sinistral offspring
  • The genotypes of the father and offspring do not affect the phenotype of the offspring

Non-Mendelian Inheritance Pattern

• This non-Mendelian inheritance pattern can be explained by the process of oogenesis
  • Maturing animal oocytes are surrounded by maternal cells that provide them with nutrients
    • These nurse cells are diploid, whereas the oocyte becomes haploid
• The snail’s body plan curvature depends on the cleavage pattern of the egg immediately after fertilization
  • If a female is heterozygous for the snail-coiling maternal effect gene:
    • The haploid oocyte can receive either the D or d allele in meiosis

Mechanism of Maternal Effect in Snail Coiling

• Transfer of gene products from nurse cells to egg
  • The nurse cells express mRNA and/or protein from genes of the D allele (green) and the d allele (red) and transfer those products to the egg.
• D gene products cause egg cleavage that promotes a right-handed body plan.
• Recessive d gene products cause egg cleavage that promotes a left-handed body plan.
  • Even if the egg is fertilized by sperm carrying the dominant D allele, the sperm’s genotype is irrelevant because the expression of the sperm’s gene would be too late to change early embryonic development.

Coiling at the Cellular Level

• Remarkably, the orientation of the cleavage plane in the earliest stages of development carries through to the adult

5.2 Epigenetic Inheritance

• Epigenetic inheritance refers to a pattern in which a modification occurs to a nuclear gene or chromosome that alters gene expression
  • However, the expression is not permanently changed over the course of many generations
  • That is because the DNA sequence does not change
• Epigenetic changes are caused by DNA and chromosomal modifications
  • These can occur during oogenesis, spermatogenesis, or early embryonic development
• We will look at Dosage Compensation and Genomic Imprinting

Dosage Compensation

• The purpose of dosage compensation is to offset differences in the number of active sex chromosomes
• Dosage compensation has been studied extensively in mammals, Drosophila and Caenorhabditis elegans
• Depending on the species, dosage compensation occurs via different mechanisms

Mechanisms of Dosage Compensation Among Different Species

• Placental mammals (XX/XY): One of the X chromosomes in the somatic cells of females is inactivated.
  • In certain species, the X chromosome from the male parent is inactivated, and in other species, such as humans, either of the two X chromosomes is randomly inactivated throughout the somatic cells of females.
• Marsupial mammals (XX/XY): The X chromosome from the male parent is inactivated in the somatic cells of females.
• Drosophila melanogaster (XX/XY): The level of expression of genes on the X chromosome in males is doubled.
• Caenorhabditis elegans (XX*/X0): The level of expression of genes on each X chromosome in hermaphrodites is decreased to 50% of the level occurring on the X chromosome in males.
  • *In C. elegans, an XX individual is a hermaphrodite, not a female.

Dosage Compensation in Birds

• 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
• It appears that the Z chromosome in males does not undergo condensation and dosage compensation like one of the X chromosomes in female mammals. Some Z-linked genes may be dosage compensated.
• Different studies have shown variation in gene expression of some Z-linked genes in male and female birds ○ Example: Males express twice as much of an enzyme, aconitase, as females
  • May lack a general mechanism, but some compensation may occur on specific genes

Dosage Compensation in Mammals

• 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
  • This structure became known as the Barr body (Figure 5.3a)
• In 1960, Susumu Ohno correctly proposed that the Barr body is a highly condensed X chromosome
• In 1961, Mary Lyon proposed that dosage compensation in mammals occurs by the inactivation of a single X chromosome in females

Dosage Compensation in Mammals Occurs by Chromosome Condensation

• (left) a Barr body in a human nucleus after staining with a DNA-specific dye
• (right) the same nucleus stained with a yellow fluorescent probe that recognizes the X chromosome

Dosage Compensation-Chromosome Condensation

• The mechanism of X chromosome inactivation (XCI), also known as the Lyon hypothesis, is schematically illustrated in Figure 5.4
• Example: A white and black variegated coat color found in certain strains of mice

Dosage Compensation-Chromosome Condensation

• A female mouse has inherited two X chromosomes:
  • One from its mother that carries an allele conferring white coat color ($X^b$)
  • One from its father that carries an allele conferring black coat color ($X^B$)

The Mechanism of X-chromosome Inactivation

• Random X inactivation occurs early in development.

The Mechanism of X-chromosome Inactivation

• During X chromosome inactivation, the DNA becomes highly compacted
  • Most genes on the inactivated X cannot be expressed
• When this inactivated X is replicated during cell division-
  • Both copies remain highly compacted and inactive
  • X inactivation is passed along to all future somatic cells

The Lyon Hypothesis Put to the Test Experiment 5A

• In 1963, Ronald Davidson, Harold Nitowsky and Barton Childs set out to test the Lyon hypothesis at the cellular level
• To do so they analyzed the expression of a human X-linked gene
  • The gene encodes glucose-6-phosphate dehydrogenase (G-6-PD), an enzyme used in sugar metabolism

Individuals Vary with Regard to the G-6-PD Enzyme

• This variation can be detected when the enzyme is subjected to gel electrophoresis
  • One G-6-PD allele encodes an enzyme that migrates very quickly
    • The “fast” enzyme
  • Another allele encodes an enzyme that migrates more slowly
    • The “slow” enzyme
• The two types of enzymes have minor differences in their structures
  • These do not significantly affect G-6-PD function

Individuals Vary with Regard to the G-6-PD Enzyme

• Heterozygous adult females produce both types of enzymes
• Hemizygous males produce either the fast or the slow type

The Hypothesis

• According to 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
• Testing the hypothesis

Figure 5.6

1. Mince the tissue to separate the individual cells.
2. Grow the cells in a liquid growth medium and then plate (sparsely) onto solid growth medium. Each cell divides to form a clone of many cells.
3. Take nine isolated clones and grow in liquid cultures. (Only three are shown here.)
4. Take cells from the liquid cultures, lyse cells to obtain proteins, and subject to gel electrophoresis. (This technique is described in the Appendix.)

The Data

• Adapted from Ronald G. Davidson, Harold M. Nitowsky, and Barton Childs (1963) Demonstration of two populations of cells in the human female heterozygous for glucose-6-phosphate dehydrogenase variants, PNAS, 50(3): 481–485, Fig. 2.

Interpreting the Data

• All nine clones expressed one of the two types of G-6-PD enzyme, not both.
• Clones 2, 3, 5, 6, 9 & 10 expressed only the slow type
• Clones 4, 7 & 8 expressed only the fast type.

Interpreting the Data

• These results are consistent with the hypothesis that
  • X inactivation has already occurred in any given epithelial cell AND
  • This pattern of inactivation is passed to all of the cell’s progeny

Mammalian Cells Allow a Single X to Remain Active

• Researchers have found that mammalian cells can count their X chromosomes and allow only one of them to remain active
  • Additional X chromosomes are converted to Barr bodies
• Phenotype Sex Chromosome Composition Number of Barr bodies
• Normal female XX 1
• Normal male XY 0
• Turner syndrome (female) X0 0
• Triple X syndrome (female) XXX 2
• Klinefelter syndrome (male) XXY 1

X-chromosome Inactivation

• X-chromosome inactivation in mammals depends on the X-inactivation center and Xist
• The genetic control of inactivation is not entirely understood at the molecular level
• However, 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
• This process will be further explained in Chapter 16

The Function of the Xic during X-chromosome Inactivation

• Nucleation: Occurs during embryonic development. The number of X-inactivation centers (Xics) is counted and one of the X chromosomes remains active and the other is targeted for inactivation.
• Spreading: Occurs during embryonic development. It begins at the Xic and progresses toward both ends until the entire chromosomes is inactivated and becomes a Barr body.
• Maintenance: Occurs from embryonic development through adult life. The inactivated X chromosomes is maintained as such during subsequent cell divisions.

Choosing an X chromosome for inactivation

• Occurs during embryonic development.
• The number of X-inactivation centers (Xics) is counted and one of the X chromosomes remains active and the other is targeted for inactivation.
• The Xist gene on the chosen X chromosome is expressed, and some Xist RNA binds to the Xic to create a nucleation site.
• Spreading: Occurs during embryonic development. It begins at the Xic and progresses toward both ends until the entire chromosome is inactivated and becomes a Barr body.
• Maintenance: Occurs from embryonic development through adult life. The inactivated X chromosome is maintained as such during subsequent cell divisions.

Some Genes May Escape Inactivation

• Some genes on the inactivated X chromosome are expressed in the somatic cells of adult female mammals
  • Pseudoautosomal genes
• Dosage compensation in this case is unnecessary because these genes are located on both the X and Y chromosomes
• Up to a quarter of X-linked genes in humans may escape full inactivation
  • The mechanism is not understood
  • May involve loosening of chromatin in specific regions

5.3 Genomic Imprinting

• Genomic imprinting is a phenomenon in which a segment of DNA is marked and the effect is maintained throughout the life of the organism inheriting the marked DNA
• Depending on how the genes are “marked”, the offspring expresses either the maternally-inherited or the paternally-inherited allele
  • Not both
  • This is termed monoallelic expression

Mouse Igf2 Gene as an Example of Genomic Imprinting

• The Igf2 gene codes a growth hormone called insulin-like growth factor 2
  • A functional Igf2 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
  • Igf2 is a loss-of-function allele that does not express a functional Igf2 protein
  • This may cause a mouse to be small size depending on whether it inherits the mutant allele from its male or female parent

An example of genomic imprinting in the mouse

• Reciprocal cross: Offspring genotypes are identical; phenotypes different

Stages of Imprinting 1

• At the cellular level, imprinting is an epigenetic process that can be divided into three stages:
  1. Establishment of the imprint during gametogenesis
  2. Maintenance of the imprint during embryogenesis and in the adult somatic cells
  3. Erasure and reestablishment of the imprint in the germ cells

Genomic imprinting during gametogenesis

• Establishment of the imprint
  • In this example, imprinting of the Igf2 gene occurs during gametogenesis. The sperm carries the Igf2 allele and the egg carries the lgf2 allele. Only the paternal allele will be expressed in offspring.
• Maintenance of the imprint
  • After fertilization, the imprint pattern is maintained throughout development. In this example, the maternal Igf2-allele will not be expressed in the somatic cells. Note that the offspring on the left is a female and the one on the right is a male; both are normal in size.
• Erasure and reestablishment
  • In the germ-line cells, the imprint is erased. The female mouse produces eggs in which the gene is silenced. The male produces sperm in which the gene can be transcribed into mRNA.

Stages of Imprinting 2

• Establishment of the imprint
  • In this example, imprinting occurs during gametogenesis in the lgf2 gene, which exists in the lgf2 allele from the male and the Igf2- allele from the female. This imprinting occurs so that only the paternal allele is expressed.
• Maintenance of the imprint
  • After fertilization, the imprint pattern is maintained throughout development. In this example, the maternal Igf2- allele will not be expressed in somatic cells.
  • Note that the offspring on the left is a female and the one on the right is a male; both are normal in size.

Stages of Imprinting 3

• Erasure and reestablishment
  • In the germ-line cells, the Imprint is erased. The female mouse produces eggs in which the gene is silenced. The male produces sperm in which the gene can be transcribed into mRNA.

Genomic Imprinting Occurs in Several Species

• Genomic imprinting occurs in several species including insects, mammals and flowering plants
  • It may involve
    • A single gene
    • A part of a chromosome
    • An entire chromosome
    • Even all the chromosomes from one parent
  • It can be used for X inactivation in some species

Imprinting and DNA Methylation

• Genomic imprinting must involve a marking process
• At the molecular level, the imprinting of several genes is known to involve an imprinting control region (ICR) located near the imprinted gene
  • The ICR is methylated either in the oocyte or sperm
    • Not both
  • The ICR contains binding sites for one or more transcription factors that regulate the imprinted gene
  • For most genes, methylation causes inhibition of transcription

Pattern of Methylation

• In figure 5.10, each parent inherits one methylated and one unmethylated gene, which is maintained in somatic cells.
• Methylation is removed in gamete forming cells

The pattern of methylation from one generation to the next

• Maintenance methylation occurs in all somatic cells.
• Erasure (demethylation)
• De novo methylation
• Formation of gametes

Imprinting in Human Disease 1

• Prader-Willi syndrome (PWS)
  • PWS is characterized by:
    • Reduced motor function
    • Obesity
    • Small hands and feet
• Angelman syndrome (AS)
  • AS is characterized by:
    • Hyperactivity and thinness
    • Unusual seizures
    • Repetitive symmetrical muscle movements
    • Cognitive impairment

Imprinting in Human Disease 2

• Most commonly, PWS and AS involve a small deletion in chromosome 15
  • If it is inherited from the male parent, it leads to PWS
  • If it is inherited from the female parent, it leads to AS

Imprinted Genes Cause AS or PWS 1

• Researchers have discovered that this region contains closely linked but distinct genes
  • These are maternally or paternally imprinted
• AS results from the lack of expression of a single gene, UBE3A
  • UBE3A codes a protein that regulates protein degradation
  • The paternal copy is silenced

Imprinted Genes Cause AS or PWS 2

• PWS appears to result from the lack of expression of several genes:
  • SNRNP codes a small nuclear ribonucleoprotein polypeptide N which is part of a complex that controls gene splicing
  • NDN codes a protein that functions as a growth suppressor for neurons
  • A cluster of genes that code snoRNAs
  • The maternal copy of each of these genes is silenced

The role of imprinting in the development of Angelman or Prader-Willi syndrome