Epigenetic phenomena Epigenetics refers to genetic inheritance that is not coded by the DNA sequence It includes changes in gene expression due to modification of DNA or change in its chromatin state (facultative heterochromatin) Lecture will illustrate this with various examples

X chromosome inactivation In female mammals with 2 X chromosomes, one X is inactivated, i.e. all its genes are switched off, and it forms the Barr body This is to prevent a double dose of X-chromosome gene products relative to that in male cells Which of the 2 X chromosomes is inactive in a cell line, is usually randomly determined early in development

The calico cat The calico cat is an example of X-chromosome inactivation She is heterozygous for a gene on the X, one allele gives orange fur, the other black Random X-inactivation in cells early in development gives patches with either the orange or black allele active White patches are due to an autosomal gene, “spotting”

Consequences of X inactivation: the calico cat

Muscular dystrophy in girls Duchenne muscular dystrophy (DMD) is an X-linked recessive disease, usually only affects boys The karyotype of girls with DMD sometimes shows an X:autosome translocation In this case, X-inactivation is not random - the normal X is always inactivated, because the translocation interferes with the inactivation process Therefore, the normal DMD gene is switched off, and the other one is disrupted by the translocation So these girls show the symptoms of DMD

Genomic imprinting Usually it does not make any difference from which parent you got a particular gene But with some genes it does matter - this is called genomic (or genetic) imprinting Example: Prader-Willi syndrome (PWS): small stature, obesity, learning difficulties Angelman syndrome (AS): epilepsy, learning difficulties, unsteady gait, “happy” appearance PWS often caused by deletion of a gene “SNRPN” on paternal chromosome 15 AS often caused by deletion of the same gene, but the maternally-derived one Therefore the gene must be expressed differently depending on which parent it came from

Father’s imprint on his daughter’s thinking? Why are boys more likely to have autism (and other disorders of social function) than girls? Turner’s syndrome (45XO) girls are of normal intelligence but often have social function problems Their single X can be either maternal or paternal in origin The ones with a maternal X are much more likely to have the social problems All boys have a maternally-derived X So, there could be imprinted gene(s) on the X, which are involved in social function When maternally inherited this could might contribute to disorders such as autism

Mechanism of imprinting The mechanisms of X-inactivation and imprinting are not fully understood but both involve DNA methylation DNA can be reversibly methylated on C bases - fig 11.22 in Hartl Methylation of a gene’s promoter tends to switch it off, due to binding of a specific protein to methylated DNA

Determination of methylation HpaII m m CCGG GGCC CCGG GGCC CCGG GGCC m m MspI

Gel electrophoresis of fragments MspI HpaII 1 2 3 4 1 5 Methylated sites which are not present in HpaII digest Non-methylated site

Is methylation state related to gene activity? Many sites within a genes are methylated some sites only in certain tissues others in all tissues A minority of sites are methylated in tissues in which the gene is not expressed, but are unmethylated in tissues in which the gene is active Experiments suggest that these sites are important regulators of gene activity

Position-effect variegation (PEV) State of chromatin (euchromatin, heterochromatin) can affect gene expression A gene could be moved to a heterochromatic region by an inversion Heterochromatin’s structure tends to switch off gene expression

An example of PEV A mutant allele of the w gene in Drosophila causes eyes to be white (wild-type is red) An inversion of part of the X chromosome causes eyes to have red and white patches (fig 7.36 in Hartl) This is because of PEV switching off w gene in some cell lines in the eye The boundary between heterochromatin and euchromatin is not exactly the same in all cell lines, hence eyes are mosaic

Summary - epigenetic gene regulation Both mammalian X inactivation and Drosophila position effect variegation are examples of epigenetic gene regulation. The repressed state caused by the chromatin rearrangement is heritable, but importantly the decision to induce the repressed state is not encoded by the genome.