Epigenetic and development

ByNadia HassanSarrah Elnour

Hamadnalla MahmoudOmer Elkarouri

Prenatal Developments

• Hundreds of millions of sperm cells are deposited in vagina during sexual intercourse.• At the end one sperm fertilizes the ova.• The embryo forms: Endoderm – lining of the gut. Mesoderm – muscle, bone and blood. Ectoderm – nerves and skin.

Differentiation

•Every cell in the adult body has the same DNA, but different types of cells have different patterns of activity.• Only those stretches of DNA relevant to the cell’s role are translated into proteins.• Only part of the genetic information of the whole is active in any cell.

Regulation Of Transcription

•Trans-acting product;

Usually protein e.g Transcription factor.

•Cis-acting sequences;

Usually sites in DNA

The interaction between these sequences regulate

the activity of the genes.

• Specific combination of transcription factors( Tran acting) leads to activation or repression of a particular cis-regulatory module, and not just the action of a single gene.

Epigenetic• Mendelian Genetics: The study of heritable changes in phenotype caused by

mutations in genes (DNA sequence)

• Epigenetics: describes the ability of different states, which may have

different phenotypic consequences ,to be inherited without any change in the sequence of DNA.“ Russo, Martienssen, and Riggs 1996’’.

• The sum of all those mechanisms is necessary for the unfolding of the genetic programme for development" Robin Holliday 2006”.

• Therefore, Epigenetic mechanism is crucial for developments .

• However, cells “remember” their epigenetic state during multiple cell divisions.

Comparison between geneticand epigenetic phenomena

GENOTYPE PHENOTYPE

Mendelian Mutation Mutant

Epigenetic Wildtype Mutant

Epigenetic landscape:• Waddington's epigenetic landscape is a metaphor for how

gene regulation modulates development. One is asked to imagine a number of marbles rolling down a hill towards a wall.

• The marbles will compete for the grooves on the slope, and come to rest at the lowest points. These points represent the eventual cell fates, that is, tissue types. This idea was actually based on experiment: Waddington found that one effect of mutation (which could modulate the epigenetic landscape was) was to affect how cells differentiated.

C. H. Waddington’s original depiction of the “Epigenetic Landscape”

•He also showed how mutation could affect the landscape and used this metaphor in his discussions on evolution - he was the first person to emphasis that evolution mainly occurred through mutations that affected developmental anatomy.

• Three different epigenetic mechanisms:

1. DNA methylation.2. Polycomb- trithorax.3. Histone modification.

DNA methylation;• An epigenetic mechanism in which chromatin is organised

into inactive closed , transcriptionally statesThe polycomb_ trithorax; The polycomb group of repressor and trithorax group of

activators maintain the correct expression of several key developmental regulators by changing the structures of chromatin into closed(inactively transcribed) or open (actively transcribed) conformation.

Histone modification;• Responsible for perpetuating expression states at specific

genomic location.

DNA Methylation

Donor: S-adenosyl-methionine; Reaction: transfer of methyl group to position 5

of the cytosine ring.

• 60% of human genes transcribed from CG rich promoters (CpG rich islands) mostly unmethylated signifying transcriptional activity.

• Methylation is usually associated with inactivation of gene

• in mammals methylated CpG dinucleotides occurs In repetitive elements or Regions of low CpG density.

• Tissue-specific patterns of CpG methylation are established during development.

DNA Methylation

Genomic imprinting

Tissue and developmental specific gene

regulation

X chromosome inactivation

Genomic Imprinting

• Genes are biallelic because both father and mother normally contribute one allele each.

• Both the paternal and maternal alleles of biallelic genes are expressed, unless one or both copies have sustained mutations which affect expression.

• However, in humans and other mammals, several biallelic genes are known where the expression of one parental allele, either the paternal or the maternal allele but not both, is normally repressed in some cells (allelic exclusion).

• Monoallelic expression

Allelic exclusion

According to parental

origin•Imprinting

Random •Xinactivation

Imprinting• Genomic imprinting involves differences in the expression of

alleles according to parent of origin

• IGF2 and H19 genes

• IGF2 that is inherited from the father is expressed but not the mother one

• H19 expresses in the maternal chromosome

H19 &IGF2

DNA methylation and developments

• Two type of methylation:1. Denovo methylation 2. Maintainance methylation• Carried out by Dnmt1 methyltransferase• Perpetuation of a pre existing methylation • Ensure that the methylation patterns in individual somatic

cells are quite stable

Cont……….• However, during development there are dramatic changes in

methylation constituting epigenetic reprogramming

• Reprogramming in germ cells• sperms, ova

• Reprogramming in the early embryo

Spermatogenesis

Cont……

• The pattern of methylation of germs cells is established in each sex during gametogenesis by two stages process:

• Existing pattern is erased by a genome wide demethylation

• Pattern specific for each sex is imposed

Changes in DNA methylation during mammalian development

Cont……

• Hypothetical locus in mouse• Paternal allele is nonmethylated and active • Maternal allele is methylated and inactive

• What happens when this mouse itself forms gametes?

Paternal allele is activeMaternal allele is inactive

Male •Allele contributed to the sperm must be non methylated•Irrespective of whether it was originally mathylated or not•Maternal allele find itself in a sperm must be demethylated

Female •Allele contributed to the egg must be methylated•Paternal allele find itself in an egg it must be methylated

Life Cycle of ImprintsThe germ line has the role of resetting imprints such that in

mature gametes they reflect the sex of that germ line.

• Establishment: during the development of germ cells into sperm or eggs.

• Maintenance: after fertilization as chromosomes duplicate and segregate in the developing organism.

• Erasure: in early germ cell development. • Re-establishment: in late germ cell development. In somatic cells imprints are maintained and modified during

development

Regulatory effect of DNA methylation in mammalian development

• 1975: Riggs, Holliday+Pugh• Prediction: programmed methylation and

demethylation of DNA might regulate expression during mammalian development

• This reprogramming is likely required for totipotency of the newly formed embryo and erasure of acquired epigenetic changes.

• It begins with a diploid cell,an oogonium.Each oogonium grows,accumulates cytoplasm,and replicates its DNA becoming a primary oocyte.

OOGENESIS(OVUM FORMATION)

Meiosis

• In meiosis I, the primary oocyte divides into two cells.a small cell with very little cytoplasm. called a first polar body, a much larger cell called a secondary oocyte. Each cell is haploid, with the chromosomes in replicated form.

• In meiosis II, the tiny first polar body may divide to yield two polar bodies of equal size, with unreplicated chromosomes; or it may simply decompose.

• The secondary oocyte, however divides unequally in meiosis II to produce another small polar body, with unreplicated chromosomes, and the mature ovum, which contains a large volume of cytoplasm.

• The secondary oocyte ,however divides unequally in meiosis II to produce another small polar body, with unreplicated chromosomes an the mature ovum, which contains a large volume of cytoplasm.

• A female ovulates about 400 oocytes between puperty and menopause.

• The woman s body absorbs the polar bodies.Rarely a sperm fertilizes a polar body,result to a disorganized clum of cells that is not an embryo grows for a few weeks and then leave the woman s body.This event a type of miscarriage called a belighted ovum.

Growth of Oocytes

•Oocytes use special mechanisms to grow to their large size .One simple strategy for rapid growth is to have extra gene copies in the cell.

•Thus ,the oocyte delays completion of the first meiotic division so as to grow while it contains the diploid chromosome set in duplicate.In this way ,it has twice as much DNA available for RNA synthesis as does average somatic cell in the G1 phase of the cell cycle.

• Oocytes may also depend partly on the synthetic activities of other cells for their growth. Yolk for example .is usually synthesized outside ovary and imported into the oocyte.

• Nutritive help can also come from neighboring accessory cells in the ovary.T hese can be of two types:

1. In Some invertebrate some of the progeny of the oogonia become nurse cells instead of becoming oocytes. These cells usually are connected to the oocyte by cytoplasmic bridges through which macromolecules can pass directly into the oocyte cytoplasm.

2. Ordinary somatic cells, called follicle cells, which are connected to acolytes by gap junctions, which permit the exchange of macromolecules, but not macromolecules.

3. Follicle cells, also secrete macromolecules that contribute to the egg coat, or act on egg-surface receptors to control the spatial patterning and axial asymmetries of the egg.

• Current concepts regarding the birth,survival,growth of oocytes that depends on: Complex patterns of cell communication

• between germline and soma.The notion of maternal inheritance”from a genetic and epigenetic perpective”.The relative value of model systems with reference to current calinincal and biotechnology applications.

FERTILIZATION

Changes in DNA methylation during mammalian development

FERTILIZATION• Reprogramming refers to erasure and remodeling of

epigenetic marks, such as DNA methylation, during mammalian development.

• After fertilization some cells of the newly formed embryo migrate to the germinal ridge and will eventually become the germ cells (sperm and oocytes).

• Due to the phenomenon of genomic imprinting, maternal and paternal genomes are differentially marked and must be properly reprogrammed every time they pass through the germline.

• Therefore, during the process of gametogenesis the primordial germ cells must have their original biparental DNA methylation patterns erased and re-established based on the sex of the transmitting parent.

• After fertilization the paternal and maternal genomes are once again demethylated and remethylated (except for differentially methylated regions associated with imprinted genes).

• This reprogramming is likely required for potency of the newly formed embryo and erasure of acquired epigenetic changes.

• The genome of the fertilized oocyte is an aggregate of the sperm and egg genomes and so it and the very early embryo are substantially methylated with methylation difference at paternal and maternal alleles of many genes.

• later on, at the morula and early blastula stage in the pre-implantation embryo, genome wide demethylation occurs.

• later still ate the pre-gastrulation stage, widespreaded de novo methylation is carried out. However the extent of this methylation varies in different cell linage: A. trophoblast-drived linage are undermethylated.B. somatic cell linage is heavily methylated.C. early primordial cells are spared (unmethylated mostly)

Imprinting in the placenta

• It is thought that genomic imprinting may play a critical role in placental biology and alterations to these imprints have been linked to severe placenta pathologies. At the same time, less well characterized are the role that imprinting alterations may play in more common, placental-related pathologies including intrauterine growth restriction and pre-eclampsia.

• Guo et al. have investigated gene expression and methylation patterns of imprinted regions in small for gestational age (SGA) placentas and have shown that loss of imprinting at H19 because of methylation alterations and subsequent effects on gene expression may be some causes of poor growth of the human fetus.

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

• The mechanism of X inactivation is also known as the Lyon hypothesis

• The example involves a white and black variegated coat color found in certain strains of mice

• A female mouse has inherited two X chromosomes1. One from its mother that carries an allele conferring white

coat color (Xb)2. One from its father that carries an allele conferring black coat

color (XB)

• X chromosome inactivation– Both coat color alleles are

originally active– One X chromosome is randomly

inactivated in each cell during early embryonic development

– X inactivation is passed along to all future somatic cells during cell division

– Patches of cells with different coloration result

• 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

• In a similar fashion, X inactivation is passed along to all future somatic cells.

• There is different mechanisms of dosage compensation among different species as seen in the coming table

Epigenetics and Links to DiseasePrader Willi Syndrome & Angelman Syndrome• Both map to 15q11 (band 11 of the long arm of chromosome

15).This region is differently imprinted in maternal and paternal chromosomes; both imprintings are needed for normal development.

• An individual may fail to inherit a properly imprinted 15q11 from one parent, as a result either of deletion of the 15q11 region from that parent's chromosome 15 or, less frequently, of uniparental disomy.

• If neither copy of 15q11 has paternal imprinting, the result is Prader-Willi syndrome (characterized by hypotonia, obesity, and hypogonadism).

• If neither copy has maternal imprinting, the result is Angelman syndrome (characterized by epilepsy, tremors, and a perpetually smiling facial expression).

lupus-like symptoms in mice :• Epigenetic immune system effects occur, and can be reversed,

according to research published in the November– December 2005 issue of the Journal of Proteome Research by Nilamadhab Mishra, an assistant professor of rheumatology at the Wake Forest University School of Medicine, and his colleagues.

• The team says it’s the first to establish a specific link between aberrant histone modification and mechanisms underlying lupus-like symptoms in mice, and they confirmed that a drug in the research stage, trichostatin A, could reverse the modifications. The drug appears to reset the aberrant histone modification by correcting hypoacetylation at two histone sites.

lung adenocarcinoma:• Accumulating evidence suggests that deregulation of imprinted

genes, including loss of imprinting (LOI), plays a role in oncogenesis.

• Kohda et al. 2001. investigated allelic expression of six imprinted genes in human lung adenocarcinomas as well as in matched normal lung tissue. LOI of the insulin-like growth factor 2 gene (IGF2) and mesoderm-specific transcript (MEST) was noted in 47% and 85% of informative cases, respectively.

• Monoallelic expression was maintained in all the matched normal tissues examined. These findings indicated that independent deregulation took place in imprinted genes and suggested that aberrant imprinting of IGF2 and MEST was involved in the development of lung adenocarcinoma.