9. Genomic imprinting - Lecture notes 9 PDF

Preview

Summary

Lecture notes from Genetics, Year 2020/21....

Description

GENOMIC IMPRINTING Genomic imprinting is an epigenetic phenomenon that causes genes to be expressed in a parent-of-origin-specific manner. Genes, however, can also be partially imprinted. Genome-wide imprinting defects- Necessity for biparental contribution. In the experiment they used a normal embryo after fertilization by a injection and then 2 types of embryos with same quantity of DNA. The first one has 2 maternal copies of the egg and we see that the growth is smaller but there is hardly any placenta. In the second one, they insert 2 sperms with the paternal copies, we see a smaller embryo and a huge placenta. This indicates that genes coming from the mother are essential for the development of the embryo, and the genes from the father for the development of the placenta.

Complete hydatidiform mole, 46, XX of paternal origin: Fertilization of enucleated oocyte by haploid sperm which duplicates or fertilization of enucleated oocyte by two sperms. This could happen (not often) in two different ways.

Ovarian Teratoma (or dermoid cyst), 46, XX of maternal origin: Parthenogenetic conceptus. 1. Epigenetic inheritance and genomic imprinting. That suggests that somewhere in the genome there are genes that are expressed either maternal or paternal origin. Imprinting: The remarkable feature of imprinted genes is that both active and inactive alleles coexist in the same cell resulting in parental of origin monoallelic expression.

The imprinted allele is the silent one. Maternally imprinted = Paternally expressed Paternally imprinted = Maternally expressed

The allele-specific expression is regulated by various epigenetic mechanisms that differentially mark the parental alleles. -

Differential DNA methylation of promoters.

If we take a look at the RNA, and we could see that the gene has to come from the paternal allele.

Question: In the above example, we know the region is imprinted because one allele is methylated. Imprinting is just utilising all of the mechanisms in the active where you have all of your open chromatin and all of the histone marks to go with the unmethylated CpG islands. In the repressed chromosome we will have all of the repressive chromatins compact. Somehow the cell is recognising the 2 different chromosomes and marking them completely differently within the same nuclear environment. We can observe this in a molecular level, with a specific antibody that recognise them.

Other important fact about imprinted genes expression. -

-

-

The monoallelic expression ca be tissue-specific: Maternal expression of UBE3A is only observed in neurons but is biallelically expressed in all other tissues, whereas in maternal expression of TFPI2 is restricted to the placenta, one of the only tissues expressing the gene. Imprinting is highly conserved between mammalian species: Approx. 50% of imprinted genes are conserved between human and mouse. Imprinted genes often cluster together: A single

ICR/DMR can influence the allelic expression, often several 100 kb away. (Maternal gene influences all the surrounding genes).

2. Historical background. The 1st imprinted gene was found by accident! -

-

Johnson 1974: The hairpin-tail allele (Thp) presents with a phenotype in heterozygous offspring depending on parental transmission. Surani et al. 1984: Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Cattanach and Kirk 1985: Generated mice with sub-chromosomal maternal duplications/paternal deficiencies (and the reciprocals) for most mouse chromosomes highlighting opposing phenotypes. De Chiara et al. 1990: Igf2 imprinting: heterozygous mice inheriting paternal deletions were small with phenotype same as homozygous null. Heterozygous mice inheriting maternal deletions were normal.

3. The life cycle of genomic imprinting. The copies of maternal and paternal in genomics are basically opposite, so within the nucleus one is active and the other is inactive (euchromatin and heterochromatin), and obviously if it is in the same nuclear environment is impossible for the cell to detect this. Imprinting is stablished in the germline, so the DNA methylation (maternal in this example) will be maintained after fertilisation. The gametes are already methylated before fertilisation, but after it, we obtain a differentially methylated region. (Which is important because up until 15 years ago we did not have the molecular techniques that analyse methylation in sperm and eggs, because a lot of DNA was needed). A lab did an experiment 10 years ago which shows that there are thousands of differences between a sperm and an egg, they have completely different epigenetic profiles. During the first days of life, the gametes are completely different, but after 5 days the cell has to be completely to differentiate (stem cells). To have this potential, it has had to eras all the memories of being an egg/sperm, its epigenetic blackboard should be completely blank. That process is what we call epigenetic programming, and it happens in every embryo. As we can see in the example, the blue line representing the dad’s methylation is decreased rapidly, due to Tet3 enzyme. Whereas, if we look at the purple one, the process is different which is a much slower profile, it takes approx. 4-5 days as it is not an active process, it is diluted by replication (every time the cell replicates, it will have half of its methylation, until getting to the point there is almost no methylation).

So, is imprinting heritable? The only exception are the regions in green which are protected from imprinting by 2 proteins, so yes, it is heritable. The imprints surviving the reprogramming in the blastocyst, are the ones that will pass to the embryo and then maintained in the adult. In the developing embryo, even the imprints that are protected during pre-implantation reprogramming are actually erased in the primordial germline cell, and that is because they have to be adjusted to the gender of that embryo. So, if it is a female, then the maternal copies will be methylated. (Only a small group of cells go through this process). Also, male and female has different timings, and it has more implications. gDMRs- germlines

Question: Genomic imprints are unique because they are methylated in one gamete and this methylation survives epigenetic reprogramming. 4. Why imprint? What is the advantage of being functional hemizygous? Imprinting may exist because of the genetic conflict. It is a way for mammals to regulate gene expression by silencing one of the alleles. In the baby, the active genes inherited are in direct conflict with those inactive. Most imprinted ICRs acquire DNA methylation from the oocyte. Therefore, parthenogenetic activation will be prevented in mammals due to the lack of paternally expressed genes. This so-called parental conflict hypothesis imagines that because a fetus growing in the womb uses tremendous maternal resources, it is in the mother’s interest for her baby to be small so as to balance her own needs with those of the child. Conversely, the father’s only interest is for his babies to be large and therefore more robust. According to the parental conflict theory, imprinting may be nature’s way of playing out this struggle in the womb. For example, Igf2 encodes a ligand that promotes growth, and it is maternally imprinted, while Igfr2 encodes a receptor for the ligand that represses growth and is paternally imprinted. Although the parental conflict hypothesis is compelling on its surface, many biologists think that it is overly simplistic, and they have very different ideas about the origins of genomic imprinting.

5. Imprinting mechanisms: different loci utilize different mechanisms. (a) Maternal imprinting of Igf2 is controlled by methylation of an insulator located between the Igf2 enhancer and promoter. On the maternal homolog, the insulator is unmethylated and is therefore functional (it binds CTCF). On the paternal homolog, the insulator is methylated and does not function. (b) Paternal imprinting of Igfr2 depends on methylation of a CpG island that controls transcription of the Air ncRNA; when Air is transcribed, Igfr2 is not expressed. The CpG island on the maternal homolog is methylated, silencing Air transcription and allowing Igfr2 expression. The paternal Igfr2 allele is silenced because the CpG island is unmethylated and Air is transcribed....