Haploid genomes illustrate epigenetic constraints and gene dosage effects in mammals

Abstract

Sequencing projects have revealed the information of many animal genomes and thereby enabled the exploration of genome evolution. Insights into how genomes have been repeatedly modified provide a basis for understanding evolutionary innovation and the ever increasing complexity of animal developmental programs. Animal genomes are diploid in most cases, suggesting that redundant information in two copies of the genome increases evolutionary fitness. Genomes are well adapted to a diploid state. Changes of ploidy can be accommodated early in development but they rarely permit successful development into adulthood. In mammals, epigenetic mechanisms including imprinting and X inactivation restrict haploid development. These restrictions are relaxed in an early phase of development suggesting that dosage regulation appears less critical. Here we review the recent literature on haploid genomes and dosage effects and try to embed recent findings in an evolutionary perspective.

Figure 1

Experimental production of haploid mammalian embryos. (A) Normal fertilization results in embryos containing genomic contributions of both parents. During this process the metaphase II arrest of the oocyte is resolved and the second polar body (PB) is extruded leaving the diploid zygote with a haploid set of chromosomes from each parent. (B) Parthenogenetic activation of oocytes can be achieved by treatment with chemicals including Strontium salts or ethanol without fertilization and results in embryos that contain only one haploid set of maternal chromosomes [62,66]. (C) Similarly, haploid gynogenetic embryos can be constructed by removing the paternal pronucleus from a fertilized zygote by micromanipulation with a glass capillary in the presence of microtubule inhibiting chemicals. (D) Removal of the maternal pronucleus from the fertilized zygote results in androgenetic embryos containing only a haploid paternal genome [64,65]. Half of these androgenetic embryos containing the Y chromosome and lacking an X chromosome do not develop. (E) An alternative way for producing haploid androgenetic embryos is to enucleate the oocyte and introduce a sperm nucleus [64,65]. Between 10 to 20% of haploid embryos containing either the maternal or paternal set of chromosomes develop to the blastocyst stage when they can be used for establishing embryonic stem cell lines.

Figure 2

Dosage imbalances in haploid mammalian cells. (A) The inequality of parental genome contributions is illustrated by the Igf2-H19 imprinted gene cluster. In bi-parental diploid cells, H19 is expressed from the maternal whereas Igf2 is expressed from the paternal inherited chromosome. Haploid cells only contain a single set of chromosomes, either the maternal or paternal, and therefore lack either Igf2 or H19 expression. (B) The cell volume of haploid cells is between 50 to 66% that of diploid cells. This leads to changes in the surface area to volume ratio and the cell diameter that can influence transport processes and extension of the mitotic spindle, respectively. In addition, dosage compensation by X inactivation is not feasible in a haploid karyotype and, as a consequence, a genetic imbalance is incurred as the X chromosome to autosome (X/A) ratio is elevated to 1:1 from 1:2 in normal diploid cells. This effect is only significant after embryonic stem (ES) cell differentiation as normal diploid ES cells are not dosage compensated by X inactivation.

Figure 3

Haploid phases are observed in human tumors. Haploid phases in human tumors could facilitate or accelerate the loss of tumor suppressor gene function. Mutations that have been introduced into the haploid tumor genome will become homozygous when the tumor cell becomes diploid or polyploid. The observation of tumors with cells at various polyploidy levels can follow a transient haploid phase, which makes recognition of haploid phases difficult.

Figure 4

The use of haploid cells in genetic screening. A primary interest in haploid cells is their use for generating mutations for assignment of gene function. In haploid cells, loss of function mutations can be readily generated as no complementation by the homologous chromosome set is encountered. Phenotypic exposure to various selection strategies can be used to investigate gene function in specific pathways. Alternatively, libraries of cells containing mutations in genes can be generated and characterized. Screening in cell culture is a distinct advantage in mammals where combination of mutations to homozygosity requires breeding efforts that are both costly and time consuming. ES, embryonic stem.