Epigenetic mechanisms underlying paternal genome elimination

Abstract

For most sexually reproducing organisms, the two parentally inherited copies of a gene are equivalent in transmission and expression. However, there are exceptions to this rule. Genomic imprinting is an epigenetic process in which expression of one gene copy is favoured depending on its parental origin. One of the most striking cases of genomic imprinting is Paternal Genome Elimination (PGE). PGE is a genomic imprinting phenomenon found in thousands of insect species and involves the silencing and elimination of an entire haploid genome in a parent-of-origin specific manner. Under PGE, both sexes develop from fertilized eggs and initially possess a diploid euchromatic chromosome complement. However, males subsequently eliminate paternally-inherited chromosomes from their germline. Different PGE species vary in the timing of the elimination of the paternal genome, and in whether it becomes transcriptionally silenced or not. As a result, male gene expression varies from haploid to diploid with various intermediates. The recognition and silencing of paternally-inherited genes under PGE appear to be regulated by the same epigenetic machinery as silencing and imprinting in mammals, namely DNA methylation and histone modifications. However, the molecular details are poorly understood. Here, I investigate the epigenetic mechanisms underlying PGE using the citrus mealybug (Planococcus citri, Hemiptera: Pseudococcidae) a small plant-feeding insect, easily reared in laboratory conditions. I utilize molecular, cytogenetic and genomic techniques to address the following questions: i) do levels & patterns of global DNA methylation differ between the sexes and does this play a role in sex-specific gene expression? ii) are key histone-mediated heterochromatin pathways (H3K9me3-HP1 and H3K27me3-PRC2 pathways) involved in the recognition and silencing of the paternal genome in PGE males? iii) do DNA methylation marks differ between paternal and maternal alleles, potentially acting as a distinguisher of parental origin during PGE? Whole genome bisulfite sequencing and transcriptome sequencing reveal evidence of sex-specific DNA methylation and gene expression. However, changes in gene methylation and expression between males and females are not correlated suggesting that this epigenetic modification may not mediate sex-specific expression. Cytogenetic studies in males show that both H3K9me3-HP1 and H3K27me3-PRC2 heterochromatin pathways are involved in the silencing of paternal alleles in PGE males but not in the recognition of paternal alleles during spermatogenesis. Finally, allele-specific bisulfite analysis in Planococcus hybrids suggests that differences in methylation on maternal and paternal alleles could potentially allow recognition of paternal alleles during PGE. My research provides insight into the putative roles of sex-specific and allele-specific epigenetic modifications in the recognition and silencing of the paternal genome during the process of PGE. Additionally, the methylome of a non-social, non-hymenopteran insect broadens understanding of the function(s) and evolution of DNA methylation within arthropods.