Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells

Chromatin diminution is the programmed elimination of specific DNA sequences during development. It occurs in diverse species, but the function(s) of diminution and the specificity of sequence loss remain largely unknown. Diminution in the nematode Ascaris suum occurs during early embryonic cleavages and leads to the loss of germline genome sequences and the formation of a distinct genome in somatic cells. We found that ∼43 Mb (∼13%) of genome sequence is eliminated in A. suum somatic cells, including ∼12.7 Mb of unique sequence. The eliminated sequences and location of the DNA breaks are the same in all somatic lineages from a single individual and between different individuals. At least 685 genes are eliminated. These genes are preferentially expressed in the germline and during early embryogenesis. We propose that diminution is a mechanism of germline gene regulation that specifically removes a large number of genes involved in gametogenesis and early embryogenesis. To profile the tissue expression of all A. suum genes, we used 8 different developmental stages/tissues of A. suum, including testis, ovary, embryo, larvae, intestine, muscle, male carcass and female carcass. In this submission there are 10 samples: 3 for early embryos (24hr, 46hr and 64hr) and the other 7 for testis, ovary, larvae, intestine, muscle, male carcass and female carcass. For each sample, 200 ug of total RNA was used for poly(A) selection and 200 ng of poly(A)+ RNA was used to make the cDNA libraries using standard Illumina protocol.