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. ⺠Over 685 (5%) of Ascaris suum genes are eliminated during chromatin diminution ⺠Eliminated genes are mainly expressed during gametogenesis and early embryogenesis ⺠The genome changes are conserved in different somatic cell lineages and sexes ⺠Diminution may be a mechanism of gene regulation that silences germline genes