DNA and histone modifications identify a putative controlling element (CE) on the X chromosome of Sciara coprophila

Chromosomal imprinting is a term first coined to describe the parent-of-origin-specific behavior of chromosomes in the fungus gnat Sciara coprophila. Parent-of-origin-specific elimination of the paternal X chromosomes (Xp) during early cleavage divisions in Sciara coprophila embryos is regulated by a controlling element (CE) mapping to heterochromomere II (H2) within the sub-telomeric short arm of polytene X-chromosomes. Using a combination of a new Sciara genome assembly, along with ChIP-Seq and MeDIP analyses, we show that a 1.2Mb region within the CE locus has a repressive epigenetic signature that is characterised by enrichments of H3K9me3, H4K20me3 and 5-methyl cytosine (5meC). These data provide evidence for a model where the H3K9me3/HP1/H4K20me3 pathway operates to assemble a heterochromatin-like complex at the CE that renders it silent on chromosomes that are not eliminated. As such, our work is consistent with the H3K9me3/HP1/H4K20me3 pathway being the most evolutionarily conserved mechanism associated with chromosomal imprinting.