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

In Sciara coprophila, paternally inherited X chromosomes are imprinted and selectively eliminated during early embryonic development. A controlling element (CE) located on the X chromosome is known to play a decisive role in this process, although the exact mechanism remains unknown. In this study, we test a proposed model in which the maternal cytoplasm regulates CE activity and thereby controls Xp elimination during embryogenesis. Using our de novo Sciara genome assembly, along with ChIP-Seq and MeDIP analyses, we identified a 1.2 Mb region within the CE locus that exhibits a repressive epigenetic signature on X chromosomes that are retained. These findings provide molecular support for the model. Remarkably, this signature also includes a unique enrichment of CpG methylation, suggesting a strong evolutionary conservation of imprinting mechanisms and identifying a promising candidate for the long-sought CE locus responsible for somatic Xp-chromosome elimination. Overall design: ChIP-seq with H3K9me3-specific antibodies in 72h Sciara coprophila embryos