Large portions of eukaryotic genomes consist of transposable elements (TEs), and the establishment of transcription-repressing heterochromatin during early development safeguards genome integrity. Repeat-rich Y chromosomes can act as reservoirs for TEs (toxic Y effect), and TEs may exploit vulnerabilities associated with incomplete genomic defenses during early development. Here, we contrast the dynamics of early TE activation in two Drosophila species with vastly different Y chromosomes of different age. Zygotic TE expression is elevated in male embryos relative to females in both species, mostly due to expression of Y-linked TEs. Interestingly, male-biased TE misexpression diminishes across development in D. pseudoobscura, but remains elevated in D. miranda, the species with the younger and larger neo-Y chromosome. In D. miranda, misexpression of TEs is associated with incomplete heterochromatin formation on the neo-Y and results in more de novo insertions of repeats in males compared to females.  We find that because the neo-Y of D. miranda still contains many actively transcribed genes embedded in TEs, the formation of silencing heterochromatin is compromised, causing elevated TE expression and mobilization. This lends support to the idea that the ‘toxic Y chromosome’ can create a mutational burden in males when genome-wide defense mechanisms are compromised, and reveals a previously unappreciated epigenetic conflict on evolving Y chromosomes between transcription of essential genes and silencing of selfish DNA. 

RNA-seq:

Read counts at TEs are normalized by the median read counts at autosomal genes then averaged across replicate libraries. Read counts at genes are inferred using featureCounts in the Subread package. Libraries are generated by Lott et al 2014.  

ChIP-seq:

Sex-specific H3K9me3 enrichment across the genome in 25kb windows. Enrichment is normalized using quantiles of spike-ins. Enrichment is averaged between libraries of the same sex and developmental stages. 

de novo TE insertions:

Genomic regions with paired-end reads that span unique sequences and TEs are provided. Insertions with both the 5' and 3' junctions found are deemd true de novo insertions.