DOI: 10.6078/d12t4p
title: Toxic Y chromosome: increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome

description: Sex-specific differences in lifespan are prevalent across the tree of life
 and influenced by heteromorphic sex chromosomes. In species with XY sex
 chromosomes, females often outlive males. Males and females can differ in
 their overall repeat content due to the repetitive Y chromosome, and
 repeats on the Y might lower survival of the heterogametic sex (toxic Y
 effect). Here, we take advantage of the well-assembled young Y chromosome
 of Drosophila miranda to study the sex-specific dynamics of chromatin
 structure and repeat expression during aging in male and female flies.
 Male D. miranda have about twice as much repetitive DNA compared to
 females, and live shorter than females. Heterochromatin is crucial for
 silencing of repetitive elements, yet old D. miranda flies lose H3K9me3
 modifications in their pericentromere, with heterochromatin loss being
 more severe during aging in males than females. Satellite DNA becomes
 de-repressed more rapidly in old vs. young male flies relative to females.
 In contrast to what is observed in D. melanogaster, we find that
 transposable elements (TEs) are expressed at higher levels in male D.
 miranda throughout their life. We show that epigenetic silencing via
 heterochromatin formation is ineffective on the large TE-rich neo-Y
 chromosome, resulting in up-regulation of Y-linked TEs already in young
 males. This is consistent with an interaction between the age of the Y
 chromosome and the genomic effects of aging. Our data support growing
 evidence that “toxic Y chromosomes” can diminish male fitness and a
 reduction in heterochromatin can contribute to sex-specific aging.
description: Lifespan assays: Flies were collected and aged for the lifespan
 assay following Linford, N. J., et al. J. Vis. Exp. (2013). We recorded
 the number of flies dying during multiple aging trials. Data represents
 fly deaths over time from 4 independent aging trials. Two files are listed
 - one recording deaths and one recording the remaining alive flies once
 the experiments stopped. RNA-Seq: Two data tables are
 processed with the DESeq2 normalization pipeline. One table contains
 normalized expression values for transposable elements (TEs) and the other
 for satellite DNA. The last table shows transposable element expression on
 a per-chromosome basis from the TECounts/TEtranscripts
 pipeline.  ChIP-Seq: Four data tables in total
 containing H3K9me3 enrichment (ChIP/Input) of different
 samples/replicates.  One table contains enrichment values for the entire
 genome of males and females, one table contains values for enrichment at
 satellite DNA, and two tables contain values for enrichment at TEs (a
 table containing male data and a table containing female data). 
description: Lifespan assay: In both files, the first column indicates the day
 of the experiment, the second represents females (0) or males (1), and the
 third represents either alive (1) or dead (2).  These plots combined will
 yield a survivorship curve.   ChIP-Seq: Combine the
 male and female data tables together to view H3K9me3 enrichment at
 TEs.