Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila

Abstract

Dosage compensation has arisen in response to the evolution of distinct male (XY) and female (XX) karyotypes. In Drosophila melanogaster, the MSL complex increases male X transcription approximately twofold. X-specific targeting is thought to occur through sequence-dependent binding to chromatin entry sites (CESs), followed by spreading in cis to active genes. We tested this model by asking how newly evolving sex chromosome arms in Drosophila miranda acquired dosage compensation. We found evidence for the creation of new CESs, with the analogous sequence and spacing as in D. melanogaster, providing strong support for the spreading model in the establishment of dosage compensation.

Figure 1.

Karyotype evolution in D. pseudoobscura and D. miranda and the acquisition of dosage compensation on newly formed X chromosomes. (A) The fusion of an autosome (chromosome 3L) with the ancestral X chromosome ∼15 million years ago formed a large metacentric X chromosome (XL + XR) that is shared between D. pseudoobscura and D. miranda. In the latter species, a more recent fusion between another autosome (2R in D. melanogaster) with the Y chromosome formed a neo-Y chromosome 1 million to 2 million years ago, leaving the remaining homolog to evolve into the neo-X. The ancestral X chromosome is shown in dark red, XR is in red, neo-X is in pink, and Y and neo-Y are in green. (B) Polytene chromosomes of a D. miranda MSL3-TAP transgenic male larva immunostained for the TAP epitope (red) and anti-H3K9me2 (green). XL, XR, and the neo-X are targeted by the MSL complex. The neo-Y, which no longer synapses with the neo-X, shows a pronounced accumulation of heterochromatin. Bar, 5 μm.

Figure 2.

Genome-wide pattern of MSL complex binding in D. miranda. (A) Enrichment profile of MSL binding in the D. miranda genome. ChIP-seq enrichment ratios are plotted for MSL3-TAP binding (Y-axis) relative to chromosomal position (X-axis). The red marks along the X-axis indicate the position of inferred CESs. (B) GBrowse screen capture of an ∼130-kb region of chromosome XL showing enrichment ratios for male third instar larval MSL binding and histone marks. Gene models are shown below. (C) Preferential binding of the MSL complex to exons on all three X chromosome arms. (D) Fraction of H3K36me3-marked active genes bound by the MSL complex on the three X chromosome arms.

Figure 3.

Evolution of the MRE motif on the D. miranda sex chromosome arms. (A) MSL enrichment at binding sites identified on XL, XR, and the neo-X. The distribution of total MSL binding is plotted on the Y axis versus enrichment level on the X axis for each X chromosome arm. Binding shows a bimodal distribution on XL and XR, with putative CESs defined as those with high MSL occupancy (to the right of the dotted line). (B) Motif searches revealed a conserved 21-bp GA-rich motif, the MRE, within CESs on XL (MEME E-value: 2.1 × 10⁻³⁴³) and XR (MEME E-value: 3.6 × 10⁻⁶⁸⁵) and an MRE-like consensus sequence, potentially still evolving, on the neo-X (MEME E-value: 1.1 × 10⁻¹⁵²).

Figure 4.

Ectopic MSL targeting by a putative CES from the D. miranda neo-X and lack of activity from the corresponding region from the neo-Y. (A) Schematic of the GA expansion found in the CES identified on the neo-X compared with its putative progenitor sequence on the neo-Y. Red boxes indicate MRE motifs. (B,C) Transgenic msl3 mutant polytene chromosomes stained with anti-MSL2 (red) to identify all CESs and DAPI to identify all chromosome arms (blue). (B, green arrow) Lack of MSL immunostaining at the 37B7 cytological location of the neo-Y transgene. (C, white arrow) Robust MSL immunostaining at the same location when the insertion contains the neo-X CES.