Facultative dosage compensation of developmental genes on autosomes in Drosophila and mouse embryonic stem cells

Abstract

Haploinsufficiency and aneuploidy are two phenomena, where gene dosage alterations cause severe defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between sexes are buffered by dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. The evolutionary origin and conservation of this process orchestrated by MSL2, the only male-specific protein within the fly MSLc, have remained unclear. Here, we report that MSL2, in addition to regulating the X chromosome, targets autosomal genes involved in patterning and morphogenesis. Precise regulation of these genes by MSL2 is required for proper development. This set of dosage-sensitive genes maintains such regulation during evolution, as MSL2 binds and similarly regulates mouse orthologues via Histone H4 lysine 16 acetylation. We propose that this gene-by-gene dosage compensation mechanism was co-opted during evolution for chromosome-wide regulation of the Drosophila male X.

Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation

“…However, the promoters of ''future'' dosage-compensated genes were already H4K16ac-positive at stages 3-4 ( Figure 7A). We also assessed whether this was true for the high-affinity sites (HASs), which are genomic loci thought to be important for MSL complex recruitment (Alekseyenko et al, 2012;Alekseyenko et al, 2008;Straub et al, 2008;Villa et al, 2016). We found that HASs were H4K16ac-positive already in early stages ( Figure 7B) and that maternal depletion of MOF or MSL3 led to a bulk decrease in their chromatin accessibility ( Figure 7C).…”

“…The embryo fixation and ChIP protocols were adapted from Zenk et al, 2017 andValsecchi et al, 2018. Briefly, 1hr embryo collections were aged at 25 C until they reached the desired developmental stage. After dechorionation using 50% bleach, the embryos were fixed in a mix containing equal volumes of heptane and 1% formaldehyde in Buffer A (60mM KCl, 15mM NaCl, 15mM HEPES pH 7.6, 4mM MgCl2) for 15min under vigorous shaking at RT.…”

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

“…In agreement with earlier findings (Meisel et al, 2012; Quinn et al, 2016), immunostainings of male and female polytene chromosomes showed a strong male-specific enrichment of MOF on the X chromosome of D. melanogaster, D. busckii and D. virilis (Figure 5A and Figure S7A). MSL recruitment to the X chromosome occurs at special binding sites termed high-affinity sites (HAS), which are particularly enriched for MSL2, MLE and roX1/2 and cluster together in space (Alekseyenko et al, 2008; Ramírez et al, 2015; Schauer et al, 2017; Straub et al, 2013; Valsecchi et al, 2018). The presence of HAS sequences and their enrichment of roX appears to be a conserved feature of the X within the Drosophila genus (Alekseyenko et al, 2013; Ellison and Bachtrog, 2013; Quinn et al, 2016).…”

“…ChIP was performed as described in (Valsecchi et al, 2018). Briefly, male and female 3rd instar larvae were separated and carcasses dissected followed by fixation with 0.2 % formaldehyde for 15 min.…”

The non‐specific lethal ( NSL ) complex at the crossroads of transcriptional control and cellular homeostasis

“…The importance of the MSL complex in mediating transcriptional regulation seems to extend beyond sex‐based dosage compensation. Recent work has established that the MSL complex drives H4K16ac and transcription of highly conserved developmental genes in D. melanogaster and mouse . Consistently, loss of just one allele of MSL3 leads to human developmental disorders typified by intellectual disability and developmental delay .…”