Here we dissect X chromosome dosage

Here, we dissect X chromosome dosage compensation (DC) in C. elegans to determine the effect of chromatin modifications on higher-order chromosome structure during long-range gene regulation. DC is exemplary because it controls hundreds of genes simultaneously, it distinguishes X chromosomes from autosomes, and it discriminates between the sexes in modulating gene expression. The C. elegans dosage compensation complex (DCC), a ten-subunit complex with five condensin subunits, binds to both hermaphrodite X chromosomes to reduce gene expression by half, thereby equalizing it with that of the single male X (Meyer, 2010). Moreover, the DCC remodels the topology of hermaphrodite X chromosomes into a spatial conformation distinct from that of Garcinol or male X chromosomes by forming topologically associating domains (TADs) (Crane et al., 2015). During that process, the chromatin modification H4K20me1 becomes enriched on the dosage-compensated X chromosomes (Kramer et al., 2015, Liu et al., 2011, Vielle et al., 2012, Wells et al., 2012). Neither the role of this modification in chromosome-wide gene control nor its effect on X chromosome structure has been determined. H4K20me1 is also enriched on the inactive X of female mammals, revealing a common feature of diverse DC strategies (Kohlmaier et al., 2004). Its contribution to transcriptional silencing is unknown. In general, the role of H4K20me1 in gene regulation has remained a puzzle due to its context-dependent contribution to both gene activation and gene repression (Beck et al., 2012). Although H4K20 methylation has been implicated in myriad nuclear functions including gene regulation, DNA replication and repair, mitotic chromosome condensation, and cell-cycle control, the mechanisms that regulate different H4K20me states (H4K20me1/me2/me3) and transduce these states into properly executed nuclear functions are not well understood (Beck et al., 2012, Jørgensen et al., 2013, van Nuland and Gozani, 2016). In principle, H4K20me1 enrichment on C. elegans X chromosomes could occur by activating the methyltransferase (SET-1) that converts H4K20 to H4K20me1, by inhibiting the methyltransferase (SET-4) that converts H4K20me1 to H4K20me2/me3, by inhibiting the demethylase (JMJD-1.1/1.2) that converts H4K20me1 to H4K20, or by activating an unknown demethylase that converts H4K20me2 to H4K20me1. Although H4K20me2 is the predominant form of H4K20 in eukaryotic cells (Pesavento et al., 2008), only a neuron-specific H4K20me2 demethylase has been reported for any organism (Wang et al., 2015). No H4K20me2 demethylase has yet been identified that could regulate H4K20me1 levels during DC. We pursued the machinery and mechanisms that catalyze H4K20me1 enrichment on X chromosomes and the role of H4K20me1 in higher-order chromosome structure and gene regulation. The key element controlling H4K20me1 levels is a DCC subunit. Apart from five condensin subunits (DPY-26, DPY-27, DPY-28, MIX-1, and CAPG-1), the DCC includes an XX-specific protein (SDC-2) that triggers the assembly of the DCC onto X chromosomes, two proteins (SDC-3 and DPY-30) that aid SDC-2 in recruiting the DCC to X, and two proteins (SDC-1 and DPY-21) required for full DCC activity, but not assembly (Meyer, 2010).
Results
Discussion Chromatin modifications can recruit specialized proteins to regulate the structure of nucleosome arrays and gene expression. In flies and mammals, malignant brain tumor repeat (MBT) proteins associate with nucleosomes enriched in H4K20me1 or H4K20me2, compact the chromatin fiber, and help repress transcription (Blanchard et al., 2014, Trojer et al., 2007). Knockout of worm MBT proteins failed to disrupt DC, implying that if H4K20me1 binding proteins modulate X chromosome conformation and gene repression, they will define a new class of H4K20me1-specific histone “readers.” Alternatively, H4K20me1 may control nucleosome or chromatin folding directly or antagonize other chromatin modifying activities.