Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans

Abstract

The adjustment of X-linked gene expression to the X chromosome copy number (dosage compensation [DC]) has been widely studied as a model of chromosome-wide gene regulation. In Caenorhabditis elegans, DC is achieved by twofold down-regulation of gene expression from both Xs in hermaphrodites. We show that in males, the single X chromosome interacts with nuclear pore proteins, while in hermaphrodites, the DC complex (DCC) impairs this interaction and alters X localization. Our results put forward a structural model of DC in which X-specific sequences locate the X chromosome in transcriptionally active domains in males, while the DCC prevents this in hermaphrodites.Supplemental material is available for this article.Received July 18, 2014; revised version accepted October 20, 2014. Throughout the animal kingdom, varied strategies have evolved to equalize expression of the X chromosome genes between sexes with different X to autosomes ratios, a process called dosage compensation (DC) (for review, see Ferrari et al. 2014). In Caenorhabditis elegans, genetic screens and RNA quantifications showed that DC occurs in hermaphrodites by twofold down-regulation of X-linked transcripts from both Xs (for review, see Strome et al. 2014). A number of mutants were isolated in which overexpression of X-linked genes led to hermaphroditespecific defects (dpy genes) or sex determination and DC deficiency (sdc genes). Remarkably, all proteins of the sex-specific Dpy and Sdc classes interact and form a single complex, the DC complex (DCC). Structurally, the DCC is similar to condensin I and loaded on the X chromosome at rex (recruitment element on X) sites characterized by a 12-base-pair (bp) MEX (motif enriched on X) consensus sequence (Ercan et al. 2009;Jans et al. 2009). Thirty-eight rex sites have been experimentally demonstrated, and sequence analysis suggests the presence of 100-300 sites on the X chromosome (Jans et al. 2009). This estimation is due to the fact that the DCC moves and spreads along the X chromosome from its nucleation sites (Csankovszki et al. 2004). The DCC accumulates at promoters upstream of transcription start sites; however, the relationship between DCC accumulation and transcriptional regulation remains disputed (Ercan et al. 2009;Jans et al. 2009). Genome-wide run-on experiments have shown that the DCC reduces transcription from the X chromosome, although RNA polymerase chromatin immunoprecipitation (ChIP) does not show a significant reduction compared with autosomes (Kruesi et al. 2013). How DCC loading regulates RNA polymerase II (Pol II) function still remains unknown. Compared with autosomes, compensated X chromatin is depleted for the histone variant HTZ-1 and H4K16 acetylation, likely a consequence of lower transcription, and carries high H4K20 monomethylation (H4K20me1), spreading with the DCC (Whittle et al. 2008;Petty et al. 2011;Vielle et al. 2012;Wells et al. 2012). Inside the nuclear space, the compensated X displays a peculiar tridimensional conformation: While all autosomes have high int...

Cell Biology of theCaenorhabditis elegansNucleus

“…This is in contrast to dosage compensation in mammals where in cells carrying two X chromosomes, one of the X chromosomes is inactivated while dosage-sensitive genes in the other are upregulated (Deng et al 2011). A key component of the dosage-compensation machinery in C. elegans is the dosage compensation complex (DCC), which is structurally similar to the condensin complex that can induce structural changes to DNA (Sharma et al 2014;Lau and Csankovszki 2015). Both FISH and Hi-C data suggest that the DCC leads to compaction of chromosome X in XX animals.…”

“…Sharma et al (2014) examined the nuclear localization of several X-chromosome loci by FISH and live imaging and found that in hermaphrodites, where the two X chromosomes are dosage compensated, there is no preferential nuclear localization. In contrast, in males the single X chromosome is preferentially localized at the nuclear periphery in a DCC-dependent manner.…”

On TADs and LADs: Spatial Control Over Gene Expression

“…downregulation on the hermaphrodite X[ 1 9 6 _ T D $ D I F F ] chromosomes away from the nuclear periphery[62] …”

Tools for DNA adenine methyltransferase identification analysis of nuclear organization during C. elegans development

“…DamID is particularly well adapted when one wants to describe chromosome or megabase scale interactions (e.g. localization close to the nuclear lamina or nuclear pores, Gonzalez-Aguilera et al, 2014;Guelen et al, 2008;Pickersgill et al, 2006;Sharma et al, 2014;Towbin et al, 2012). However, many profiles were achieved with nuclear proteins which bind smaller regions, such as transcription factors, RNA polymerase, chromatin remodellers or insulators (Filion et al, 2010;Southall et al, 2013).…”