X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation

Abstract

Introductory paragraphAmong organisms with chromosome-based mechanisms of sex determination, failure to equalize expression of X-linked genes between the sexes is typically lethal. In C. elegans, XX hermaphrodites halve transcription from each X chromosome to match the output of XO males 1 . Here, we mapped the binding location of the condensin homolog DPY-27 and the zinc finger protein SDC-3, two components of the C. elegans dosage compensation complex (DCC) 2,3 . Strong foci of DCC binding were observed on X, around which broader regions of localization were centered. Binding foci, but not adjacent regions of localization, were distinguished by clusters of a stereotypic 10-bp DNA sequence, suggesting a recruitment-andspreading mechanism for X recognition. In contrast to the Drosophila DCC, the C. elegans DCC was bound preferentially upstream of genes, suggesting modulation of transcriptional initiation and polymerase-coupled spreading. A mechanism for tuning DCC activity at specific loci was indicated by stronger DCC binding upstream of genes with high transcriptional activity. These data provide a basis for understanding how proteins involved in higher-order chromosome dynamics can regulate transcription at individual loci. Main TextTo compensate for differences in X-linked gene dosage between XY males and XX females, mammals inactivate most genes on one of the two female X chromosomes 4 . In contrast, C. elegans XX hermaphrodites dosage compensate by reducing transcription from each X chromosome by a factor of two to match the expression of XO males 1 . This mechanism is remarkable in that the subtle two-fold downregulation is imposed upon X-linked genes expressed over a large dynamic range 5,6 . The dosage compensation complex (DCC) required for C. elegans X-repression is composed of proteins encoded by the genes sdc-1, sdc-2, sdc-3, dpy-21, dpy-26, dpy-27, dpy-28, dpy-30 and mix-1 7 . DPY-26, DPY-27, DPY-28 and MIX-1 are homologous to members of the condensin complex, which is required for chromosome condensation and segregation in organisms ranging from bacteria to humans 8 . While the *Correspondence should be addressed to: Jason D. Lieb jlieb@bio.unc.edu (919) 843-3228. AUTHOR CONTRIBUTIONS This study was designed by SE and JDL. SE conducted the experiments. SE, PGG, CMW, and JDL conducted the data analysis. XZ and RDG designed, manufactured, and hybridized the DNA microarrays. SE and JDL wrote the paper. COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript molecular parallels to mitotic chromosome condensation broadly suggest a mechanism for reducing X-linked transcription 9,10 , the features of X that control DCC binding have proven more difficult to investigate. Four loci on X (rex-1-4) sufficient for DCC recruitment were identified recently by using confocal microscopy to detect DCC binding to multiple-copy extrachromosomal transgenic DNA 11,12 . Here, we take an ...

Broad chromosomal domains of histone modification patterns in C. elegans

“…Consistent with extensive evidence that these proteins collaborate to repress expression of X-linked genes in XX hermaphrodites (Meyer 2005;Ercan et al 2007), their ChIP data sets show higher signals on the X chromosome than on autosomes (Supplemental Fig. S2), as observed previously for some of these factors (Ercan et al 2007(Ercan et al , 2009Jans et al 2009). Interestingly, two histone modifications, H3K27me1 and H4K20me1, also group with the dosage compensation proteins (Supplemental Fig.…”

“…For an antibody to pass dot blot analysis required that at least 75% of the total signal be specific to the cognate peptide. Mouse monoclonal antibodies against H3K9me2 (clone 6D11), H3K9me3 (clone 2F3), H3K27me3 (clone1E7), H3K36me2 (2C3), and H3K36me3 (13C9) were gifts from Hiroshi Kimura (Osaka University) (Kimura et al 2008 , MES-4 (SDI SDQ0791) , SDC-3 and DPY-27 (Ercan et al 2007), DPY-26 and MIX-1 (Ercan et al 2009), and HTZ-1 (Whittle et al 2008). DPY-28 antibody was kindly provided by Kirsten Hagstrom.…”

“…Extracts were prepared from N2 (wild-type) embryos and L3 larvae as described previously: early embryo (EE) extracts , mixed embryo (MxE) extracts (Ercan et al 2007), and L3 extracts (Kolasinska-Zwierz et al 2009). Eight different matched EE extracts (containing an average of 37% <28-cell embryos, 30% 28-100-cell embryos, and 33% ;100-300-cell embryos), seven different matched MxE extracts, and four different matched L3 extracts were prepared.…”

“…The first C. elegans chromatin factors whose distributions were analyzed genome-wide were DPY-27 and SDC-3, members of the dosage compensation complex (Ercan et al 2007). That and subsequent studies (Ercan et al 2009;Jans et al 2009) revealed that the dosage compensation complex is recruited to and spreads from specific sites on the X chromosome and is most concentrated upstream of active X-linked genes.…”

Condensins: universal organizers of chromosomes with diverse functions

“…The DCC is composed of a condensin I-like complex (known as condensin I DC ) and another five-subunit complex containing SDC-1, SDC-2, SDC-3, DPY-21, and DPY-30. Experiments combining genome-wide chromatin precipitation assays have revealed that the DCC is enriched at ;1500 sites scattered along the length of the X chromosomes that can be categorized into two different classes: rex (recruiting element on X) sites and dox (dependent on X) sites (McDonel et al 2006;Ercan et al 2007;Blauwkamp and Csankovszki 2009;Jans et al 2009). The rex sites contain a 12-base-pair sequence motif called MEX (motif enriched on X) and are able to recruit the DCC when detached from the X.…”