High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.

DRM complex mutant lin-54 vs. H3K36 methyltransferase mutant mes-4 vs. lin-54; mes-4 double mutant vs. wild type C.elegans germline

Here we uncover antagonistic regulation of transcript levels in the germline of Caenorhabditis elegans hermaphrodites. The histone methyltransferase MES-4 marks genes expressed in the germline with methylated Lys36 on histone H3 (H3K36me) and promotes their transcription; MES-4 also represses genes normally expressed in somatic cells and genes on the X chromosomes. The DRM complex, which includes E2F/DP and Retinoblastoma homologs, affects germline gene expression and prevents excessive repression of X-chromosome genes. Using genome-scale analyses of germline tissue, we show that common germline-expressed genes are activated by MES-4 and repressed by DRM, and that MES-4 and DRM co-bind many germline-expressed genes. Reciprocally, MES-4 represses and DRM activates a set of autosomal soma-expressed genes and overall X-chromosome gene expression. Mutations in mes-4 or the DRM subunit lin-54 oppositely skew target transcript levels and cause sterility; a double mutant restores near wild-type transcript levels and germ cell development. Together, yin-yang regulation by MES-4 and DRM ensures transcript levels appropriate for germ cell function, elicits robust but not excessive dampening of X-chromosome-wide transcription, and may poise genes for future expression changes. Our study reveals that conserved transcriptional regulators implicated in development and cancer counteract each other to fine-tune transcript dosage.

C. elegans mixed stage embryo total RNA levels by microarray: L4440 RNAi, smo-1 RNAi and sdc-2 (y93)+RNAi

The essential process of dosage compensation equalizes X-chromosome gene expression between C. elegans XO males and XX hermaphrodites through a dosage compensation complex (DCC) that resembles condensin. The DCC binds to both X chromosomes of hermaphrodites to repress transcription by half. Here we show that post-translational modification by the SUMO conjugation pathway is essential for sex-specific assembly of the DCC onto X. Depletion of the SUMO peptide in vivo severely disrupts binding of particular DCC subunits and causes changes in X-linked gene expression similar to those caused by disrupting genes encoding DCC subunits. Three DCC subunits are themselves SUMOylated, and depletion of SUMO preferentially reduces their binding to X, suggesting that SUMOylation of DCC subunits is essential for robust association with X. DCC SUMOylation is triggered by the signal that initiates DCC assembly onto X. The initial step of assembly--binding of X-targeting factors to recruitment sites on X (rex sites)--is independent of SUMOylation, but robust binding of the complete complex requires SUMOylation. SUMOylated DCC subunits are enriched at rex sites, and SUMOylation enhances interactions between X-targeting factors and condensin subunits that facilitate DCC binding beyond the low level achieved without SUMOylation. DCC subunits also participate in condensin complexes essential for chromosome segregation, but their SUMOylation occurs only in the context of the DCC. Our results reinforce a newly emerging theme in which multiple proteins of a complex are SUMOylated in response to a specific stimulus, leading to accelerated complex formation and enhanced function.

An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression.

An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression.

Analysis of expression of genes regulated by DAF-19

By screening for genes possessing canonical X-box sequences in promoters of three Caenorhabditis species, namely C. elegans, C. briggsae and C. remanei, we identified 93 genes (including known X-box regulated genes) that encode putative components of ciliated neurons in C. elegans and are subject to the same regulatory control. For many of these genes, restricted anatomical expression in ciliated cells was confirmed, and control of transcription by the ciliogenic DAF-19 RFX transcription factor was demonstrated by comparative transcriptional profiling of daf-19(+) and daf-19(-) animals. Keywords: Microarry analysis; DAF-19; X-box motif; C. elegans; transcription; comparative genomics

Analysis of SDC-2, DPY-26, MIX-1, DPY-27 and RNA Polymerase II ChIP-chip and RNA abundance in C. elegans

In C. elegans, a condensin-like protein complex associates specifically with both X chromosomes of XX animals to execute dosage compensation. Dosage Compensation Complex (DCC) reduces the level of transcripts arising from each of the two X chromosomes. Recruitment to X is specified in part by discrete DNA sequence motifs, but following recruitment, the DCC is targeted to the promoters of individual active genes by an unknown mechanism. Here, we investigated three outstanding questions regarding the molecular mechanism of DCC recruitment and spreading along X. By examining the genome-wide binding patterns of several DCC subunits in different stages of C. elegans development, and in strains harboring X:Autosome chromosomal fusions, we provide evidence that: (1) DCC binding is dynamically specified according to gene activity during development (2) The condensin-like subunits of the DCC spread from recruitment sites to active promoters more readily than the non-conserved SDC subunits, which are involved in initial X-targeting and (3) the mechanism of DCC spreading is independent of X-chromosome DNA sequence, and will proceed onto any active promoter near a recruitment site. Our results contribute to understanding how chromatin complexes can be targeted to achieve domain-scale transcriptional regulation during development. For data usage terms and conditions, please refer to http:

MES-4, an autosome-associated HMT that participates in silencing the X chromosomes in the C. elegans germ line

Microarray-based expression profiling of dissected gonads from mes-4 mutants reveals that MES-4 is required to repress expression of a set of X-linked genes. Keywords: Mutant analysis of mes-4 in dissected C. elegans gonads

Fasting induced changes in gene expression profiles of C. elegans

Many species undergo sexual reproduction to distribute the parental genomes and increase the genomic diversity of the progeny. Among such species, sexual dimorphism is often displayed through morphology, size, behavior, and life-span, depending on the survival and reproduction strategies of the species. The nematode Caenorhabditis elegans has two sexes, hermaphrodite and male, and only the hermaphrodites, which produce both oocytes and sperm, are essential for the perpetuation of the species. In this study, we found that dietary restriction, which is the most reproducible way to retard aging in many species, extends the life-span of C. elegans hermaphrodites but not that of males. Our analysis revealed that fasting induces male-enriched genes in hermaphrodites and that the sex determination pathway affects life-span regulation, even after the completion of development, and is regulated by food availability. Furthermore, fasting activates the entire X-chromosome only in hermaphrodites. Our tiling array analysis identified a fasting-inducible, X-linked non-coding RNA for which expression positively correlated with the activation level of the X-chromosome and longevity. These links between the sex determination mechanism and dietary restriction at multiple levels may give priority to the survival of hermaphrodites during food shortages in C. elegans.

Global profile of germline gene expression in C. elegans

We used DNA microarrays to profile gene expression patterns in the C. elegans germline and identified 1416 germline-enriched transcripts that define three groups. The sperm-enriched group contains an unusually large number of protein kinases and phosphatases. The oocyte-enriched group includes potentially new components of embryonic signaling pathways. The germline-intrinsic group, defined as genes expressed similarly in germlines making only sperm or only oocytes, contains a family of piwi-related genes that may be important for stem cell proliferation. Finally, examination of the chromosomal location of germline transcripts revealed that sperm-enriched and germline-intrinsic genes are nearly absent from the X chromosome, but oocyte-enriched genes are not. This research has been described more fully in Reinke V et al.(2000) Mol Cell 6:605-16 Keywords: other

SGF3165_FLAG_MES4FLAG_EEMB

The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome function