Silence in the germ

Gene expression in C. elegans germline cells is subject to strict controls. A set of MES proteins, including SET domain proteins and two homologs of Polycomb group proteins, establish an epigenetically transmitted silenced state that affects X chromosome gene expression.

Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites

Enhancer of Zeste is a Polycomb Group protein essential for the establishment and maintenance of repression of homeotic and other genes. In the early embryo it is found in a complex that includes ESC and is recruited to Polycomb Response Elements. We show that this complex contains a methyltransferase activity that methylates lysine 9 and lysine 27 of histone H3, but the activity is lost when the E(Z) SET domain is mutated. The lysine 9 position is trimethylated and this mark is closely associated with Polycomb binding sites on polytene chromosomes but is also found in centric heterochromatin, chromosome 4, and telomeric sites. Histone H3 methylated in vitro by the E(Z)/ESC complex binds specifically to Polycomb protein.

TheDrosophilaTrithorax protein is a coactivator required to prevent re-establishment of Polycomb silencing

Polycomb group (PcG) and Trithorax (TRX) complexes assemble at Polycomb response elements (PREs) and maintain respectively the repressed and active state of homeotic genes. Although PcG and TRX complexes are distinct, their binding to some PRE fragments in vitro depends on GAGA motifs. GAGA factor immunoprecipitates with both complexes. In presence of a PRE, TRX stimulates expression and prevents the return of repression at later stages. When TRX levels are reduced, repression is re-established in inappropriate regions of imaginal discs, suggesting that TRX insufficiency impairs the epigenetic memory of the active state. Targeting a GAL-TRX fusion shows that TRX is a coactivator that stimulates expression of an active gene but cannot initiate expression by itself. Targeting a histone acetylase to a PRE does not affect embryonic silencing but causes a loss of memory in imaginal discs, suggesting that deacetylation is required to establish the memory of the repressed state.

The Drosophila suppressor of underreplication protein binds to late-replicating regions of polytene chromosomes

In many late-replicating euchromatic regions of salivary gland polytene chromosomes, DNA is underrepresented. A mutation in the SuUR gene suppresses underreplication and leads to normal levels of DNA polytenization in these regions. We identified the SuUR gene and determined its structure. In the SuUR mutant stock a 6-kb insertion was found in the fourth exon of the gene. A single SuUR transcript is present at all stages of Drosophila development and is most abundant in adult females and embryos. The SuUR gene encodes a protein of 962 amino acids whose putative sequence is similar to the N-terminal part of SNF2/SWI2 proteins. Staining of salivary gland polytene chromosomes with antibodies directed against the SuUR protein shows that the protein is localized mainly in late-replicating regions and in regions of intercalary and pericentric heterochromatin.

Extensive conservation of sequences and chromatin structures in the bxd polycomb response element among Drosophilid species

The Polycomb Response Element (PRE) is the nucleation site for the Polycomb silencing complexes. The sequences responsible for the recruitment of the components of the Polycomb complex are not well understood. A comparison of the bxd PRE sequences from several different Drosophila species shows that some changes have occurred during phylogeny but large blocks of sequence are conserved after a divergence of some 60 million years. We compare the PRE sequences, the sites of some known PRE binding proteins, the conservation of DNasel hypersensitive sites and relate them to the sequence of the Ultrabithorax promoter which these PREs regulate.

Establishment of Polycomb silencing requires a transient interaction between PC and ESC

Two distinct types of Polycomb complexes have been identified in flies and in vertebrates, one containing ESC and one containing PC. Using LexA fusions, we show that PC and ESC can establish silencing of a reporter gene but that each requires the presence of the other. In early embryonic extracts, we find PC transiently associated with ESC in a complex that includes EZ, PHO, PH, GAGA, and RPD3 but not PSC. In older embryos, PC is found in a complex including PH, PSC, GAGA, and RPD3, whereas ESC is in a separate complex including EZ, PHO, and RPD3.

Painting of fourth, a chromosome-specific protein in Drosophila

Chromosome-specific gene regulation is known thus far only as a mechanism to equalize the transcriptional activity of the single male X chromosome with that of the two female X chromosomes. In Drosophila melanogaster, a complex including the five Male-Specific Lethal (MSL) proteins, "paints" the male X chromosome, mediating its hypertranscription. Here, with the molecular cloning of Painting of fourth (Pof), we describe a previously uncharacterized gene encoding a chromosome-specific protein in Drosophila. Unlike the MSL proteins, POF paints an autosome, the fourth chromosome of Drosophila melanogaster. Chromosome translocation analysis shows that the binding depends on an initiation site in the proximal region of chromosome 4 and spreads in cis to involve the entire chromosome. The spreading depends on sequences or structures specific to chromosome 4 and cannot extend to parts of other chromosomes translocated to the fourth. Spreading can also occur in trans to a paired homologue that lacks the initiation region. In the related species Drosophila busckii, POF paints the entire X chromosome exclusively in males, suggesting relationships between the fourth chromosome and the X and between POF complexes and dosage-compensation complexes.

Loss of insulator activity by paired Su(Hw) chromatin insulators

Chromatin insulators are regulatory elements that block the action of transcriptional enhancers when interposed between enhancer and promoter. The Drosophila Suppressor of Hairy wing [Su(Hw)] protein binds the Su(Hw) insulator and prevents enhancer-promoter interaction by a mechanism that is not understood. We show that when two copies of the Su(Hw) insulator element, instead of a single one, are inserted between enhancer and promoter, insulator activity is neutralized and the enhancer-promoter interaction may instead be facilitated. This paradoxical phenomenon could be explained by interactions between protein complexes bound at the insulators.

Recruitment of components of Polycomb Group chromatin complexes in Drosophila

Polycomb Group complexes assemble at polycomb response elements (PREs) in vivo and silence genes in the surrounding chromatin. To study the recruitment of silencing complexes, we have targeted various Polycomb Group (PcG) proteins by fusing them to the LexA DNA binding domain. When LexA-PC, -PSC, -PH or -SU(Z)2 are targeted to a reporter gene, they recruit functional PcG-silencing complexes that recapitulate the silencing behavior of a PRE: silencing is sensitive to the state of activity of the target chromatin. When the target is transcriptionally active, silencing is not established but when the target is not active at syncytial blastoderm, it becomes silenced. The repressed state persists through embryonic development but cannot be maintained in larval imaginal discs even when the LexA-PcG fusion is constitutively expressed, suggesting a discontinuity in the mechanism of repression. These proteins also interact with other PC-containing complexes in embryonic nuclear extracts. In contrast LexA-PHO is neither able to silence nor to interact with PC-containing complexes. Analysis of pho mutant embryos and of PRE constructs whose PHO-binding sites are mutated suggests that, while PHO is important for silencing in imaginal discs, it is not necessary for embryonic PcG silencing.

[Effect of four doses of the Su(UR)ES gene on intercalary heterochromatin in Drosophila melanogaster]

Polytene chromosomes of salivary glands of various Drosophila melanogaster strains containing two doses of the normal Su(UR)ES allele have a constant set of intercalary heterochromatin (IHC) sites. Their DNA is underreplicated, which leads to breaks and ectopic contacts emerging at a certain rate. Almost no underreplication, breaks, or ectopic conjugation are present in mutants lacking the normal Su(UR)ES gene product. It could be expected that an increase in the number of the Su(UR)ES+ gene doses would, in turn, drastically increase ectopic conjugation and breakage. To test this hypothesis, a strain of D. melanogaster was obtained with two additional doses of Su(UR)ES+ introduced into its genome. The flies with four gene doses exhibited a considerable increase in ectopic conjugation: both the proportion of regions participating in conjugation and the number of chromosomes with numerous contact nodes were increased. As a result, chromosomes that were straight and well-stretched in homozygotes for the mutation in Su(UR)ES became twisted and wound and contained many loops or nodes. Many chromosomes were wound too tightly for cytological analysis. Four doses of Su(UR)ES+ considerably increased the number of weak "points." For example, the 2R chromosome has only 3 weak points in strains with two doses of Su(UR)ES+ and as many as 22 weak points in the strain with four doses. In the transgenic strain, the frequency of breaks in previously known weak points increased, and new breaks appeared in 19 additional sites. All new break points appeared in the regions that were earlier described as regions of late replication in the S phase.

Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor

Polycomb response elements (PREs) are regulatory sites that mediate the silencing of homeotic and other genes. The bxd PRE region from the Drosophila Ultrabithorax gene can be subdivided into subfragments of 100 to 200 bp that retain different degrees of PRE activity in vivo. In vitro, embryonic nuclear extracts form complexes containing Polycomb group (PcG) proteins with these fragments. PcG binding to some fragments is dependent on consensus sequences for the GAGA factor. Other fragments lack GAGA binding sites but can still bind PcG complexes in vitro. We show that the GAGA factor is a component of at least some types of PcG complexes and may participate in the assembly of PcG complexes at PREs.

The mcp element from the Drosophila melanogaster bithorax complex mediates long-distance regulatory interactions

In the studies reported here, we have examined the properties of the Mcp element from the Drosophila melanogaster bithorax complex (BX-C). We have found that sequences from the Mcp region of BX-C have properties characteristic of Polycomb response elements (PREs), and that they silence adjacent reporters by a mechanism that requires trans-interactions between two copies of the transgene. However, Mcp trans-regulatory interactions have several novel features. In contrast to classical transvection, homolog pairing does not seem to be required. Thus, trans-regulatory interactions can be observed not only between Mcp transgenes inserted at the same site, but also between Mcp transgenes inserted at distant sites on the same chromosomal arm, or even on different arms. Trans-regulation can even be observed between transgenes inserted on different chromosomes. A small 800-bp Mcp sequence is sufficient to mediate these long-distance trans-regulatory interactions. This small fragment has little silencing activity on its own and must be combined with other Polycomb-Group-responsive elements to function as a "pairing-sensitive" silencer. Finally, this pairing element can also mediate long-distance interactions between enhancers and promoters, activating mini-white expression.

Chromatin insulator elements block the silencing of a target gene by the Drosophila polycomb response element (PRE) but allow trans interactions between PREs on different chromosomes

Polycomb response elements (PREs) can establish a silenced state that affects the expression of genes over considerable distances. We have tested the ability of insulator or boundary elements to block the repression of the miniwhite gene by the Ubx PRE. The gypsy element and the scs element interposed between PRE and miniwhite gene protect it against silencing but the scs' is only weakly effective. When the PRE-miniwhite gene construct is insulated from flanking chromosomal sequences by gypsy elements at both ends, it can still establish efficient silencing in some lines but not others. We show that this can be caused by interactions in trans with PREs at other sites. PRE-containing transposons inserted at different sites or even on different chromosomes can interact, resulting in enhanced silencing. These trans interactions are not blocked by the gypsy insulator and reveal the importance of nonhomologous associations between different regions of the genome for both silencing and activation of genes. The similarity between the behavior of PREs and enhancers suggests a model for their long-distance action.

Chromatin-silencing mechanisms in Drosophila maintain patterns of gene expression

The Polycomb-Group proteins form chromatin complexes that can silence gene expression over large distances. The formation of these complexes at homeotic genes depends on early developmental events but the repressed state is then maintained through many cell divisions. In vivo, complexes formed at one genomic site can interact with those at other sites, suggesting that they, like heterochromatin complexes, affect the folding of chromatin and the organization of chromosomes in the nucleus.

PcG complexes and chromatin silencing

Silencing complexes in yeast and in the fly have many similarities. This repressive complex is assembled by a chain of recruitment; its extent and stability depend on the concentration of components and affect an extended chromatin region, probably through interactions with nucleosomes. Recent results show that assembly of the complex is antagonized by transcriptional activity in the region but is favored by interactions with other complexes nearby or in other regions that associate in the same nuclear environment. How such a complex interferes with transcriptional activity is not entirely clear but current evidence suggests that they compete with the chromatin structure required for the binding of activators.

Hunchback-independent silencing of late Ubx enhancers by a Polycomb Group Response Element

Drosophila homeotic genes are kept silent outside of their appropriate expression domains by a repressive chromatin complex formed by the Polycomb Group proteins. In the case of the Ubx gene, it has been proposed that the early repressor HB, binding at enhancers, recruits the Polycomb complex and specifies the domain of repression. We show that some Ubx enhancers are activated after blastoderm. If a Polycomb Response Element (PRE) is combined with such late enhancers, repression of a reporter gene can be established everywhere in the embryo, irrespective of the presence or absence of hunchback protein. If, however, these late enhancers are combined with a Ubx early enhancer, as well as a PRE, repression is established only where the reporter gene was inactive at early stages. These results imply that the Polycomb complex is not dependent on hunchback and suggest that the pattern of silencing reflects rather the state of activity of the gene at the time the Polycomb complex is formed.

Distinct parasegmental and imaginal enhancers and the establishment of the expression pattern of the Ubx gene

The expression domain of the Ubx gene in Drosophila embryos is bounded by the product of the hb gene, acting as a repressor. We show that all Ubx fragments that bind Hb protein in vitro contain parasegmental enhancers active in the embryo in specific parasegmental patterns. We have found three new embryonic enhancer elements in the upstream region, in addition to the two previously identified. Each produces a pattern initially bounded at PS6 by Hb but sooner or later breaks down this boundary and begins to express in the anterior region. These enhancers do not respond to the long-term maintenance mediated by the Polycomb group of genes. They also cease functioning after germ band extension. Expression in imaginal tissues is due to a set of entirely separate and independent imaginal disc enhancers. These do not contain Hb binding sites and by themselves have no anterior/posterior positional information, although some distinguish between ventral and dorsal discs. A third kind of element, the Polycomb Response Element (PRE), has no enhancer activity but causes long-term maintenance of the expression domain of other enhancers present in the vicinity. The interaction of these elements results in the correct expression of Ubx in imaginal tissues.

Chromatin complexes regulating gene expression in Drosophila

Polycomb-group proteins form chromatin complexes at target genes such as Ubx, providing a cellular memory of gene activity in early development and determining the later activity of the gene. The complexes, whose constituents vary depending on site and genomic context, initiate at specific sites, but can extend to involve larger chromatin domains. How they persist through cell proliferation and how they silence gene activity are still open issues.

Dosage compensation of the Drosophila white gene requires both the X chromosome environment and multiple intragenic elements

The X-linked white gene when transposed to autosomes retains only partial dosage compensation. One copy of the gene in males expresses more than one copy but less than two copies in females. When inserted in ectopic X chromosome sites, the mini-white gene of the CaspeR vector can be fully dosage compensated and can even achieve hyperdosage compensation, meaning that one copy in males gives more expression than two copies in females. As sequences are removed gradually from the 5' end of the gene, we observe a progressive transition from hyperdosage compensation to full dosage compensation to partial dosage compensation. When the deletion reaches -17, the gene can no longer dosage compensate fully even on the X chromosome. A deletion reaching +173, 4 bp preceding the AUG initiation codon, further reduces dosage compensation both on the X chromosome and on autosomes. This truncated gene can still partially dosage compensate on autosomes, indicating the presence of dosage compensation determinants in the protein coding region. We conclude that full dosage compensation requires an X chromosome environment and that the white gene contains multiple dosage-compensation determinants, some near the promoter and some in the coding region.

White gene expression, repressive chromatin domains and homeotic gene regulation in Drosophila

The use of Drosophila chromosomal rearrangements and transposon constructs involving the white gene reveals the existence of repressive chromatin domains that can spread over considerable genomic distances. One such type of domain is found in heterochromatin and is responsible for classical position-effect variegation. Another type of repressive domain is established, beginning at specific sequences, by complexes of Polycomb Group proteins. Such complexes, which normally regulate the expression of many genes, including the homeotic loci, are responsible for silencing, white gene variegation, pairing-dependent effects and insertional targeting.

A Polycomb response element in the Ubx gene that determines an epigenetically inherited state of repression

Segmentation genes provide the signals for the activation and regulation of homeotic genes in Drosophila but cannot maintain the resulting pattern of expression because their activity ceases halfway through embryogenesis. Maintenance of the pattern is due to the Polycomb group of genes (Pc-G) and the trithorax group of genes (trx-G), responsible for the persistence of the active or repressed state of homeotic genes. We have identified a regulatory element in the Ubx gene that responds to Pc-G and trx-G genes. Transposons carrying this element create new binding sites for Pc-G products in the polytene chromosomes. This Pc-G maintenance element (PRE), establishes a repressive complex that keeps enhancers repressed in cells in which they were originally repressed and maintains this state through many cell divisions. The trx-G products stimulate the expression of enhancers in cells in which they were originally active. This mechanism is responsible for the correct regulation of imaginal disc enhancers, which lack themselves antero-posterior positional information. The PRE also causes severe variegation of the mini-white gene present in the transposon, a phenomenon very similar to heterochromatic position-effect variegation. The significance of this mechanism for homeotic gene regulation is discussed.