Domains of Heterochromatin Protein 1 Required for Drosophila melanogaster Heterochromatin Spreading

Centric regions of eukaryotic genomes are packaged into heterochromatin, which possesses the ability to spread along the chromosome and silence gene expression. The process of spreading has been challenging to study at the molecular level due to repetitious sequences within centric regions. A heterochromatin protein 1 (HP1) tethering system was developed that generates “ectopic heterochromatin” at sites within euchromatic regions of the Drosophila melanogaster genome. Using this system, we show that HP1 dimerization and the PxVxL interaction platform formed by dimerization of the HP1 chromo shadow domain are necessary for spreading to a downstream reporter gene located 3.7 kb away. Surprisingly, either the HP1 chromo domain or the chromo shadow domain alone is sufficient for spreading and silencing at a downstream reporter gene located 1.9 kb away. Spreading is dependent on at least two H3K9 methyltransferases, with SU(VAR)3-9 playing a greater role at the 3.7-kb reporter and dSETDB1 predominately acting at the 1.9 kb reporter. These data support a model whereby HP1 takes part in multiple mechanisms of silencing and spreading.HETEROCHROMATIN protein 1 (HP1) was identified in Drosophila as a nonhistone chromosomal protein enriched in centric heterochromatin (James and Elgin 1986; James et al. 1989). On polytene chromosomes, HP1 localizes near centromeres and telomeres, along the fourth chromosome and at ∼200 sites within the euchromatic arms (James et al. 1989; Fanti et al. 2003). Heterochromatin has the ability to “spread,” or propagate in cis, along the chromosome (Weiler and Wakimoto 1995). Spreading is observed when a chromosomal rearrangement places a euchromatic domain next to a heterochromatic domain. Cytologically, spreading is visualized as densely compact chromatin that emanates from the chromocenter, the structure formed by the fusion of centromeres, and extends into the banded regions of polytene chromosomes (Belyaeva and Zhimulev 1991). Euchromatic genes brought into juxtaposition with heterochromatin by chromosomal rearrangements exhibit gene silencing, termed position effect variegation (PEV) (Weiler and Wakimoto 1995). Mutations in Su(var)2-5, the gene encoding HP1, suppress silencing, suggesting HP1 plays a key role in spreading (Eissenberg et al. 1990). The molecular processes of spreading are not well understood.Repetitive sequences within heterochromatin make it difficult to study spreading at the molecular level. In addition, specific repetitive elements are thought to function as initiation sites for heterochromatin formation (Sun et al. 2004; Haynes et al. 2006), making it challenging to separate initiation from spreading. To overcome these problems, we generated a system that nucleates small domains (<20 kb) of repressive chromatin that share many properties with centric heterochromatin. Here we refer to these as ectopic heterochromatin domains. These domains are generated by expressing a fusion protein, consisting of the DNA binding domain of the Escherichia coli lac repressor (LacI) fused to HP1, in stocks possessing lac operator (lacO) repeats upstream of a reporter gene cassette (Danzer and Wallrath 2004). LacI-HP1 associates with the lacO repeats and causes silencing of the adjacent reporter genes. Silencing correlates with alterations in chromatin structure that include the generation of regular nucleosome arrays similar to those observed in centric heterochromatin (Sun et al. 2001; Danzer and Wallrath 2004). Chromatin immunoprecipitation (ChIP) experiments demonstrated that HP1 spreads bidirectionally, 5–10 kb from the lacO repeats, encompassing the reporter genes (Danzer and Wallrath 2004). Thus, HP1 is sufficient to nucleate small heterochromatin-like domains at genomic locations devoid of repetitious sequences, allowing for molecular studies of spreading.HP1 contains an amino terminal chromo domain (CD) and a carboxy chromo shadow domain (CSD), separated by a flexible hinge (Li et al. 2002). The CD forms a hydrophobic pocket implicated in chromosomal association through binding to di- and trimethylated lysine 9 of histone H3 (H3K9me2 and me3, respectively), an epigenetic mark generated by the histone methyltransferases (HMT) SU(VAR)3-9 and dSETDB1 (also known as Egg) (Jacobs et al. 2001; Schotta et al. 2002; Schultz et al. 2002; Ebert et al. 2004; Clough et al. 2007; Seum et al. 2007; Tzeng et al. 2007). Association with methylated H3 is one mechanism of HP1 chromosome association; however, other mechanisms involving interactions with DNA and/or partner proteins likely exist (Fanti et al. 1998; Li et al. 2002; Cryderman et al. 2005). In Drosophila HP1, a single amino acid substitution within the CD (V26M) is present in the Su(var)2-5⁰² allele; flies heterozygous for this allele show suppression of gene silencing by heterochromatin (Eissenberg et al. 1990). Furthermore, flies trans-heterozygous for Su(var)2-5⁰² and a null allele of Su(var)2-5 show dramatic reduction of HP1 near centromeres and do not survive past the third larval stage (Fanti et al. 1998). Consistent with these observations, structural studies show that V26 plays a critical role in forming the hydrophobic pocket of the CD that binds to H3K9me (Jacobs et al. 2001).The HP1 CSD dimerizes and mediates interactions with a variety of nuclear proteins (Cowieson et al. 2000; Yamamoto and Sonoda 2003; Thiru et al. 2004). CSD dimerization sets up an interaction platform for the binding of proteins possessing a penta-peptide motif, PxVxL (where x represents any amino acid) (Thiru et al. 2004; Lechner et al. 2005). Amino acid substitutions within HP1 have been identified that disrupt dimerization, and interaction with PxVxL proteins (Lechner et al. 2000; Thiru et al. 2004). For example, a single amino acid substitution within the CSD (I161E) disrupts dimerization of mouse HP1beta (Brasher et al. 2000). The lack of dimerization also caused the loss of interactions with nuclear factors containing PxVxL motifs and non-PxVxL partners (Yamamoto and Sonoda 2003; Lechner et al. 2005). In contrast, a single amino acid substitution elsewhere in the CSD (W170A) of mouse HP1beta does not prevent dimerization, but disrupts the interaction with PxVxL partner proteins (Brasher et al. 2000). Therefore, the requirement for HP1 dimerization and binding to the PxVxL proteins can be functionally separated. Here, we investigate effects of HP1 domain deletions and amino acid substitutions on HP1 localization, partner protein interactions, and heterochromatin spreading.     

Essential Genes in Autosomal Heterochromatin of Drosophila Melanogaster

We are taking two approaches to understanding the structure, function and regulation of essential genes within Drosophilaheterochromatin. In the first, we have undertaken a genetic and molecular characterization of essential genes within proximal 3L heterochromatin. The expression of such ‘resident’ genes within a heterochromatic environment is paradoxical and poorly understood, given that the same environment can inactivate euchromatic sequences (position effect variegation, or PEV). A second approach involves the study of the local chromosomal environment of heterochromatic (het) genes, as assayed both biochemically, and via the effects of genetic modifiers of PEV, the latter being putative components important for het gene expression. Our results to date suggest that the three most proximal genes in 3L heterochromatin have key roles in development, and indicate strong effects of combinations of genetic modifiers of PEV on het gene expression. This revised version was published online in July 2006 with corrections to the Cover Date.     

Knockdown of SCFSkp2 Function Causes Double-Parked Accumulation in the Nucleus and DNA Re-Replication in Drosophila Plasmatocytes

In Drosophila, circulating hemocytes are derived from the cephalic mesoderm during the embryonic wave of hematopoiesis. These cells are contributed to the larva and persist through metamorphosis into the adult. To analyze this population of hemocytes, we considered data from a previously published RNAi screen in the hematopoietic niche, which suggested several members of the SCF complex play a role in lymph gland development. eater-Gal4;UAS-GFP flies were crossed to UAS-RNAi lines to knockdown the function of all known SCF complex members in a plasmatocyte-specific fashion, in order to identify which members are novel regulators of plasmatocytes. This specific SCF complex contains five core members: Lin-19-like, SkpA, Skp2, Roc1a and complex activator Nedd8. The complex was identified by its very distinctive large cell phenotype. Furthermore, these large cells stained for anti-P1, a plasmatocyte-specific antibody. It was also noted that the DNA in these cells appeared to be over-replicated. Gamma-tubulin and DAPI staining suggest the cells are undergoing re-replication as they had multiple centrioles and excessive DNA content. Further experimentation determined enlarged cells were BrdU-positive indicating they have progressed through S-phase. To determine how these cells become enlarged and undergo re-replication, cell cycle proteins were analyzed by immunofluorescence. This analysis identified three proteins that had altered subcellular localization in these enlarged cells: Cyclin E, Geminin and Double-parked. Previous research has shown that Double-parked must be degraded to exit S-phase, otherwise the DNA will undergo re-replication. When Double-parked was titrated from the nucleus by an excess of its inhibitor, geminin, the enlarged cells and aberrant protein localization phenotypes were partially rescued. The data in this report suggests that the SCF^Skp2 complex is necessary to ubiquitinate Double-parked during plasmatocyte cell division, ensuring proper cell cycle progression and the generation of a normal population of this essential blood cell type.     

Chromosomal Polymorphisms of Constitutive Heterochromatin and Inversions in Drosophila

A simple technique for preparing mitotic metaphases from a larval ganglion of Drosophila is described. Parallel examination of polytene and metaphase chromosome groups shows that inversion polymorphism in chromosome 3 of D. recticilia from East Maui (Hawaii) manifests a one-to-one correlation with a metaphase karyotype polymorphism due to the presence of an extra heterochromatic portion. These observations are consistent with the previous findings on other species of Hawaiian Drosophila. They strongly support the hypothesis that when one breakpoint of a long inverted segment of a chromosome element occurs in the vicinity of the constitutive heterochromatin, it may exert an effect in eliciting the production of heterochromatic material in the same chromosome.     

Cytogenetic Analysis of the Second Chromosome Heterochromatin of Drosophila Melanogaster

This paper reports the cytogenetic characterization of the second chromosome heterochromatin of Drosophila melanogaster. High resolution cytological analysis of a sample of translocations, inversions, deficiencies and free duplications involving the pericentric regions of the second chromosome was achieved by applying sequential Hoechst 33258 and N-chromosome banding techniques to larval neuroblast prometaphase chromosomes. Heterochromatic rearrangements were employed in a series of complementation assays and the genetic elements previously reported to be within or near the second chromosome heterochromatin were thus precisely assigned to specific heterochromatic bands. The results of this analysis reveal a nonhomogeneous distribution of loci along the second chromosome heterochromatin. The l(2)41Aa, l(2)41Ab, rolled (l(2)41Ac) and l(2)41Ad loci are located within the proximal heterochromatin of 2R, while the nine remaining loci in the left arm and two (l(2)41Ae and l(2)41Ah) in the right arm map to h35 and to h46, respectively, the most distal heterochromatic regions. In addition, a common feature of these loci revealed by the cytogenetic analysis is that they map to specific heterochromatic blocks but do not correspond to the blocks themselves, suggesting that they are not as large as the Y fertility factors or the Rsp locus. Mutations of the proximal most heterochromatic loci, l(2)41Aa and rolled, were also examined for their phenotypic effects. Extensive cell death during imaginal disc development was observed in individuals hemizygous for either the EMS 31 and rolled mutations, leading to a pattern of phenotypic defects of adult structures.     

Drosophila Telomere Transposons: Genetically Active Elements in Heterochromatin

In Drosophilatwo non-LTR retrotransposons, HeT-Aand TART, offer a novel experimental system for the study of heterochromatin. These elements, found only in heterochromatin, form Drosophilatelomeres by repeated transposition onto chromosome ends. Their transposition yields arrays of repeats larger and more irregular than the repeats produced by telomeras; nevertheless, the transpositions are, in principle, equivalent to the telomere-building action of telomerase. The identification of the HeT-Apromoter has given the first view of the molecular structure of a promoter active in heterochromatin. These telomere-specific elements are unusual in having a large amount of non-coding sequence. Like many other heterochromatic sequences, the HeT-Anon-coding sequence has a repetitive organization strongly conserved within the species, although the sequence itself can undergo significant change between species (atypical example of concerted evolution). Such heterochromatic sequences could be important for the cell, perhaps as docking stations for essential proteins. This revised version was published online in July 2006 with corrections to the Cover Date.     

Mapping Simple Repeated DNA Sequences in Heterochromatin of Drosophila Melanogaster

Heterochromatin in Drosophila has unusual genetic, cytological and molecular properties. Highly repeated DNA sequences (satellites) are the principal component of heterochromatin. Using probes from cloned satellites, we have constructed a chromosome map of 10 highly repeated, simple DNA sequences in heterochromatin of mitotic chromosomes of Drosophila melanogaster. Despite extensive sequence homology among some satellites, chromosomal locations could be distinguished by stringent in situ hybridizations for each satellite. Only two of the localizations previously determined using gradient-purified bulk satellite probes are correct. Eight new satellite localizations are presented, providing a megabase-level chromosome map of one-quarter of the genome. Five major satellites each exhibit a multichromosome distribution, and five minor satellites hybridize to single sites on the Y chromosome. Satellites closely related in sequence are often located near one another on the same chromosome. About 80% of Y chromosome DNA is composed of nine simple repeated sequences, in particular (AAGAC)(n) (8 Mb), (AAGAG)(n) (7 Mb) and (AATAT)(n) (6 Mb). Similarly, more than 70% of the DNA in chromosome 2 heterochromatin is composed of five simple repeated sequences. We have also generated a high resolution map of satellites in chromosome 2 heterochromatin, using a series of translocation chromosomes whose breakpoints in heterochromatin were ordered by N-banding. Finally, staining and banding patterns of heterochromatic regions are correlated with the locations of specific repeated DNA sequences. The basis for the cytochemical heterogeneity in banding appears to depend exclusively on the different satellite DNAs present in heterochromatin.     

Islands of Complex DNA Are Widespread in Drosophila Centric Heterochromatin

Heterochromatin is a ubiquitous yet poorly understood component of multicellular eukaryotic genomes. Major gaps exist in our knowledge of the nature and overall organization of DNA sequences present in heterochromatin. We have investigated the molecular structure of the 1 Mb of centric heterochromatin in the Drosophila minichromosome Dp1187. A genetic screen of irradiated minichromosomes yielded rearranged derivatives of Dp1187 whose structures were determined by pulsed-field Southern analysis and PCR. Three Dp1187 deletion derivatives and an inversion had one breakpoint in the euchromatin and one in the heterochromatin, providing direct molecular access to previously inaccessible parts of the heterochromatin. End-probed pulsed-field restriction mapping revealed the presence of at least three ``islands' of complex DNA, Tahiti, Moorea, and Bora Bora, constituting approximately one half of the Dp1187 heterochromatin. Pulsed-field Southern analysis demonstrated that Drosophila heterochromatin in general is composed of alternating blocks of complex DNA and simple satellite DNA. Cloning and sequencing of a small part of one island, Tahiti, demonstrated the presence of a retroposon. The implications of these findings to heterochromatin structure and function are discussed.     

Accumulation of Transposable Elements in the Heterochromatin and on the Y Chromosome of Drosophila simulans and Drosophila melanogaster

The elements of the transposon families G, copia, mdg 1, 412, and gypsy that are located in the heterochromatin and on the Y chromosome have been identified by the Southern blotting technique in Drosophila simulans and D. melanogaster populations. Within species, the abundance of such elements differs between transposon families. Between species, the abundance in the heterochromatin and on the Y chromosome of the elements of the same family can differ greatly suggesting that differences within a species are unrelated to structural features of elements. By shedding some new light on the mechanism of accumulation of transposable elements in the heterochromatin, these data appear relevant to the understanding of the long-term interaction between transposable elements and the host genome. Received: 8 August 1997 / Accepted: 11 December 1997     

Replication Fork Stability Is Essential for the Maintenance of Centromere Integrity in the Absence of Heterochromatin

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Highlights? Fork protection complex protects centromeric repeats when heterochromatin is lost ? Mutants lacking heterochromatin and fork protection exhibit increased recombination ? Prolonged condensation in mutants lacking both heterochromatin and fork protection     

Preferential adhesion maintains separation of ommatidia in the Drosophila eye

In the Drosophila eye, neighboring ommatidia are separated by inter-ommatidial cells (IOCs). How this ommatidial spacing emerges during eye development is not clear. Here we demonstrate that four adhesion molecules of the Irre cell recognition module (IRM) family play a redundant role in maintaining separation of ommatidia. The four IRM proteins are divided into two groups: Kirre and Rst are expressed in IOCs, and Hbs and Sns in primary pigment cells (1°s). Kirre binds Hbs and Sns in vivo and in vitro. Reducing activity of either Rst or Kirre alone had minimal effects on ommatidial spacing, but reducing both together led to direct ommatidium:ommatidium contact. A similar phenotype was also observed when reducing both Hbs and Sns. Consistent with the role of these factors in sorting ommatidia, mis-expression of Hbs plus Sns within a single IOC led to complete separation of the cell from neighboring ommatidia. Our results indicate mutual preferential adhesion between ommatidia and IOCs mediated by four IRM proteins is both necessary and sufficient to maintain separation of ommatidia.