A TATA binding protein regulatory network that governs transcription complex assembly

A portion of the assembly process involving the regulation of the TATA binding protein (TBP) throughout the yeast genome is modeled and experimentally tested

Targeting of P-Element Reporters to Heterochromatic Domains by Transposable Element 1360 in Drosophila melanogaster

Heterochromatin is a common DNA packaging form employed by eukaryotes to constitutively silence transposable elements. Determining which sequences to package as heterochromatin is vital for an organism. Here, we use Drosophila melanogaster to study heterochromatin formation, exploiting position-effect variegation, a process whereby a transgene is silenced stochastically if inserted in proximity to heterochromatin, leading to a variegating phenotype. Previous studies identified the transposable element 1360 as a target for heterochromatin formation. We use transgene reporters with either one or four copies of 1360 to determine if increasing local repeat density can alter the fraction of the genome supporting heterochromatin formation. We find that including 1360 in the reporter increases the frequency with which variegating phenotypes are observed. This increase is due to a greater recovery of insertions at the telomere-associated sequences (∼50% of variegating inserts). In contrast to variegating insertions elsewhere, the phenotype of telomere-associated sequence insertions is largely independent of the presence of 1360 in the reporter. We find that variegating and fully expressed transgenes are located in different types of chromatin and that variegating reporters in the telomere-associated sequences differ from those in pericentric heterochromatin. Indeed, chromatin marks at the transgene insertion site can be used to predict the eye phenotype. Our analysis reveals that increasing the local repeat density (via the transgene reporter) does not enlarge the fraction of the genome supporting heterochromatin formation. Rather, additional copies of 1360 appear to target the reporter to the telomere-associated sequences with greater efficiency, thus leading to an increased recovery of variegating insertions

Genome-wide changes in expression upon perturbation of the TBP regulatory network

<p><b>Copyright information:</b></p><p>Taken from "A TATA binding protein regulatory network that governs transcription complex assembly"</p><p>Genome Biology 2007;8(4):R46-R46.</p><p>Published online 2 Apr 2007</p><p>PMCID:PMC1896006.</p><p></p> We grouped 2,903 ORFs (rows) that changed expression by at least 1.5-fold in at least one of the 63 conditions (columns) examined into 10 clusters using the K-means algorithm [63]. Clusters 1-10 contained the following number of ORFs, respectively: 338, 333, 225, 330, 344, 359, 259, 282, 127, 306; 3,323 ORFs did not meet the filtering criteria. Changes are relative to a galactose-induced null TBP in a wild-type TBP background. Red, green, and black denote increased, decreased, and no change in gene expression. Gray denotes no data. Color intensity reflects the magnitude of change on a logscale. Columns were arranged by hierarchical clustering [63]. Color boxes above each column indicate the relevant strain genotypes. All mutations are located on TBP except where designated '', and 'ΔTAND', which signify deletion of and the TAND domain. Boxes with dashed outlines indicate null TBP. All strains harbor a chromosomal copy of the endogenous wild-type TBP gene ()

The 'flow' of PIC assembly through the TBP regulatory network at different gene clusters

<p><b>Copyright information:</b></p><p>Taken from "A TATA binding protein regulatory network that governs transcription complex assembly"</p><p>Genome Biology 2007;8(4):R46-R46.</p><p>Published online 2 Apr 2007</p><p>PMCID:PMC1896006.</p><p></p> Each assembly model corresponds to the indicated cluster number in Figure 3. The same prototype model described in Figure 1 is applied to all clusters. Line and arrow thickness reflect the magnitude of flux through the system

Multiple SET Methyltransferases Are Required to Maintain Normal Heterochromatin Domains in the Genome of Drosophila melanogaster

Methylation of histone H3 lysine 9 (H3K9) is a key feature of silent chromatin and plays an important role in stabilizing the interaction of heterochromatin protein 1 (HP1) with chromatin. Genomes of metazoans such as the fruit fly Drosophila melanogaster generally encode three types of H3K9-specific SET domain methyltransferases that contribute to chromatin homeostasis during the life cycle of the organism. SU(VAR)3-9, dG9a, and dSETDB1 all function in the generation of wild-type H3K9 methylation levels in the Drosophila genome. Two of these enzymes, dSETDB1 and SU(VAR)3-9, govern heterochromatin formation in distinct but overlapping patterns across the genome. H3K9 methylation in the small, heterochromatic fourth chromosome of D. melanogaster is governed mainly by dSETDB1, whereas dSETDB1 and SU(VAR)3-9 function in concert to methylate H3K9 in the pericentric heterochromatin of all chromosomes, with dG9a having little impact in these domains, as shown by monitoring position effect variegation. To understand how these distinct heterochromatin compartments may be differentiated, we examined the developmental timing of dSETDB1 function using a knockdown strategy. dSETDB1 acts to maintain heterochromatin during metamorphosis, at a later stage in development than the reported action of SU(VAR)3-9. Surprisingly, depletion of both of these enzymes has less deleterious effect than depletion of one. These results imply that dSETDB1 acts as a heterochromatin maintenance factor that may be required for the persistence of earlier developmental events normally governed by SU(VAR)3-9. In addition, the genetic interactions between dSETDB1 and Su(var)3-9 mutations emphasize the importance of maintaining the activities of these histone methyltransferases in balance for normal genome function