ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF.

Drosophila NURF is an ATP-dependent chromatin remodeling complex that contains ISWI, a member of the SWI2/SNF2 family of ATPases. We demonstrate that NURF catalyzes the bidirectional redistribution of mononucleosomes reconstituted on hsp70 promoter DNA. In the presence of NURF, nucleosomes adopt one predominant position from an ensemble of possible locations within minutes. Movements occur in cis, with no transfer to competing DNA. Migrating intermediates trapped by Exo III digestion reveal progressive nucleosome motion in increments of several base pairs. All four core histones are retained quantitatively during this process, indicating that the general integrity of the histone octamer is maintained. We suggest that NURF remodels nucleosomes by transiently decreasing the activation energy for short-range sliding of the histone octamer.

Inorganic pyrophosphatase is a component of the Drosophila nucleosome remodeling factor complex.

The Drosophila nucleosome remodeling factor (NURF) is a protein complex consisting of four polypeptides that facilitates the perturbation of chromatin structure in vitro in an ATP-dependent manner. The 140-kD NURF subunit, imitation switch (ISWI), is related to the SWI2/SNF2 ATPase. Another subunit, NURF-55, is a 55-kD WD repeat protein homologous to the human retinoblastoma-associated protein RbAp48. Here, we report the cloning and characterization of the smallest (38 kD) component of NURF. NURF-38 is strikingly homologous to known inorganic pyrophosphatases. Both recombinant NURF-38 alone and the purified NURF complex are shown to have inorganic pyrophosphatase activity. Inhibition of the pyrophosphatase activity of NURF with sodium fluoride has no significant effect on chromatin remodeling, indicating that these two activities may be biochemically uncoupled. Our results suggest that NURF-38 may serve a structural or regulatory role in the complex. Alternatively, because accumulation of unhydrolyzed pyrophosphate during nucleotide incorporation inhibits polymerization, NURF may also have been adapted to deliver pyrophosphatase to chromatin to assist in replication or transcription by efficient removal of the inhibitory metabolite.

Drosophila NURF-55, a WD repeat protein involved in histone metabolism.

The Drosophila nucleosome remodeling factor (NURF) is a protein complex of four distinct subunits that assists transcription factor-mediated chromatin remodeling. One NURF subunit, ISWI, is related to the transcriptional regulators Drosophila brahma and yeast SWI2/SNF2. We have determined peptide sequences and isolated cDNA clones for a second NURF component (the 55-kDa subunit). Immunological studies show that p55 is an integral subunit of NURF and is generally associated with polytene chromosomes. The predicted sequence of p55 reveals a WD repeat protein that is identical with the 55-kDa subunit of the Drosophila chromatin assembly factor (CAF-1). Given that WD repeat proteins related to p55 are associated with histone deacetylase and histone acetyltransferase, our findings suggest that p55 and its homologs may function as a common platform for the assembly of protein complexes involved in chromatin metabolism.

Characterization of functional domains of the su(Hw) protein that mediate the silencing effect of mod(mdg4) mutations.

The suppressor of Hairy-wing [su(Hw)] protein represses enhancer function in a unidirectional fashion: enhancers segregated from the promoter by the su(Hw) binding region are rendered inactive. whereas those in the same domain are unaffected. In the case of the gypsy-induced y2 allele, the repressive effect of su(Hw) is rendered bidirectional in mod(mdg4) mutant flies, and all enhancers of the affected gene become inactive. This silencing of enhancer elements might be due to exposure of specific domains of su(Hw) when the mod(mdg4) protein is absent. Two of three regions of su(Hw) that are located adjacent to the leucine zipper motif and are conserved across Drosophila species are necessary for both the unidirectional and bidirectional repression of transcription by su(Hw). In contrast, two acidic domains that are dispensable for the unidirectional repression of enhancer elements are critical for the bidirectional silencing of enhancer activity observed in mutants lacking functional mod(mdg4) protein.

Genetic and molecular analysis of the gypsy chromatin insulator of Drosophila.

Boundary or insulator elements set up independent territories of gene activity by establishing higher order domains of chromatin structure. The gypsy retrotransposon of Drosophila contains an insulator element that represses enhancer-promoter interactions and is responsible for the mutant phenotypes caused by insertion of this element. The gypsy insulator inhibits the interaction of promoter-distal enhancers with the transcription complex without affecting the functionality of promoter-proximal enhancers; in addition, these sequences can buffer a transgene from chromosomal position effects. Two proteins have been identified that bind gypsy insulator sequences and are responsible for their effects on transcription. The suppressor of Hairy-wing [su(Hw)] protein affects enhancer function both upstream and downstream of its binding site by causing a silencing effect similar to that of heterochromatin. The modifier of mdg4 [mod(mdg4)] protein interacts with su(Hw) to transform this bi-directional repression into the polar effect characteristic of insulators. These effects seem to be modulated by changes in chromatin structure.

A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation.

The suppressor of Hairy wing (su(Hw)) protein inhibits the function of transcriptional enhancers located distally from the promoter with respect to the location of su(Hw)-binding sites. This polarity is due to the ability of the su(Hw)-binding region to form a chromatin insulator. Mutations in modifier of mdg4 (mod(mdg4)) enhance the effect of su(Hw) by inhibiting the function of enhancers located on both sides of the su(Hw)-binding region. This inhibition results in a variegated expression pattern, and mutations in mod(mdg4) act as classical enhancers of position-effect variegation. The mod(mdg4) and su(Hw) proteins interact with each other. The mod(mdg4) protein controls the nature of the repressive effect of su(Hw): in the absence of mod(mdg4) protein, su(Hw) exerts a bidirectional silencing effect, whereas in the presence of mod(mdg4), the silencing effect is transformed into unidirectional repression.

A leucine zipper domain of the suppressor of Hairy-wing protein mediates its repressive effect on enhancer function.

The suppressor of Hairy-wing [su(Hw)] protein mediates the mutagenic effect of the gypsy retrotransposon by repressing the function of transcriptional enhancers controlling the expression of the mutant gene. A structural and functional analysis of su(Hw) was carried out to identify domains of the protein responsible for its negative effect on enhancer action. Sequence comparison among the su(Hw) proteins from three different species allows the identification of evolutionarily conserved domains with possible functional significance. An acidic domain located in the carboxy-terminal end of the Drosophila melanogaster protein is not present in su(Hw) from other species, suggesting a nonessential role for this part of the protein. A second acidic domain located in the amino-terminal region of su(Hw) is present in all species analyzed. This domain is dispensable in the D. melanogaster protein when the carboxy-terminal acidic domain is present, but the protein is nonfunctional when both regions are simultaneously deleted. Mutations in the zinc fingers result in su(Hw) protein unable to interact with DNA in vivo, indicating a functional role for this region of the protein in DNA binding. Finally, a region of su(Hw) homologous to the leucine zipper motif is necessary for the negative effect of this protein on enhancer function, suggesting that su(Hw) might exert this effect by interacting, directly or indirectly, with transcription factors bound to these enhancers.

Structural basis of the subtype selectivity of muscarinic antagonists: a study with chimeric m2/m5 muscarinic receptors.

The five muscarinic receptors (m1-m5), although structurally closely related, can be distinguished pharmacologically by the use of subtype-selective ligands. Various tricyclic muscarinic antagonists, including the AF-DX derivative AQ-RA 741 and the alkaloid himbacine, for example, have been shown to display up to 200-fold higher affinities for m2 and m4 than for m5 receptors. On the other hand, antagonists such as sila-hexocyclium and the pirenzepine derivative UH-AH 37 exhibit lower affinities for m2 than for m5 and all other muscarinic receptors. To identify receptor epitopes that contribute to the subtype selectivities of these antagonists, we prepared a series of chimeric m2/m5 muscarinic receptors in which regions of the m5 receptor were systematically replaced with the homologous regions of the m2 receptor. AQ-RA 741, himbacine, and sila-hexocyclium bound to the various chimeric receptors, expressed in COS-7 cells, with affinity profiles indicative of multiple receptor domains contributing to the subtype selectivities of these antagonists. On the other hand, the higher affinity of UH-AH 37 for m5 than for m2 receptors appears to be largely dependent on a short stretch of 31 amino acids comprising most of transmembrane region VI and the third extracellular loop, a region that does not contribute to the subtype selectivity of AQ-RA 741 and himbacine. Our data indicate that different receptor epitopes are involved in conferring subtype selectivity on structurally different muscarinic antagonists.

Site-directed mutagenesis of the m3 muscarinic receptor: identification of a series of threonine and tyrosine residues involved in agonist but not antagonist binding.

The hydrophobic core of all muscarinic receptors contains several conserved serine, threonine and tyrosine residues, most of which do not occur in any other G-protein coupled receptor. Since these amino acids can serve as potential hydrogen bond donors or acceptors, we have tested the hypothesis that they may be involved in the selective binding of muscarinic ligands. To eliminate the OH groups present in these residues, we have created nine single point mutations in the rat m3 muscarinic receptor by converting serine and threonine residues to alanine, and tyrosine residues to phenylalanine. The ligand binding and functional properties of these receptors were studied after transient expression in COS-7 cells. Six out of the nine mutant receptors (threonine and tyrosine mutations) showed strong reductions (approximately 10- to 40-fold lower than the wild-type receptor) in agonist binding affinities and reduced potencies in agonist-induced activation of phosphoinositide hydrolysis. Their antagonist binding properties, however, were similar to those of the wild-type m3 receptor. Despite their location on different transmembrane domains (III, V, VI and VII), all six mutations are positioned at a similar level (one to two helical turns away from the membrane surface) within the outer leaflet of the plasma membrane and may thus define the plain in which muscarinic agonists (but not antagonists) bind to their target receptor.

Human nonmuscle myosin heavy chains are encoded by two genes located on different chromosomes.

We report the cloning of cDNAs encoding two different human nonmuscle myosin heavy chains designated NMMHC-A and NMMHC-B. The mRNAs encoding NMMHC-A and NMMHC-B are both 7.5 kb in size but are shown to be the products of different genes, which are localized to chromosome 22q11.2 and chromosome 17q13, respectively. In aggreement with previously reported results using avian tissues, we show that the mRNAs encoding the two myosin heavy chain isoforms are differentially expressed in rat nonmuscle and muscle tissues as well as in a number of human cell lines. The cDNA sequence encoding the 5' portion of the NMMHC-A isoform completes the previously published 3' cDNA sequence encoding a human myosin heavy chain, thus providing the cDNA sequence encoding the entire NMMHC-A amino acid sequence. Comparison of this sequence to cDNA clones encoding the amino-terminal one third of the NMMHC-B sequence (amino acids 58-718) shows them to be 89% identical at the amino acid level and 74% identical at the nucleotide level.

Molecular cloning and expression of a dopamine D2 receptor from human retina.

Based on the sequence of a dopamine D2 receptor cloned from rat brain, we prepared a series of oligodeoxynucleotide probes. A mixture of these probes hybridized with a 2.6-kilobase species of mRNA extracted from several rat tissues including retina and, using in situ hybridization of these probes to cryostat sections of rat retina, they densely label the inner nuclear and outer plexiform layers. Labeling was also observed in the inner plexiform and ganglion cell layers. No hybridization was observed to the photoreceptor layers. A similar pattern of labeling was observed in monkey retina, indicating that the probes also hybridize with a homologous primate mRNA. The probes were used to screen a lambda gt10 library of human retina. A 2.5-kilobase clone was isolated, which encodes a protein that differs from the rat brain protein by 18 amino acids. The 5' and 3' untranslated regions of the human retinal cDNA were also strongly homologous with the rat brain cDNA. The clone was subcloned into the pCD-PS expression vector and transfected into COS-7 cells. The transfected cells bound [3H]-raclopride with a pharmacology expected of dopamine D2 receptors. These data indicate that D2 receptors expressed in the inner retina and outer plexiform layer have genetic identity with those expressed by brain and that the human and rat D2 receptors are derived from highly related genes.