Chromatin structure of simian virus 40-pBR322 recombinant plasmids in COS-1 cells

The v-ErbA oncoprotein quenches the activity of an erythroid-specific enhancer

v-ErbA is a mutated variant of thyroid hormone receptor (TRalpha/NR1A1) borne by the Avian Erythroblastosis virus causing erythroleukemia. TRalpha is known to activate transcription of specific genes in the presence of its cognate ligand, T3 hormone, while in its absence it represses it. v-ErbA is unable to bind ligand, and hence is thought to contribute to leukemogenesis by actively repressing erythroid-specific genes such as the carbonic anhydrase II gene (CA II). In the prevailing model, v-ErbA occludes liganded TR from binding to its cognate elements and constitutively interacts with the corepressors NCoR/SMRT. We previously identified a v-ErbA responsive element (VRE) within a DNase I hypersensitive region (HS2) located in the second intron of the CA II gene. We now show that HS2 fulfils all the requirements for a genuine enhancer that functions independent of its orientation and position with a profound erythroid-specific activity in normal erythroid progenitors (T2ECs) and in leukemic erythroid cell lines. We find that the HS2 enhancer activity is governed by two adjacent GATA-factor binding sites. v-ErbA as well as unliganded TR prevent HS2 activity by nullifying the positive function of factors bound to GATA-sites. However, v-ErbA, in contrast to TR, does not convey active repression to silence the transcriptional activity intrinsic to a heterologous tk promoter. We propose that depending on the sequence and context of the binding site, v-ErbA contributes to leukemogenesis by occluding liganded TR as well as unliganded TR thereby preventing activation or repression, respectively.

Cloning and characterization of a novel human class I histone deacetylase that functions as a transcription repressor

Histone acetylation alters chromatin state by modifying lysines on histone and plays an important role in modulating gene transcription. A dynamic balance of histone acetylation/deacetylation is maintained by histone acetyltransferases and histone deacetylases. Emerging evidence suggests that a family of histone deacetylases may exist to regulate diverse cellular functions, including chromatin structure, gene expression, cell cycle progression, and oncogenesis. We describe here a novel human histone deacetylase, named HDAC8, cloned from human kidney. HDAC8 encodes 377 amino acid residues and shares extensive homology to several known HDACs, in particular a histone deacetylase from Arabidopsis thaliana. Northern blot analyses revealed that HDAC8 expression pattern for HDAC8 is distinct from that for HDAC1 and HDAC3, and expression of HDAC8 mRNA occurs in multiple organs including heart, lung, kidney, and pancreas. HDAC8 mRNA was also observed in several cell lines derived from cancerous tissues. When expressed in HEK293 cells, HDAC8 exhibited deacetylase activity toward acetylated histone, indicating that this protein is a bona fide histone deacetylase. Its histone deacetylase activity was inhibited by trichostatin and other known histone deacetylase inhibitors. Furthermore, active recombinant HDAC8 was expressed and purified from Escherichia coli. When ectopically expressed in cells, HDAC8 was found to be localized to the nucleus. Co-transfection experiments demonstrated that expression of HDAC8 repressed a viral SV40 early promoter activity. These results indicate that HDAC8 is a novel member of the histone deacetylase family, which may play a role in the development of a broad range of tissues and potentially in the etiology of cancer.

Subcellular localization of prostaglandin endoperoxide H synthases-1 and -2 by immunoelectron microscopy

Prostaglandin endoperoxide H synthases-1 and -2 (PGHS-1 and -2) are the major targets of nonsteroidal anti-inflammatory drugs like aspirin and ibuprofen. These enzymes catalyze the committed step in the formation of prostanoids from arachidonic acid. Although PGHS-1 and -2 are similar biochemically, a number of studies suggest that PGHS-1 and PGHS-2 function independently to form prostanoids that subserve different cellular functions. We have hypothesized that these isozymes may reside, at least in part, in different subcellular compartments and that their compartmentation may affect their access to arachidonic acid and serve to separate the functions of the enzymes. To obtain high resolution data on the subcellular locations of PGHS-1 and -2, we employed immunoelectron microscopy with multiple antibodies specific to each isozyme. Both PGHS-1 and -2 were found on the lumenal surfaces of the endoplasmic reticulum (ER) and nuclear envelope of human monocytes, murine NIH 3T3 cells, and human umbilical vein endothelial cells. Within the nuclear envelope, PGHS-1 and -2 were present on both the inner and outer nuclear membranes and in similar proportions. Western blotting data showed a similar distribution of PGHS-1 and -2 in subcellular fractions, and product analysis using isozyme-specific inhibitors suggested that both enzymes generate the same products in NIH 3T3 cells. Thus, we are unable to attribute the independent functioning of PGHS-1 and PGHS-2 to differences in their subcellular locations. Instead, the independent operation of these isozymes may be attributable to subtle kinetic differences (e.g. negative allosteric regulation of PGHS-1 at low concentrations of arachidonate (500-1000 nM)). A further conclusion of importance from a cell biological perspective is that membrane proteins such as PGHS-1 and -2, which are located on the lumenal surface of the ER, are able to diffuse freely among the ER and the inner and outer membranes of the nuclear envelope.

Activation of SRF-regulated chromosomal templates by Rho-family GTPases requires a signal that also induces H4 hyperacetylation

Constitutively active forms of the small GTPases RhoA (RhoA.V14) and Cdc42 (Cdc42.V12) induce expression of extrachromosomal SRF reporter genes in microinjection experiments, but only Cdc42.V12 can efficiently activate a chromosomal template. Both SAPK/JNK-dependent or -independent signals can cooperate with RhoA.V14 to activate chromosomal SRF reporters, and it is SAPK/JNK activation by Cdc42.V12 that allows it to activate chromosomal templates. Cooperating signals can be bypassed by deacetylase inhibitors. Three findings show that histone H4 hyperacetylation is one target for cooperating signals, although it alone is not sufficient: (1) Cdc42.V12, but not RhoA.V14, induces H4 hyperacetylation; (2) cooperating signals use the same SAPK/JNK-dependent or -independent pathways to induce H4 hyperacetylation; (3) growth factor and stress stimuli induce substantial H4 hyperacetylation, detectable in reporter gene chromatin. These data establish a link between signal-regulated acetylation events and gene transcription.

Construction of nucleosome cores from defined sequence DNA of viral origin

The de novo construction of defined nucleosomes from two DNA fragments of simian virus SV40 is described. One fragment spans the region containing the origin of replication of the virus from base -16 to base 161, a region which is nucleosome-free during virus replication. The other fragment, of 142 bp (1352 to 1493), is within the region coding for viral proteins VP2 and VP3, and serves for comparison. Both fragments form nucleosomes with similar efficiency when combined with histone cores as well as when exchanged with existing core particles. The DNase I digestion pattern and exonuclease III analysis both indicate that true nucleosome cores are formed, and that a prolonged tail is not protruding from the constructs. The efficient formation of a nucleosome core particle from the origin region of DNA implies that the absence of nucleosomes from this region during viral infection is not prescribed by the specific base sequence of origin DNA, and is therefore likely to be determined by non-histone nuclear factors associated with the SV40 replication process.

Determinants for the DNase I-hypersensitive chromatin structure 5' to a human HSP70 gene

A DNase I hypersensitive site was detected in chromatin formed over a human hsp70 gene segment after amplification in COS7 cells. Deletion mutant analysis was used to evaluate the sequence requirements for this chromatin structure. Determinants sufficient to form the hypersensitive site are contained in a 280 base-pair sequence corresponding approximately to the region that is hypersensitive. Deletion of sequences from either end of this region resulted in reduced hypersensitivity, suggesting that multiple genetic elements contribute to the formation of this chromatin structure. As has been reported for other heat shock genes, the hypersensitive chromatin structure is present prior to heat treatment and does not change in intensity or position after heat shock, in spite of the fact that hsp70 gene expression is completely dependent on heat induction. Sequence requirements for hypersensitivity were generally similar to those for heat-induced gene expression when mutant plasmids were tested at low copy number (e.g. in HeLa cells or in COS cells without amplification); however, deletion of sequences between -223 and -162 with respect to the start of transcription abolished the hypersensitive site but had no effect on gene expression. A barrier to exonuclease III digestion was detected within this region (near an imperfect inverted repeat sequence centered at position -202), suggesting that proteins are tightly bound to the DNA at this location.

Expression of transfected DNA depends on DNA topology

Supercoiled DNAs, especially those containing enhancers, yield markedly higher levels of expression than linearized DNA when transfected into CV-1 cells or L cells. Different templates, linear or supercoiled, enhancer-containing or not, saturate for expression at 2 micrograms DNA per dish, suggesting that one role for enhancers and supercoiling is to increase the efficiency with which the same limiting component is used. Plasmids containing only enhancers or only promoters do not compete for expression with an enhancer-driven gene. However, plasmids that contain both enhancers and promoters do complete, suggesting that a second role for enhancers is to increase the binding of a limiting transcription factor. Linear and supercoiled enhancer-promoter plasmids compete equivalently. This suggests that supercoiling affects the ability of transcription factors to activate a given promoter, once bound.

Structure of transcriptionally active chromatin

Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.

Simian virus 40 early promoter mutations that affect promoter function and autoregulation by large T antigen

A set of nine mutants containing point mutations, and small deletions or insertions, were constructed in the early promoter region of simian virus 40 (SV40) to determine the role of the DNA sequences between the TATA box and the six upstream G + C-rich clusters in early transcription. The mutant templates were tested for transcription activity in vitro in HeLa cell extracts and in vivo in CV-1 and COS cells using the chloramphenicol acetyl transferase gene (CAT) assay. Both in vitro and in vivo results show that the narrow region from nucleotide positions 38 to 41 is an important domain of the early promoter. Deletion and insertion mutations most strongly affect the level of transcription. Specifically a four base-pair deletion in the promoter region enhances the level of transcription four- to sixfold in vitro, but causes a fourfold suppression of CAT gene expression in the in vivo assay. These opposite effects may result from changes in spacing under in vitro and in vivo conditions between the TATA box and the G + C-rich motifs where transcription factors may make simultaneous contact. Of the three T antigen binding sites (I, II and III), sites I and II have already been shown to be involved in the autoregulation of early transcription. Our mutational analyses demonstrate the role of site III, which partially overlaps with nucleotide positions 38 to 41, in the autoregulation of the SV40 early promoter.