Characterization of basal and estrogen-regulated antisense transcription in breast cancer cells: Role in regulating sense transcription

Estrogen-responsive breast cancer cells exhibit both basal and estrogen-regulated transcriptional programs, which lead to the transcription of many different transcription units (i.e., genes), including those that produce coding and non-coding sense (e.g., mRNA, lncRNA) and antisense (i.e., asRNA) transcripts. We have previously characterized the global basal and estrogen-regulated transcriptomes in estrogen receptor alpha (ERα)-positive MCF-7 breast cancer cells. Herein, we have mined genomic data to define three classes of antisense transcription in MCF-7 cells based on where their antisense transcription termination sites reside relative to their cognate sense mRNA and lncRNA genes. These three classes differ in their response to estrogen treatment, the enrichment of a number of genomic features associated with active promoters (H3K4me3, RNA polymerase II, open chromatin architecture), and the biological functions of their cognate sense genes as analyzed by DAVID gene ontology. We further characterized two estrogen-regulated antisense transcripts arising from the MYC gene in MCF-7 cells, showing that these antisense transcripts are 5'-capped, 3'-polyadenylated, and localized to different compartments of the cell. Together, our analyses have revealed distinct classes of antisense transcription correlated to different biological processes and response to estrogen stimulation, uncovering another layer of hormone-regulated gene regulation.

Stress-induced glucocorticoids suppress the antisense molecular regulation of FGF-2 expression

Psychological stress can upregulate basic fibroblast growth factor (FGF-2) expression. Because glucocorticoids can also upregulate FGF-2 expression, the present studies investigated whether stress-induced glucocorticoids mediate the effects of stress on FGF-2. FGF-2 is regulated by an FGF-2 antisense (AS) molecular mechanism and so the present experiments also, for the first time, assessed the effects of stress on FGF-2-AS mRNA, as well as the mediating role of glucocorticoids. The effects of either escapable shock (ES) or yoked-inescapable tail shock (IS) on FGF-2 and FGF-2-AS were determined. To test whether glucocorticoids mediate the effect of stress on FGF-2 and FGF-2-AS, animals were pretreated with temporary corticosterone (CORT) synthesis inhibitors and exposed to IS. To test whether glucocorticoids are sufficient to modulate FGF-2 and FGF-2-AS mRNA, animals were injected with CORT and mRNA measured. ES and IS similarly downregulated FGF-2-AS mRNA at 0 h post-stress and upregulated FGF-2 mRNA 2 h post-stress. Inhibition of CORT synthesis abrogated the effect of IS on both FGF-2-AS and FGF-2 mRNA. Exogenous CORT mimicked the effects of ES and IS on FGF-2, but not FGF-2-AS mRNA. The present study demonstrates that glucocorticoids mediate the effects of stress on FGF-2 and FGF-2-AS.

Bcl-2 down-regulation causes autophagy in a caspase-independent manner in human leukemic HL60 cells

To understand the roles of bcl-2 for the survival of leukemic cells, we constructed human leukemic HL60 transformant lines in which full length bcl-2 antisense message was conditionally expressed by a tetracycline-regulatable expression system. Cell growth was completely inhibited after antisense message induction and massive cell death was induced. Electron microscopic examinations show that cells died by autophagy, but not by apoptosis. The morphology and the function of mitochondria remained intact: neither the reduction in mitochondrial membrane potential nor the nuclear translocation of AIF, a mitochondrial protein that translocates to nuclei in cases of apoptosis, was observed. Caspase inhibitors did not rescue bcl-2-antisense-mediated autophagy. Thus, bcl-2 is essential for leukemic cell survival and its down-regulation results in autophagy. Cell Death and Differentiation (2000) 7, 1263 - 1269.

Repressible antisense inhibition in B lymphocytes

The tetracycline-responsive promoter (TRP) system has been adopted in an attempt to obtain repressible antisense inhibition in a B lymphocyte model in vitro. Levels of secreted IgM protein and mRNA were assessed following the stable transfection of B cell line, HO-2.2, with a series of plasmid constructs containing antisense or sense target sequence DNA (the 3'-untranslated region adjacent to the secreted exon of IgM gene) under the control of the TRP. Significant reduction (approximately 90%) in IgM secretion was observed for clones transfected with antisense plasmids driven by the TRP and containing the IgH enhancer element and the polyadenylation signal sequence from membrane IgM, when compared with untransfected and sense controls. Tetracycline (1 microgram/ml) addition to the culture medium restored the level of IgM secretion in these clones to control values, demonstrating repressibility of antisense inhibition. Transfection of HO-2.2 cells with antisense (or sense) constructs had no detectable effect on membrane IgM protein levels. Hybridisation studies demonstrated that decreased protein production observed in the antisense-transfected clones was most likely attributable to reduced RNA levels. These data show that the TRP can be used for repressible and specific antisense inhibition of gene product expression in B lymphocytes.

[A new class of small RNP (alpha-RNP) containing antisense RNA in K-562 cells. IV. The coordinated regulation of the expression of Alu-containing mRNA and alpha-RNA during differentiation]

Small alpha-RNP of K-562 cells contain a small RNA as an RNA component, this RNA is homologous to Alu-repeating sequences of human DNA. When cells are exposed to dimethylsulfoxide, an agent inducing cell differentiation along the erythroid pathway, the content of both high-molecular-weight (heterogeneous nuclear and messenger) RNA enriched with Alu repeats and low-molecular-weight specific RNA, small Alu-homologous alpha-RNA undergoes a coordinated decrease. Using the technique of northern blot hybridization, we have demonstrated nonuniform distribution of Alu repeats both in the fraction of total low-molecular-weight RNA of the cytoplasm as well as in the fraction of messenger RNA. It is proposed that alpha-RNA (alpha-RNP) participates in the control of expression of non-linked Alu-containing genes.

Dual function of the copR gene product of plasmid pIP501

Replication of plasmid pIP501 is regulated at a step subsequent to transcription initiation by an antisense RNA (RNAIII) and transcriptionally by a repressor protein, CopR. Previously, it had been shown that CopR binds to a 44-bp DNA fragment upstream of and overlapping the repR promoter pII. Subsequently, we found that high-copy-number pIP501 derivatives lacking copR and low-copy-number derivatives containing copR produced the same intracellular amounts of RNAIII. This suggested a second, hitherto-unknown function of CopR. In this report, we show that CopR does not affect the half-life of RNAIII. Instead, we demonstrate in vivo that, in the presence of both pII and pIII, CopR provided in cis or in trans causes an increase in the intracellular concentration of RNAIII and that this effect is due to the function of the protein rather than its mRNA. We suggest that, in the absence of CopR, the increased (derepressed) RNAII transcription interferes, in cis, with initiation of transcription of RNAIII (convergent transcription), resulting in a lower RNAIII/plasmid ratio. When CopR is present, the pII promoter is repressed to >90%, so that convergent transcription is mostly abolished and RNAIII/plasmid ratios are high. The hypothesis that RNAII transcription influences promoter pIII through induced changes in DNA supercoiling is supported by the finding that the gyrase inhibitor novobiocin affects the accumulation of both sense and antisense RNA. The dual role of CopR in repression of RNAII transcription and in prevention of convergent transcription is discussed in the context of replication control of pIP501.

Naturally occurring antisense RNA

Within the last few years a number of mammalian genes have been found for which there exist naturally occurring "antisense" RNA species with complementarity to mRNAs. Effects of antisense RNA on "sense" RNA have yet to be established. Nevertheless, it is apparent that mammalian cells have devoted genetic information and machinery to processing RNA:RNA hybrids, and it is becoming clear that there may be many more genes than previously suspected to which natural antisense RNAs exist. If naturally occurring antisense RNAs are mediators of alterations in gene expression, the question arises as to whether these pathways can be exploited pharmacologically.

The antisense bcl-2-IgH transcript is an optimal target for synthetic oligonucleotides

In most human follicular B cell lymphomas the bcl-2 gene is up-regulated as a result of the t(14;18) chromosomal translocation generating a hybrid bcl-2-IgH mRNA. Recently, we have identified in t(14;18)-positive cells a bcl-2-IgH mRNA in the antisense orientation, putatively responsible for the overexpression of bcl-2. Herein we show that this chimeric antisense transcript is an optimal target for synthetic oligodeoxynucleotides (ODNs). A variety of sense-oriented oligonucleotides have been designed that target the antisense transcript in regions endowed with a sequence specificity presumably restricted to an individual cell line (the bcl-2-IgH fusion regions) or extended to all t(14;18) cells (the ectopic bcl-2 segment upstream from the major breakpoint region and the IgH segment). All sense-oriented ODNs complementary to the antisense transcript induced an early strong inhibition of cell growth and a late fulminant cell death. As expected, the activity of ODNs targeting the fusion region was restricted to each individual cell line, whereas the activity of all ODNs targeting the common bcl-2 and IgH segments was extended to all t(14;18) cell lines tested. These sense ODNs were not effective in untranslocated cell lines. Antisense-oriented ODNs, complementary to the bcl-2-IgH mRNA, and control ODNs (scrambled, inverted, or mismatched) were biologically ineffective. The selectivity and efficacy of all sense ODNs tested provide support for the development of therapeutic ODNs targeting the bcl-2-IgH antisense transcript expressed in human follicular lymphomas.

[A new class of small RNP (alpha-RNP) containing antisense RNA in K-562 cells. III. The DNA-binding activity of nuclear alpha-RNP. The Signal Transmission from Growth Factors Group of the Medical Faculty, F. Schiller University, Jena, Germany]

DNA-binding activity of small nuclear alpha-RNP identified in acid-soluble fraction of chromatin of human proerythroleukemic cell line K-562 was studied using the technique of gel retardation. We found that nuclear alpha-RNP isolated from K-562 cells through treatment with dimethylsulfoxide, an agent inducing differentiation, acquire a capacity to specific interaction with Alu repeats of DNA leading to the formation of alpha-RNP-Alu-DNA complexes; nuclear alpha-RNP from cells that were not treated with dimethylsulfoxide do not show such capacity, although they are tightly bound with chromatin in the cell. Thus, the capacity of nuclear alpha-RNP to direct interaction with DNA Alu repeats appearing after the induction of K-562 cells to differentiation along erythroid pathway is an inducible property. We discuss hypothesis about the involvement of nuclear alpha-RNP in the control of expression of inducible genes at the level of chromatin and interaction with DNA.

Expression of the 25-kDa heat-shock protein (HSP27) correlates with resistance to the toxicity of cadmium chloride, mercuric chloride, cis-platinum(II)-diammine dichloride, or sodium arsenite in mouse embryonic stem cells transfected with sense or antisense HSP27 cDNA

Embryonic stem (ES) cells were transfected with the protein-coding region of rat HSP27 cDNA placed in sense or antisense orientation in vector pcDNA3 under the control of the constitutive cytomegalovirus (CMV) promoter. Compared with nontransfected ES cells, five sense HSP27 cDNA-transfected ES cell clones displayed up to fourfold increases in expression of HSP27 mRNA and up to sixfold increases in expression of HSP27 protein, whereas four antisense HSP27 cDNA-transfected ES cell lines exhibited synthesis of antisense HSP27 RNA and a 50-85% decrease in HSP27 protein expression. Compared to the parental ES cell lines or ES cells transfected with the vector lacking any HSP27 sequence, all ES cell lines overexpressing HSP27 were resistant to killing by cadmium chloride (CdCl2), mercuric chloride (HgCl2), cis-platinum(II)-diammine dichloride (cDDP), sodium arsenite (NaAsO2), and heat while ES cell lines expressing reduced HSP27 were more sensitive to metal toxicity and heat. The relative toxicities of the tested metals to ES cells were cDDP > NaAsO2 > HgCl2 > CdCl2. Protection of ES cells against metal or heat toxicity was positively correlated with the level of HSP27. These data confirm in ES cells previous reports of the ability of HSP27 to protect other cell types against heat and demonstrate that HSP27 protects mammalian cells against the toxic effects of diverse metals.

[A new class of small RNP (alpha-RNP) containing antisense RNA in K-562 cells. I. Their characteristics and changes during erythroid differentiation]

A new class of small RNP (alpha-RNP) has been detected and identified in nuclei and cytoplasm of A-562 erythroid leukemia cell line; these RNPs have a characteristic spectrum of proteins containing conservative and specific components and a special RNA component, which contains a small antisense component (alpha-RNA), a homolog of short dispersed Alu repeats. alpha-RNP is highly stable, tightly associated with chromatin in the nucleus, and is found in the free state in cytoplasm. The composition of nuclear and cytoplasmic alpha-RNP differ and have a specific pattern of changes in response to dimethylsulfoxide, an agent causing differentiation.

[A new class of small RNP (alpha-RNP) containing antisense RNA in K-562 cells. II. The interaction of the RNA--the alpha-RNP component--with heterogeneous nuclear and messenger RNA in the normal state and under DMSO exposure]

Small antisense RNA (alpha-RNA), components of a new class of small nuclear and cytoplasmic RNP (alpha-RNP) identified in the cells of K-562 human proerythroleukemia cell line, are capable of hybridizing under stringent conditions with precursors of mRNA (heterogeneous nuclear RNA or mRNA) and with mRNA of these cells. We found that DMSO, an agent inducing differentiation in K-562 cells, is capable of regulating the composition of alpha-RNA population and concomitantly changes the content of mRNA that has regions homologous (complementary) to alpha-RNA. Specifically, it has been demonstrated that DMSO decreases the level of alpha-RNA, which hybridizes with the actin gene. Results of restriction mapping of regions of complementary interaction of alpha-RNA with the actin gene point out that alpha-RNA hybridizes with regions containing the promotor area and 3'-nontranslated area of the gene. It is proposed that small antisense alpha-RNA (alpha-RNP) participates in the control of gene expression at posttranscriptional level in cell cytoplasm.

Model systems for the study of the role of PADPRP in essential biological processes

The nuclear enzyme poly(ADP-ribose) polymerase (PADPRP) is implicated in a number of cellular processes, including DNA repair, replication, and differentiation. We have been using several model systems to examine these potential roles of PADPRP. A human keratinocyte model system has been developed in which stable lines of epidermal cells contain an inducible construct harboring the antisense cDNA to PADPRP. When PADPRP antisense RNA is induced in culture, endogenous PADPRP mRNA, protein, and enzymatic activity is lowered, and the pattern of poly(ADP) ribosylation in response to alkylating agents is altered. When keratinocyte clones containing the antisense construct or empty vector alone were grafted onto nude mice, they formed histologically normal human skin. The PADPRP antisense construct was also inducible in vivo by the topical application of dexamethasone to the reconstituted epidermis, as determined by in situ hybridization. In addition, poly(ADP-ribose) polymer could be induced and detected in vivo following the topical application of a DNA alkylating agent to the grafted transfected skin layers. Thus, a model system has been developed in which the levels of PADPRP can be selectively manipulated in human keratinocytes in cell culture, and potentially in reconstituted epidermis as these keratinocyte lines can be grafted to nude mice, whereupon they form a histologically and immunocytochemically normal human epidermis. Another system that we have been utilizing to examine the role of PADPRP in proliferation and differentiation is stable lines of mouse preadipocytes that contain an inducible antisense PADPRP RNA. Similar to the keratinocyte system, these cells can inducibly express antisense PADPRP RNA, and subsequently lower levels of endogenous PADPRP.(ABSTRACT TRUNCATED AT 250 WORDS)

Regulation of pp60c-src expression in rat and mouse fibroblasts by an inducible antisense gene: effects on serum regulation of growth and polyoma virus middle T function

Expression of antisense c-src RNAs in rat and mouse fibroblasts had a dramatic effect on the function of polyoma virus middle T (mT). Antisense c-src RNA decreased the amount of mT:pp60c-src complexes in de novo virus-infected cells and prevented expression of the transformed phenotype in rat F111 cells. Expression of antisense c-src RNA in infected NIH3T3 cells also reduced the formation of mT:pp60c-src complexes but did not affect the ability of polyoma virus to carry out a productive infection. Further analysis of the effects of antisense c-src RNA in uninfected cells revealed that pp60c-src is required for cell growth. When pp60c-src synthesis was reduced, F111 cells stopped proliferating and showed decreased S6 phosphorylation in response to serum. However, F111 cells expressing reduced pp60c-src could be efficiently transformed by v-rasHa, even in the presence of low serum. Thus, pp60c-src appears to function as a component of a signal transduction pathway which regulates cell proliferation in response to serum.