Introduction

In response to stressful environmental conditions, mammalian cells elicit a series of adaptive changes collectively termed the stress response. Central to the stress response is the implementation of changes in gene expression patterns, which critically influence the cellular outcome. In turn, such gene regulatory events will dictate whether the stressed cell will engage in events such as growth arrest, proliferation, repair of damaged macromolecules, differentiation, or apoptotic death.

Post-transcriptional gene regulatory processes such as RNA splicing and maturation, as well as mRNA transport, stability, and translation, are gaining increasing recognition as key mechanisms controlling gene expression during the stress response (Sheikh and Fornace, 1999; Mitchell and Tollervey, 2000; Kaufman, 2002; Kedersha and Anderson, 2002). Such control mechanisms typically involve the association of transcripts with specific RNA-binding proteins (RBPs) that affect their subcellular localization, stability, and translation rate (Keene, 2001). A growing number of these ribonucleoprotein (RNP) associations have been found to be dependent on the presence of particular RNA sequences rich in adenines and uracils (also known as AU-rich elements or AREs), present in the 5' or 3' untranslated regions (UTRs) of the mRNA (Zhang et al, 2002; Bevilacqua et al, 2003). ARE-dependent RNPs have been described for many transcripts encoding proteins that directly influence cell survival upon exposure to damaging stimuli, such as p53, p27, bcl-2, and p21 (Wang et al, 2000a; Kullmann et al, 2002; Lapucci et al, 2002; Galbán et al, 2003; Mazan-Mamczarz et al, 2003). The ubiquitous member of the Hu/ELAV family of RBPs (which also comprises the primarily neuronal proteins HuB, HuC, and HuD), HuR binds target ARE-bearing mRNA subsets through its RNA-recognition motifs (RRMs), and has been proposed to participate in their export to the cytoplasm, where it increases their stability, modulates their translation, or performs both functions. Through its post-transcriptional influence on target mRNAs such as those encoding c-fos, c-myc, cyclooxygenase-2, tumor necrosis factor-, GM-CSF, -catenin, eotaxin, p27, cyclin A, cyclin B1, cyclin D1, p21, p27, p53, HuR has been proposed to play major roles in cell proliferation, tumorigenesis, the immune response, and the stress response (Brennan and Steitz, 2001; Dixon et al, 2001; Esnault and Malter, 2003; Gorospe, 2003).

The prothymosin (ProT) mRNA was recently identified as one of the major putative targets of HuR (Lal et al, 2004). The encoded ProT is a small, highly acidic protein with a wide tissue distribution and a high degree of conservation among mammals (reviewed in Hannappel and Huff, 2003). ProT was isolated from thymus extracts three decades ago, but progress in elucidating ProT expression and function has been slow and surrounded by controversies regarding its subcellular localization, structural properties, post-translational modifications, related family members, immunomodulatory effects, and mechanisms controlling its expression (Pineiro et al, 2000). Nonetheless, there is a general agreement that ProT promotes cell proliferation, is closely associated with neoplastic growth, and is capable of preventing cell death; consequently, ProT is considered to be an oncoprotein (Eilers et al, 1991; Sburlati et al, 1991; Dosil et al, 1993; Smith et al, 1993; Wu et al, 1997; Rodriguez et al, 1998; Magdalena et al, 2000; Pineiro et al, 2000; Orre et al, 2001). An important breakthrough in elucidating ProT function was the discovery that ProT inhibited the formation of the apoptosome, a cytosolic macromolecular complex (700–1400-kDa) that assembles in cells committed to apoptotic death. In response to apoptogenic stimuli, cytochrome c is released from the mitochondria and binds apoptotic protease activating factor (Apaf)-1 monomers; Apaf-1 then oligomerizes to form the apoptosome, a heptameric structure that recruits and activates caspase-9, which in turn activates effector caspases (caspase-3, -6, -7), culminating in apoptotic cell death (Li et al, 1997; Rodriguez and Lazebnik, 1999; Kaufmann and Hengartner, 2001). ProT was found to hinder the assembly of the apoptosome complex and thereby prevented the activation of caspase-9 and the ensuing apoptotic cascade of events (Jiang et al, 2003).

In this investigation, we set out to formally examine the association of HuR with target ProT mRNA, to study HuR's influence on ProT expression, and to assess the consequences of this interaction on apoptosis. Our results support a role for HuR in enhancing both the abundance of cytoplasmic ProT mRNA and the translation of ProT in response to irradiation with short-wavelength ultraviolet light (UVC), an apoptotic stimulus. We present evidence highlighting a functional interdependence between the prosurvival effects of HuR and those of ProT following stressful stimulation, and propose that ProT is a major effector of the antiapoptotic effects of HuR.

Results

Antiapoptotic effects of HuR in unstimulated and UVC-irradiated cells

In previous studies aimed at modulating HuR expression in cancer cells (Wang et al, 2000a, 2000b; Lal et al, 2004), we consistently noted increased cell death in populations expressing reduced HuR levels (not shown). Here, we systematically investigated the effects of HuR on cell survival in response to UVC, a proapoptotic stimulus that damages DNA and other macromolecules. HuR abundance in the cytoplasm of HeLa cells increased rapidly (by 2 h) following UVC irradiation, remained elevated for at least 12 h, and decreased thereafter (Figure 1A), in keeping with earlier findings in other cell types (Wang et al, 2000a); UVC irradiation also triggered the appearance of cleaved poly(ADP-ribose) polymerase (PARP), a well-established marker of apoptosis. RNAi-based interventions to lower HuR expression in untreated (Untr.) HeLa cells (HuR siRNA group, Figure 1B and D) caused the appearance of nuclei with condensed and fragmented chromatin, distinct hallmarks of apoptosis, while no such nuclei were seen in the control population (Ctrl. siRNA). Following UVC irradiation, apoptotic nuclei were strikingly more abundant in cells expressing reduced HuR levels (Figure 1C). The changes in surviving cells as well as in the condensed/fragmented nuclei in each transfection and treatment group (Figure 1C) further revealed that HuR prevented cell death both in unstressed and in UVC-treated cells. The apoptotic features of populations expressing lower HuR levels were also observed when employing three other sequences targeting different regions of the HuR mRNA (not shown). Western blot analysis further revealed the different apoptotic response of these populations: in Ctrl. siRNA cells, PARP cleavage was only visible after UVC treatment, while in HuR siRNA cells, PARP cleavage was readily visible in unirradiated cells and increased markedly after UVC irradiation. Additional characterization of the apoptotic response by monitoring cleaved caspase-9 and cleaved caspase-3 (two additional apoptotic markers, Figure 1D) further indicated that knockdown of HuR triggered apoptosis in unirradiated cells and potentiated the toxicity of UVC irradiation.

Conversely, ectopic overexpression of HuR by transfection (pHuR-T) reduced the number of apoptotic nuclei detected in control, vector-transfected (Vector) cells by 24 h after UVC irradiation, and largely prevented the cleavage of caspase-9, caspase-3, and PARP (Figure 2A–C). Further evidence of the protective influence of HuR was obtained from 'rescue' experiments. When endogenous HuR expression levels were specifically knocked down by using an siRNA directed to the HuR 3'UTR (HuR(3)), cell survival was strongly reduced (Figure 2D), as anticipated (Figure 1); ectopic overexpression of HuR-T, using a vector that lacked the HuR 3'UTR and hence was insensitive to the effects of HuR(3) siRNA, significantly lowered the apoptotic phenotype (Figure 2D). Together, these results uncover an antiapoptotic function for HuR in both unstimulated and stress-treated cells.

HuR binds the 3'UTR of the ProT mRNA

Earlier studies had identified the ProT mRNA, which bears a long, AU-rich 3'UTR (Figure 3, Schematic), as an HuR target transcript (Lal et al, 2004). In order to directly examine the formation of (HuR-ProT mRNA) RNP complexes, binding assays were performed. First, cDNAs corresponding to either the 5'UTR, the coding region (CR), or the 3'UTR of the ProT mRNA were prepared for use as templates for in vitro transcription and the corresponding biotinylated RNAs used in pulldown assays (Materials and methods). As shown, HuR prominently bound the 3'UTR transcript, but not the CR or 5'UTR transcripts; by contrast, the RBP hnRNP A1 was found to bind the 5'UTR transcript somewhat more strongly than the other two fragments (Figure 3A). Second, an immunoprecipitation (IP) assay was carried out under conditions that preserved endogenous RNP associations. Following RT–PCR analysis of the IP material employing ProT-specific oligomers, a ProT product was readily detected in the IP material obtained using an anti-HuR antibody, while only residual amplification of ProT was observed in both the IgG1 control IP and in control RT–PCR reactions to amplify housekeeping genes GAPDH and SDHA (Figure 3B). These observations indicate that HuR can specifically bind the ProT 3'UTR.

ProT mRNA cytoplasmic abundance and association with HuR in the translating cell fraction increase after UVC

The levels of ProT mRNA (as detected by Northern blotting, Figure 4A) and ProT protein in whole-cell lysates (as detected by Coomassie staining due to unique ProT characteristics that preclude its analysis by Western blotting (Pineiro et al, 2000; Sukhacheva et al, 2002), Figure 4B) remained unchanged following UVC irradiation. However, the cytoplasmic levels of ProT mRNA increased approximately three-fold by 6 h after UVC irradiation, as assessed by either RT+real-time PCR analysis or by Northern blotting, while a concomintant three-fold reduction of ProT mRNA in the nuclear compartment was measured (Figure 4C). The levels of positive control p21 mRNA increased in both compartments after UVC treatment, while the levels of negative control GAPDH mRNA remained unchanged (Figure 4C). These observations suggested that UVC increased ProT mRNA levels in the cytoplasm and decreased them in the nucleus, possibly via a UVC-enhanced mRNA export. That HuR likely contributed to this increase in cytoplasmic ProT mRNA was supported by the findings that cells overexpressing HuR (pHuR-T group) had overall higher levels of cytoplasmic ProT mRNA and lower levels of nuclear ProT mRNA than did control populations (Vector group, Figure 4D).

A closer analysis of the cytoplasmic components of HeLa cells, separated through sucrose gradients to discriminate the nontranslating and the translating fractions, revealed an increase in the ProT mRNA in the translationally engaged, polysomal fractions (fractions 6–10) of UVC-irradiated cells, as monitored by both Northern blotting (Figure 5A, quantified in Supplementary data) and by RT+real-time PCR analysis (Figure 5B). The latter set of experiments also examined the abundance of UVC-regulated mRNAs encoding p21 or cyclin D1 (previously reported; Lal et al, 2004), as well as that of negative controls UBC, GAPDH, and SDHA mRNAs, whose levels and relative distribution on polysomes did not change significantly with UVC irradiation (Lal et al, 2004). The heightened presence of ProT mRNA in the translating fractions further suggested that UVC might enhance the biosynthesis of ProT protein.

Given the association of HuR with ProT transcripts (Figure 3) and the UVC-triggered increase in HuR in actively translating polysomes (Figure 5A), direct evidence for the existence of (HuR-ProT mRNA) complexes was sought in the various cell fractions following UVC irradiation. As shown in Figure 5C, IP followed by RT+real-time PCR analysis revealed a marked increase in the abundance of the (HuR-ProT mRNA) complex, particularly in the polysomes (fractions 6–10). Taking into consideration the aforementioned reports describing a role for HuR in modulating the translation of target mRNAs, we hypothesized that ProT translation could be regulated by HuR and set out to examine this possibility experimentally.

UVC increases ProT translation in an HuR-dependent fashion

ProT is predominantly a nuclear protein (Watts et al, 1989, 1990; Clinton et al, 1991) but its antiapoptotic effects are elicited in the cytoplasm (Jiang et al, 2003). While no UVC-triggered changes in global ProT levels have been reported (Enkemann et al, 2000; Evstafieva et al, 2003; Figure 4B), it was possible that ProT levels increased in the cytoplasm following irradiation. Accordingly, we investigated if the translation and cytoplasmic abundance of ProT were altered following UVC irradiation. These studies were carried out by employing constructs that expressed chimeric EGFP-ProT (pEGFP-ProT, Figure 5D) for several reasons: first, to avoid using the endogenous ProT promoter, which is activated by transcription factor c-myc (Eilers et al, 1991), itself encoded by an mRNA that is a target of HuR (Ma et al, 1996); second, to be able to transfer the protein onto filters for Western blot analysis (ProT fails to bind to nitrocellulose membranes because it lacks sufficient hydrophobic amino acids); third, to be able to use anti-EGFP antibodies for analysis, thereby overcoming the limited usefulness of anti-ProT antibodies available, which poorly detect it by Western blotting; and fourth, because the ProT protein lacks any methionine or cysteine residues, needed for monitoring nascent translation (Materials and methods), an approach that allows the direct measurement of newly synthesized protein and thereby circumvents additional processes influencing protein levels (degradation, cleavage, etc.). Nascent translation of EGFP and EGFP-ProT was assayed by performing a brief (20-min long) incubation in the presence of [³⁵S]-labeled amino acids followed by IP using either an anti-EGFP antibody or control IgG. As shown, UVC did not influence EGFP translation, as determined by monitoring the rate of nascent EGFP translation from construct pEGFP, but strongly elevated the translation of EGFP-ProT (Figure 5E). Importantly, when assessing the levels of the chimeric ProT protein following UVC irradiation, a sizeable increase was detected in the cytoplasm (the cell fraction where ProT inhibits the formation of the apoptosome) of UVC-treated cells (Figure 5F). These observations strongly support the notion that the translation of ProT increased after UVC irradiation.

In order to investigate whether HuR was directly implicated in regulating ProT translation by UVC, interventions to either elevate or knock down HuR levels were undertaken. Following HuR knockdown by siRNA, EGFP-ProT expression was significantly reduced in the HuR siRNA populations, whereas EGFP expression was unchanged between the Ctrl. and HuR siRNA transfection groups (Figure 6A). That this reduction in EGFP-ProT expression was due, at least in part, to a decrease in EGFP-ProT translation in the HuR siRNA population was again determined through the assessment of nascent protein synthesis. After a pulse incubation with ³⁵S-amino acids followed by IP, EGFP-ProT translation was found to be markedly reduced in HuR-knockdown populations, while EGFP translation was unaffected by the reduction in HuR levels (Figure 6B). Conversely, HuR overexpression increased the steady-state abundance of EGFP-ProT (Figure 6C) and its translation rate (Figure 6D), but not those of control EGFP (Figure 6C and D). Northern blot analyses of EGFP mRNA and EGFP-ProT mRNA revealed that the levels of the chimeric transcripts were unchanged among the populations expressing different ectopic HuR levels (not shown). These results underscore a role for HuR in regulating the translation of ProT and hence its cytoplasmic abundance.

Interdependence of prosurvival effects of ProT and HuR

Finally, the influence of ProT and HuR on cell survival was investigated directly. Overexpression of ProT (performed as described in Figure 6) was found to partly rescue the apoptosis triggered by HuR knockdown, both in unirradiated and in UVC-irradiated cells (Figure 7A). Similarly, in UVC-irradiated cells, ProT overexpression potentiated the antiapoptotic phenotype of cells expressing higher HuR levels (Figure 7B). More significantly, a reduction of ProT expression by using oligomers that did not change mRNA levels but suppressed ProT translation (AS oligo, (Sburlati et al, 1991), as determined by Western blotting and ³⁵S incorporation (Figure 7C)) largely abrogated the protective influence of HuR overexpression (compare HuR-T groups between the S oligo and AS oligo populations) and further contributed to enhancing apoptosis (Figure 7D). Assessment of PARP cleavage (Figure 7D, right) served to confirm the relative extent of apoptosis in the S and AS oligo treatment groups. Together, these findings support an antiapoptotic role of HuR that is elicited through HuR-mediated increases in the levels of cytoplasmic ProT mRNA and ProT translation.

Discussion

This report describes the antiapoptotic influence of HuR and examines the mechanisms whereby HuR modulates the expression of ProT, a protein that critically enhances cell survival (Jiang et al, 2003) and is encoded by an HuR target mRNA (Lal et al, 2004). Using UVC-irradiated HeLa cells as model system, HuR was found to strongly promote cell survival after UVC irradiation, and these effects were linked to HuR-mediated increases in cytoplasmic ProT mRNA levels and in ProT translation. Based on these observations, we investigate the existence of molecular and functional associations between the expression and prosurvival effects of HuR and ProT during the stress response.

Post-transcriptional upregulation of HuR target transcripts

While a role for HuR in export of target mRNAs to the cytoplasm has been suggested (Keene, 1999; Gallouzi and Steitz, 2001), HuR has been extensively characterized as a protein that stabilizes target mRNAs, as described for transcripts such as those encoding c-fos, VEGF, cyclooxygenase-2, p21, cyclin A, cyclin B1, matrix metalloprotease 9, GM-CSF, eotaxin, IL-2, c-myc, etc. (reviewed in Brennan and Steitz, 2001). However, HuR and other Hu/ELAV members have also been found to promote the translation of growing number of target transcripts. In addition to enhancing the ProT translation, as described here, HuR was proposed to stimulate the translation of p53 and p27^Kip1 (Millard et al, 2000; Mazan-Mamczarz et al, 2003) (although one study instead reports the repression of p27^Kip1 translation by HuR; Kullmann et al, 2002), while HuB binds to and increases the translation of NF-M and Glut-1 mRNAs (Jain et al, 1997; Antic et al, 1999). The precise mechanisms mediating the enhanced translation of ProT, p53, and p27^Kip1 by HuR are unclear, but may be linked to a mechanism of recruitment of these mRNAs to translationally active polysomes. In the present investigation, no differences in ProT mRNA abundance (Figure 4A) or stability (Supplementary data) were observed, and only an HuR-mediated promotion of ProT translation was apparent (Figure 6). To date, no studies addressing specific links between HuR-mediated stabilization and translation of target transcripts on a global level have been reported, but single-gene studies lend support to an emerging model whereby HuR binds to a given mRNA, likely assists in its nuclear export, protects it from degradation in the cytoplasm, and directs it to ribosomes, enhancing its translation (Keene 1999; Brennan and Steitz, 2001; Lal et al, 2004).

During the cellular response to genotoxic stresses, the presence of damaged DNA causes an inhibition of general transcription (reviewed in Svejstrup, 2002). Paradoxically, while the transcriptional machinery is inhibited, certain proteins participating in the DNA damage response, including those that control the cell division cycle, apoptosis, and DNA repair, must continue to be synthesized. How then does the cell modify its gene expression patterns to adequately sense the damage and elicit a proper response? Several studies support the notion that post-transcriptional events may provide leading mechanisms to control the expression of critical genes in response to DNA damage. For example, recent studies provide systematic demonstration that mRNA turnover accounted for at least one-half of the changes in mRNA steady-state levels following exposure to stresses (Fan et al, 2002; Kawai et al, 2004). Other post-transcriptional mechanisms (such as enhanced mRNA export, heightened translation, or increased protein stability) may likewise provide such regulation of specific DNA damage response proteins, thereby temporarily obviating the need for new transcription (Gorospe, 2003). In addition, post-transcriptional gene regulatory mechanisms would ensure that DNA damage affecting critical genes is not perpetuated by the production of defective proteins and would help preserve conditions of cellular homeostasis during a period of DNA repair. We propose that HuR is a key participant in the execution of such post-transcriptional regulation: it binds to mRNAs encoding proteins that regulate cell proliferation, repair, and apoptosis, likely functions in their nuclear export, helps preserve their cytoplasmic half-life, and enhances their translation. Accordingly, a broad post-transcriptional function for HuR will help ensure that key response proteins such as ProT or p53 are in place through post-transcriptional mechanisms at a critical time of damage assessment and implementation of survival or apoptotic responses.

Antiapoptotic influence of RNA-binding protein HuR

Our findings also uncover ProT as a critical downstream effector of the HuR-elicited survival program. Damaging stimuli such as UVC (Nijhawan et al, 2003) trigger apoptosis by causing the release of cytochrome c from the mitochondria to the cytosol, where it activates Apaf-1 and promotes it oligomerization into the apoptosome. The antiapoptotic function of ProT is attributed to its ability to inhibit the function of the apoptosome (Jiang et al, 2003; Nicholson and Thornberry, 2003), thereby blocking the cleavage of caspase-9 and preventing the ensuing cascade of events. In the present investigation, HuR was found to associate with the ProT mRNA and to enhance its translation and cytoplasmic abundance in response to UVC. ProT-mediated survival was reduced when its translation and cytoplasmic accumulation were diminished in cells that either expressed reduced HuR (Figures 5, 6 and 7) or had been treated with oligomers that blocked ProT translation (Figure 7C and D; Sburlati et al, 1991). The ProT-elicited protection might have been more robust if ProT had been used instead of EGFP-ProT, although the chimeric protein does appear to retain functional characteristics of the endogenous protein (Rubtsov et al, 1997; Sukhacheva et al, 2002; Karetsou et al, 2004). Moreover, the antiapoptotic effects of HuR relied on the enhanced translation of ProT, since interventions to decrease ProT production abrogated the prosurvival effects of HuR (Figure 7).

HuR and cancer

In order to become malignant, cancer cells must acquire a number of traits, including proliferation without growth signals, insensitivity to growth inhibitory signals, avoidance of replicative senescence, evasion of apoptosis, tissue invasion and metastasis, maintenance of angiogenesis, and evasion of antitumor immune response (Hanahan and Weinberg, 2000; Dunn et al, 2004). HuR levels are elevated in cancer (Audic and Hartley, 2004) and, interestingly, it has been proposed to regulate genes critical to the development of each of the aforementioned traits. It can help cells attain the ability to proliferate without external growth signals through its positive influence on the expression of growth factors such as EGF (Sheflin et al, 2004); it can assist cells in eluding growth inhibitory signals and avoiding replicative senescence by promoting the expression of proliferative and proto-oncogenic factors such as c-myc, c-fos, cyclin A, cyclin B, and cyclin D1 (Ma et al, 1996; Wang et al, 2000b; Wang et al, 2001); it can augment the cell's ability to invade and metastasize by elevating the expression of target mRNAs encoding matrix metalloproteases such as MMP-9 (Akool et al, 2003) and metastasis-associated protein 1 (MTA1, López de Silanes et al, 2004); it can promote angiogenesis through its ability to bind to the HIF-1 and VEGF mRNAs and enhance its expression (Levy et al, 1998, Sheflin et al, 2004); and finally, by regulating mRNAs that encode the immunosuppressive cytokine TGF- and the T-cell inhibitor galectin-1 (Nabors et al, 2001; López de Silanes et al, 2004), HuR can help the tumor evade immune recognition, another common adaptive mechanism in malignancy.

The finding that HuR regulates ProT expression reported in the present study strongly supports the notion that HuR can actively enable cancer cells to evade apoptosis. Together with its ability to enhance the expression of genes critical to the other biological traits of malignancy, we hypothesize that HuR plays a central, multidirectional role in the path to cancer development. Substantiating this concept are reports indicating that HuR expression was universally elevated in cancers derived from a wide range of tissues examined (Blaxall et al, 2000; Erkinheimo et al, 2003; López de Silanes et al, 2003). Indeed, the HuR family of proteins was initially identified as specific tumor antigens present in individuals with paraneoplastic neurological disorder, providing the first indication that they could have a cancer-regulatory function (Dalmau et al, 1990; Szabo et al, 1991). Furthermore, the human HuR gene has been localized to chromosome 19p13.2, a locus that is associated with a number of translocations and oncogenic gains in human tumors (Larramendy et al, 1997; Ma and Furneaux 1997; Mao et al, 2002). Investigation of the tumorigenic potential of cells expressing varying levels of HuR using nude mice revealed that heightened HuR levels led to the development of larger and faster-growing tumors, while low HuR-expressing cells gave rise to significantly smaller and slow-developing tumors (López de Silanes et al, 2003). An assessment of whether such a pivotal function for HuR in colon carcinogenesis can be extended to cancer growth arising from other tissues is underway.

In summary, we propose that HuR exerts an antiapoptotic function through mechanisms that rely on binding the ProT mRNA, elevating its cytoplasmic levels, and enhancing the translation of the encoded prosurvival protein. In light of the regulatory paradigm presented here, a reassessment of HuR's impact on the cell's response to immune, proliferative, differentiation, and stressful stimuli is warranted, as we seek a more complete understanding of the post-transcriptional events contributing to the maintenance of cellular homeostasis.

Materials and methods

Cell culture, treatment, RNA interference, and scoring of apoptotic nuclei

Human cervical carcinoma HeLa cells were cultured in Dulbecco's modified essential medium (Gibco-BRL) supplemented with 10% fetal bovine serum and antibiotics. Unless otherwise indicated, irradiated cells received 30 J/m² UVC. For HuR RNAi analysis, cells were transfected with 20 nM of siRNAs in medium containing 3% fetal bovine serum described under ' Supplementary data'. At 48 h after transfection, cells were treated with UVC, allowed to recover for the times indicated, and then either collected for analysis or stained with Hoechst 33342 (1 g/ml, 30 min) to visualize nuclei. To score apoptotic nuclei, 500 cells were counted from duplicate plates; experiments were performed three times independently.

Plasmids and transient transfections

Cloning of the coding region and 3'UTR of ProT downstream of the EGFP coding region in plasmid pEGFP-C1 (BD Biosciences), and cloning of the coding region of HuR upstream of TAP (pcDNA3-TAP, a kind gift from C-Y Chen, (Chen et al, 2001)) are described as ' Supplementary data'. Plasmids pEGFP-ProT and pHuRT (8 g each when used separately, 4 g each when used jointly) were transfected using Lipofectamine 2000; 48 h after transfection cells received 30 J/m² UVC, and were analyzed at varying times afterwards.

Cell fractionation

For the preparation of cytosolic fractions, 5 10⁶ cells were scraped in 400 l of lysis buffer (10 mM Tris–HCl (pH 7.5), 100 mM NaCl, 2.5 mM MgCl₂, and 40 g/ml digitonin). The lysate was incubated in ice for 5 min and centrifuged (2000 g, 8 min), and the supernatant was designated as the soluble cytosolic fraction. Whole-cell lysates were prepared using RIPA buffer as described (Lal et al, 2004). To monitor ProT mRNA levels in the cytoplasm and the nucleus, cytoplasmic extracts were made using digitonin (described above), and nuclear extracts were prepared by resuspending the resulting nuclear pellet in RIPA buffer and lysing by mild sonication. RNA was isolated from these fractions using the Trizol reagent (Invitrogen).

Linear sucrose gradient fractionation was performed as described (Lal et al, 2004; Supplementary data). For Western blot analysis, SDS–PAGE sample buffer was added to an aliquot of each fraction. For Northern blotting and RT–PCR, RNA was isolated from 500 l of each fraction using 3 ml Trizol.

Detection of RNA and protein

RNA was isolated using the Trizol reagent and Northern blot analysis to detect mRNAs encoding p21 and cyclin D1, as well as to detect 18S rRNA was performed as previously described (Wang et al, 2000a), using excess oligomer probes in each case. For the detection of ProT transcripts, a ProT PCR product was labeled using random primers, [-³²P]dATP, and Klenow enzyme.

For Western blot analysis, proteins were resolved by 12% SDS–PAGE and transferred onto PVDF membranes (Invitrogen). Commercial antibodies are described (Supplementary data); a monoclonal anti-hnRNP A1 antibody was a generous gift from Dr G Dreyfuss. Following incubation with appropriate secondary antibodies, signals were detected by enhanced chemiluminescence. Endogenous ProT was isolated from whole-cell lysates by phenol:chlorofom (1:1) extraction followed by SDS–PAGE and Coomassie blue staining of the polyacrylamide gel (Evstafieva et al, 2003).

The RNA isolated from either IP material or from pooled polysomal fractions was reverse-transcribed using random hexamers and SSII RT (Invitrogen), and the resulting cDNA amplified by PCR using gene-specific primer pairs for 25–30 cycles (oligomer sequences and PCR conditions described as Supplementary data).

Binding assays

IP of ribonucleoprotein complexes was previously described (Lal et al, 2004; Supplementary data). In vitro transcription and biotin pulldown assays were described previously (Lal et al, 2004) except that whole-cell lysates (40 g) and equimolar transcript concentrations (16.8 pmol per reaction) were used here. Primers used to prepare templates for in vitro transcription are listed (Supplementary data).

Analysis of nascent protein

Newly translated EGFP or EGFP-ProT proteins were measured by incubating 5 10⁶ cells with 1 mCi L-[³⁵S]methionine and L-[³⁵S]cysteine (Easy Tag ™EXPRESS, NEN/Perkin Elmer) per 60-mm plate for 20 min, whereupon cells were lysed using TSD lysis buffer (50 mM Tris (pH 7.5), 1% SDS, and 5 mM DTT) and EGFP or EGFP-ProT were immunoprecipitated using polyclonal anti-GFP antibody for 18 h at 4°C; IgG was used in control IP reactions. Beads were washed in TNN buffer (50 mM Tris (pH 7.5), 250 mM NaCl, 5 mM EDTA, 0.5% NP-40) and IP material was resolved by 12% SDS–PAGE, transferred onto PVDF membranes, and visualized using a PhosphorImager.

Supplementary data

Supplementary data are available at The EMBO Journal Online.

Acknowledgements

We are grateful to JL Martindale and K Abdelmohsen for helpful discussions.

References

Akool el-S, Kleinert H, Hamada FM, Abdelwahab MH, Forstermann U, Pfeilschifter J, Eberhardt W (2003) Nitric oxide increases the decay of matrix metalloproteinase 9 mRNA by inhibiting the expression of mRNA-stabilizing factor HuR. Mol Cell Biol 23: 4901−4916 | Article |

Antic D, Lu N, Keene JD (1999) ELAV tumor antigen, Hel-N1, increases translation of neurofilament M mRNA and induces formation of neurites in human teratocarcinoma cells. Genes Dev 13: 449−461

Audic Y, Hartley RS (2004) Post-transcriptional regulation in cancer. Biol Cell 96: 479−498 | Article |

Bevilacqua A, Ceriani MC, Capaccioli S, Nicolin A (2003) Post-transcriptional regulation of gene expression by degradation of messenger RNAs. J Cell Physiol 195: 356−372 | Article |

Blaxall BC, Dwyer-Nield LD, Bauer AK, Bohlmeyer TJ, Malkinson AM, Port JD (2000) Differential expression and localization of the mRNA binding proteins, AU-rich element mRNA binding protein (AUF1) and Hu antigen R (HuR), in neoplastic lung tissue. Mol Carcinog 28: 76−83 | Article |

Brennan CM, Steitz JA (2001) HuR and mRNA stability. Cell Mol Life Sci 58: 266−277

Chen CY, Gherzi R, Ong SE, Chan EL, Raijmakers R, Pruijn GJ, Stoecklin G, Moroni C, Mann M, Karin M (2001) AU-binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107: 451−464 | Article |

Clinton M, Graeve L, el-Dorry H, Rodriguez-Boulan E, Horecker BL (1991) Evidence for nuclear targeting of prothymosin and parathymosin synthesized in situ. Proc Natl Acad Sci USA 88: 6608−6612

Dalmau J, Furneaux HM, Gralla RJ, Kris MG, Posner JB (1990) Detection of the anti-Hu antibody in the serum of patients with small cell lung cancer—a quantitative western blot analysis. Ann Neurol 27: 544−552 | Article |

Dixon DA, Tolley ND, King PH, Nabors LB, McIntyre TM, Zimmerman GA, Prescott SM (2001) Altered expression of the mRNA stability factor HuR promotes cyclooxygenase-2 expression in colon cancer cells. J Clin Invest 108: 1657−1665 | Article |

Dosil M, Alvarez-Fernandez L, Gomez-Marquez J (1993) Differentiation-linked expression of prothymosin gene in human myeloid leukemic cells. Exp Cell Res 204: 94−101 | Article |

Dunn GP, Old LJ, Schreiber RD (2004) The immunobiology of cancer immunosurveillance and immunoediting. Immunity 21: 137−148 | Article |

Eilers M, Schirm S, Bishop JM (1991) The MYC protein activates transcription of the -prothymosin gene. EMBO J 10: 133−141

Enkemann SA, Wang RH, Trumbore MW, Berger SL (2000) Functional discontinuities in prothymosin caused by caspase cleavage in apoptotic cells. J Cell Physiol 182: 256−268 | Article |

Erkinheimo TL, Lassus H, Sivula A, Sengupta S, Furneaux H, Hla T, Haglund C, Butzow R, Ristimaki A (2003) Cytoplasmic HuR expression correlates with poor outcome and with cyclooxygenase 2 expression in serous ovarian carcinoma. Cancer Res 63: 7591−7594

Esnault S, Malter JS (2003) Hyaluronic acid or TNF- plus fibronectin triggers granulocyte macrophage-colony-stimulating factor mRNA stabilization in eosinophils yet engages differential intracellular pathways and mRNA binding proteins. J Immunol 171: 6780−6787

Evstafieva AG, Belov GA, Rubtsov YP, Kalkum M, Joseph B, Chichkova NV, Sukhacheva EA, Bogdanov AA, Pettersson RF, Agol VI, Vartapetian AB (2003) Apoptosis-related fragmentation, translocation, and properties of human prothymosin . Exp Cell Res 284: 211−223

Fan J, Yang X, Wang W, Wood III WH, Becker KG, Gorospe M (2002) Global analysis of stress-regulated mRNA turnover using cDNA arrays. Proc Natl Acad Sci USA 99: 10611−10616 | Article |

Galbán S, Martindale JL, Mazan-Mamczarz K, López de Silanes I, Fan J, Wang W, Decker J, Gorospe M (2003) Influence of the RNA-binding protein HuR in pVHL-regulated p53 expression in renal carcinoma cells. Mol Cell Biol 23: 7083−7095 | Article |

Gallouzi IE, Steitz JA (2001) Delineation of mRNA export pathways by the use of cell-permeable peptides. Science 294: 1895−1901 | Article |

Gorospe M (2003) HuR in the mammalian genotoxic response: post-transcriptional multitasking. Cell Cycle 2: 412−414

Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57−70 | Article |

Hannappel E, Huff T (2003) The thymosins Prothymosin , parathymosin, and -thymosins: structure and function. Vitam Horm 66: 257−296

Jain RG, Andrews LG, McGowan KM, Pekala PH, Keene JD (1997) Ectopic expression of Hel-N1, an RNA-binding protein, increases glucose transporter (GLUT1) expression in 3T3-L1 adipocytes. Mol Cell Biol 17: 954−962

Jiang X, Kim HE, Shu H, Zhao Y, Zhang H, Kofron J, Donnelly J, Burns D, Ng SC, Rosenberg S, Wang X (2003) Distinctive roles of PHAP proteins and prothymosin- in a death regulatory pathway. Science 299: 223−226 | Article |

Karetsou Z, Martic G, Tavoulari S, Christoforidis S, Wilm M, Gruss C, Papamarcaki T (2004) Prothymosin associates with the oncoprotein SET and is involved in chromatin decondensation. FEBS Lett 577: 496−500 | Article |

Kaufman RJ (2002) Orchestrating the unfolded protein response in health and disease. J Clin Invest 110: 1389−1398 | Article |

Kaufmann SH, Hengartner MO (2001) Programmed cell death: alive and well in the new millennium Trends. Cell Biol 11: 526−534

Kawai T, Fan J, Mazan-Mamczarz K, Gorospe M (2004) Global mRNA stabilization preferentially linked to translational repression during the endoplasmic reticulum stress response. Mol Cell Biol 24: 6773−6787 | Article |

Kedersha N, Anderson P (2002) Stress granules: sites of mRNA triage that regulate mRNA stability and translatability. Biochem Soc Trans 30: 963−969 | Article |

Keene JD (1999) Why is Hu where? Shuttling of early-response-gene messenger RNA subsets. Proc Natl Acad Sci USA 96: 5−7 | Article |

Keene JD (2001) Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 98: 7018−7024 | Article |

Kullmann M, Gopfert U, Siewe B, Hengst L (2002) ELAV/Hu proteins inhibit p27 translation via an IRES element in the p27 5'UTR. Genes Dev 16: 3087−3099 | Article |

Lal A, Mazan-Mamczarz K, Kawai T, Yang X, Martindale JL, Gorospe M (2004) Concurrent versus individual binding of HuR and AUF1 to common labile target mRNAs. EMBO J 23: 3092−3102 | Article |

Lapucci A, Donnini M, Papucci L, Witort E, Tempestini A, Bevilacqua A, Nicolin A, Brewer G, Schiavone N, Capaccioli S (2002) AUF1 Is a bcl-2 A+U-rich element-binding protein involved in bcl-2 mRNA destabilization during apoptosis. J Biol Chem 277: 16139−16146 | Article |

Larramendy ML, Tarkkanen M, Valle J, Kivioja AH, Ervasti H, Karaharju E, Salmivalli T, Elomaa I, Knuutila S (1997) Gains, losses, and amplifications of DNA sequences evaluated by comparative genomic hybridization in chondrosarcomas. Am J Pathol 150: 685−691

Levy NS, Chung S, Furneaux H, Levy AP (1998) Hypoxic stabilization of vascular endothelial growth factor mRNA by the RNA-binding protein HuR. J Biol Chem 273: 6417−6423 | Article |

Li P, Nijhawan D, Budihardjo I, Srinivasula SM, Ahmad M, Alnemri ES, Wang X (1997) Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade. Cell 91: 479−489 | Article |

López de Silanes I, Fan J, Yang X, Potapova O, Zonderman AB, Pizer ES, Gorospe M (2003) Role of the RNA-binding protein HuR in colon carcinogenesis. Oncogene 22: 7146−7154 | Article |

López de Silanes I, Zhan M, Lal A, Yang X, Gorospe M (2004) Identification of a target RNA motif for RNA-binding protein HuR. Proc Natl Acad Sci USA 101: 2987−2992 | Article |

Ma WJ, Cheng S, Campbell C, Wright A, Furneaux H (1996) Cloning and characterization of HuR, a ubiquitously expressed Elav-like protein. J Biol Chem 271: 8144−8151 | Article |

Ma WJ, Furneaux H (1997) Localization of the human HuR gene to chromosome 19p13.2. Hum Genet 99: 32−33

Magdalena C, Dominguez F, Loidi L, Puente JL (2000) Tumour prothymosin content, a potential prognostic marker for primary breast cancer. Br J Cancer 82: 584−590 | Article |

Mao X, Lillington D, Child F, Russell-Jones R, Young B, Whittaker S (2002) Comparative genomic hybridization analysis of primary cutaneous B-cell lymphomas: identification of common genomic alterations in disease pathogenesis. Genes Chromosomes Cancer 35: 144−155 | Article |

Mazan-Mamczarz K, Galban S, Lopez de Silanes I, Martindale JL, Atasoy U, Keene JD, Gorospe M (2003) RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiation. Proc Natl Acad Sci USA 100: 8354−8359 | Article |

Millard SS, Vidal A, Markus M, Koff A (2000) A U-rich element in the 5' untranslated region is necessary for the translation of p27 mRNA. Mol Cell Biol 20: 5947−5959 | Article |

Mitchell P, Tollervey D (2000) mRNA stability in eukaryotes. Curr Opin Genet Dev 10: 193−198 | Article |

Nabors LB, Gillespie GY, Harkins L, King PH (2001) HuR, a RNA stability factor, is expressed in malignant brain tumors and binds to adenine- and uridine-rich elements within the 3' untranslated regions of cytokine and angiogenic factor mRNAs. Cancer Res 61: 2154−2161

Nicholson DW, Thornberry NA (2003) Apoptosis. Life and death decisions. Science 299: 214−215 | Article |

Nijhawan D, Fang M, Traer E, Zhong Q, Gao W, Du F, Wang X (2003) Elimination of Mcl-1 is required for the initiation of apoptosis following ultraviolet irradiation. Genes Dev 17: 1475−1486 | Article |

Orre RS, Cotter II MA, Subramanian C, Robertson ES (2001) Prothymosin functions as a cellular oncoprotein by inducing transformation of rodent fibroblasts in vitro. J Biol Chem 276: 1794−1799

Pineiro A, Cordero OJ, Nogueira M (2000) Fifteen years of prothymosin : contradictory past and new horizons. Peptides 21: 1433−1446 | Article |

Rodriguez J, Lazebnik Y (1999) Caspase-9 and APAF-1 form an active holoenzyme. Genes Dev 13: 3179−3184 | Article |

Rodriguez P, Vinuela JE, Alvarez-Fernandez L, Buceta M, Vidal A, Dominguez F, Gomez-Marquez J (1998) Overexpression of prothymosin accelerates proliferation and retards differentiation in HL-60 cells. Biochem J 331: 753−761

Rubtsov YP, Zolotukhin AS, Vorobjev IA, Chichkova NV, Pavlov NA, Karger EM, Evstafieva AG, Felber BK, Vartapetian AB (1997) Mutational analysis of human prothymosin reveals a bipartite nuclear localization signal. FEBS Lett 413: 135−141 | Article |

Sburlati AR, Manrow RE, Berger SL (1991) Prothymosin antisense oligomers inhibit myeloma cell division. Proc Natl Acad Sci USA 88: 253−257

Sheflin LG, Zou AP, Spaulding SW (2004) Androgens regulate the binding of endogenous HuR to the AU-rich 3'UTRs of HIF-1 and EGF mRNA. Biochem Biophys Res Commun 322: 644−651 | Article |

Sheikh MS, Fornace Jr AJ (1999) Regulation of translation initiation following stress. Oncogene 18: 6121−6128 | Article |

Smith MR, al-Katib A, Mohammad R, Silverman A, Szabo P, Khilnani S, Kohler W, Nath R, Mutchnick MG (1993) Prothymosin gene expression correlates with proliferation, not differentiation, of HL-60 cells. Blood 82: 1127−1132

Sukhacheva EA, Evstafieva AG, Fateeva TV, Shakulov VR, Efimova NA, Karapetian RN, Rubtsov YP, Vartapetian AB (2002) Sensing prothymosin origin, mutations and conformation with monoclonal antibodies. J Immunol Methods 266: 185−196 | Article |

Svejstrup JQ (2002) Mechanisms of transcription-coupled DNA repair. Nat Rev Mol Cell Biol 3: 21−29 | Article |

Szabo A, Dalmau J, Manley G, Rosenfeld M, Wong E, Henson J, Posner JB, Furneaux HM (1991) HuD, a paraneoplastic encephalomyelitis antigen, contains RNA-binding domains and is homologous to Elav and Sex-lethal. Cell 67: 325−333 | Article |

Wang W, Furneaux H, Cheng H, Caldwell MC, Hutter D, Liu Y, Holbrook N, Gorospe M (2000a) HuR regulates p21 mRNA stabilization by UV light. Mol Cell Biol 20: 760−769 | Article |

Wang W, Lin S, Caldwell CM, Furneaux H, Gorospe M (2000b) HuR Regulates Cyclin A and cyclin B1 mRNA Stability During the Cell Division Cycle. EMBO J 19: 2340−2350 | Article |

Wang W, Yang X, Cristofalo VJ, Holbrook NJ, Gorospe M (2001) Loss of HuR influences gene expression during replicative senescence. Mol Cell Biol 21: 5889−5898 | Article |

Watts JD, Cary PD, Crane-Robinson C (1989) Prothymosin is a nuclear protein. FEBS Lett 245: 17−20 | Article |

Watts JD, Cary PD, Sautiere P, Crane-Robinson C (1990) Thymosins: both nuclear and cytoplasmic proteins. Eur J Biochem 192: 643−651 | Article |

Wu CG, Habib NA, Mitry RR, Reitsma PH, van Deventer SJ, Chamuleau RA (1997) Overexpression of hepatic prothymosin , a novel marker for human hepatocellular carcinoma. Br J Cancer 76: 1199−1204

Zhang T, Kruys V, Huez G, Gueydan C (2002) AU-rich element-mediated translational control: complexity and multiple activities of trans-activating factors. Biochem Soc Trans 30: 952−958 | Article |