We have purified distinct complexes of nine to 12 proteins [referred to as BRG1‐associated factors (BAFs)] from several mammalian cell lines using an antibody to the SWI2‐SNF2 homolog BRG1. Microsequencing revealed that the 47 kDa BAF is identical to INI1. Previously INI1 has been shown to interact with and activate human immunodeficiency virus integrase and to be homologous to the yeast SNF5 gene. A group of BAF47‐associated proteins were affinity purified with antibodies against INI1/BAF47 and were found to be identical to those co‐purified with BRG1, strongly indicating that this group of proteins associates tightly and is likely to be the mammalian equivalent of the yeast SWI‐SNF complex. Complexes containing BRG1 can disrupt nucleosomes and facilitate the binding of GAL4‐VP16 to a nucleosomal template similar to the yeast SWI‐SNF complex. Purification of the complex from several cell lines demonstrates that it is heterogeneous with respect to subunit composition. The two SWI‐SNF2 homologs, BRG1 and hbrm, were found in separate complexes. Certain cell lines completely lack BRG1 and hbrm, indicating that they are not essential for cell viability and that the mammalian SWI‐SNF complex may be tailored to the needs of a differentiated cell type.

Cells have evolved multiple mechanisms to inhibit viral replication. To identify previously unknown antiviral activities, we screened mammalian complementary DNA (cDNA) libraries for genes that prevent infection by a genetically marked retrovirus. Virus-resistant cells were selected from pools of transduced clones, and an active antiviral cDNA was recovered. The gene encodes a CCCH-type zinc finger protein designated ZAP. Expression of the gene caused a profound and specific loss of viral messenger RNAs (mRNAs) from the cytoplasm without affecting the levels of nuclear mRNAs. The finding suggests the existence of a previously unknown machinery for the inhibition of virus replication, targeting a step in viral gene expression.

Summary The selective degradation of mRNAs by the nonsense-mediated decay pathway is a quality control process with important consequences for human disease. From initial studies using RNA hairpin-tagged mRNAs for purification of messenger ribonucleoproteins assembled on transcripts with HIV-1 3′ untranslated region (3′UTR) sequences, we uncover a two-step mechanism for Upf1-dependent degradation of mRNAs with long 3′UTRs. We demonstrate that Upf1 associates with mRNAs in a 3′UTR length-dependent manner and is highly enriched on transcripts containing 3′UTRs known to elicit NMD. Surprisingly, Upf1 recruitment and subsequent RNA decay can be antagonized by retroviral RNA elements that promote translational readthrough. By modulating the efficiency of translation termination, recognition of long 3′UTRs by Upf1 is uncoupled from the initiation of decay. We propose a model for 3′UTR length surveillance in which equilibrium binding of Upf1 to mRNAs precedes a kinetically distinct commitment to RNA decay.

The rat zinc-finger antiviral protein (ZAP) was recently identified as a host protein conferring resistance to retroviral infection. We analyzed ZAP's ability to inhibit viruses from other families and found that ZAP potently inhibits the replication of multiple members of the Alphavirus genus within the Togaviridae, including Sindbis virus, Semliki Forest virus, Ross River virus, and Venezuelan equine encephalitis virus. However, expression of ZAP did not induce a broad-spectrum antiviral state as some viruses, including vesicular stomatitis virus, poliovirus, yellow fever virus, and herpes simplex virus type 1, replicated to normal levels in ZAP-expressing cells. We determined that ZAP expression inhibits Sindbis virus replication after virus penetration and entry, but before the amplification of newly synthesized plus strand genomic RNA. Using a temperature-sensitive Sindbis virus mutant expressing luciferase, we further showed that translation of incoming viral RNA is blocked by ZAP expression. Elucidation of the antiviral mechanism by which ZAP inhibits Sindbis virus translation may lead to the development of agents with broad activity against alphaviruses.A previously unknown rat protein, designated zinc-finger antiviral protein (ZAP), was recently found to exhibit antiviral activity against Moloney murine leukemia virus (MMLV), a member of the Retroviridae. When challenged with an ecotropic MMLV carrying a luciferase reporter, cells expressing ZAP expressed 30 times less luciferase than did control cells. Expression of either the full-length rat ZAP or the aminoterminal one-third fused to the product of the zeocin resistance gene (NZAP-Zeo) was inhibitory, and the mechanism of the block was found to be a dramatic and specific loss of viral mRNAs from the cytoplasm, but not the nuclei, of cells (5). In our effort to better understand virus-host interactions, we tested ZAP's ability to inhibit infection by other viruses. Our studies indicate that, in addition to inhibiting MMLV replication, ZAP's range of targets also includes multiple members of the Alphavirus genus of the Togaviridae.Alphaviruses cause significant morbidity and mortality worldwide (reviewed in reference 7). The broad host range for these viruses includes vertebrates and invertebrates, with arthropods being the usual vectors of transmission to mammals. Infection with Sindbis virus (SIN), the type alphavirus, can lead to a painful polyarthritis, while disease caused by Venezuelan equine encephalitis virus (VEE) ranges from a mild influenzatype illness to fatal encephalitis. Alphaviruses are small, enveloped RNA viruses with an icosahedral nucleocapsid (reviewed in reference 22). The SIN genome consists of a single, capped, positive-sense RNA molecule of approximately 11.7 kb and contains a 5Ј untranslated region (UTR) as well as a 3Ј UTR and a poly(A) tail. The 5Ј-terminal two-thirds of the genomic 49S RNA is directly translated to produce the four nonstructural proteins (nsPs), while the structural proteins are encoded by a subgenomic 26S ...

The zinc finger antiviral protein (ZAP) is a recently isolated host antiviral factor. It specifically inhibits the replication of Moloney murine leukemia virus (MLV) and Sindbis virus (SIN) by preventing the accumulation of viral RNA in the cytoplasm. For this report, we mapped the viral sequences that are sensitive to ZAP inhibition. The viral sequences were cloned into a luciferase reporter and analyzed for the ability to mediate ZAP-dependent destabilization of the reporter. The sensitive sequence in MLV was mapped to the 3 long terminal repeat; the sensitive sequences in SIN were mapped to multiple fragments. The fragment of SIN that displayed the highest destabilizing activity was further analyzed by deletion mutagenesis for the minimal sequence that retained the activity. This led to the identification of a fragment of 653 nucleotides. Any further deletion of this fragment resulted in significantly lower activity. We provide evidence that ZAP directly binds to the active but not the inactive fragments. The CCCH zinc finger motifs of ZAP play important roles in RNA binding and antiviral activity. Disruption of the second and fourth zinc fingers abolished ZAP's activity, whereas disruption of the first and third fingers just slightly lowered its activity.The zinc finger antiviral protein (ZAP) was originally recovered from a screen for genes conferring resistance to the infection of cells by Moloney murine leukemia virus (MLV) (11). The overexpression of ZAP rendered cells 30-fold more resistant to viral infection. An analysis to determine the step at which ZAP blocked virus infection revealed that in ZAP-expressing cells, reverse transcription and nuclear entry of the viral DNA were normal but the production of viral RNA in the cytoplasm was inhibited (11). In addition to its inhibition of MLV, ZAP potently inhibits the replication of multiple members of the Alphavirus genus of the Togaviridae family, including Sindbis virus (SIN), Semliki Forest virus, Ross River virus, and Venezuelan equine encephalitis virus (3). The expression of ZAP does not induce a broad-spectrum antiviral state, as some viruses, including herpes simplex virus type 1 and yellow fever virus, grow normally in ZAP-expressing cells (3). ZAP targets SIN at a stage after binding and penetration, and it prevents translation of the incoming viral RNA (3). Given that alphaviruses are replicated entirely in an RNA state in the cytoplasm (19) and that the production of MLV viral RNA was inhibited only in the cytoplasm, it is tempting to propose that a common mechanism occurring in the cytoplasm underlies the ZAPmediated elimination of MLV and SIN viral RNAs. However, since there is no obvious sequence homology between MLV and SIN, the common feature(s) shared by these two divergent viruses to account for their sensitivity to ZAP remained elusive.Sequence analysis revealed that in the N terminus of ZAP there are four CCCH-type zinc finger motifs. A fragment of 254 amino acids of the N terminus (NZAP) containing the four zinc finger motifs displa...

Moloney murine leukemia virus (M-MLV) replication is restricted in embryonic carcinoma (EC) and embryonic stem (ES) cells, likely to protect the germ line from insertional mutagenesis. Proviral DNAs are potently silenced at the level of transcription in these cells. This silencing is largely due to an unidentified trans-acting factor that is thought to bind to the primer binding site (PBS) of M-MLV and repress transcription from the viral promoter. We have partially purified a large PBS-mediated silencing complex and identified TRIM28 (Kap-1), a known transcriptional silencer, as an integral component of the complex. We show that RNAi-mediated knockdown of TRIM28 in EC and ES cells relieves the restriction and that TRIM28 is bound to the PBS in vivo when restriction takes place. The identification of TRIM28 as a retroviral silencer adds to the growing body of evidence that many TRIM family proteins are involved in retroviral restriction.

Dopaminergic (DA) neurons of substantia nigra in the midbrain control voluntary movement, and their degeneration is the cause of Parkinson's disease. The complete set of genes required to specifically determine the development of midbrain DA subgroups is not known yet. We report here that mice lacking the bicoidrelated homeoprotein Pitx3 fail to develop DA neurons of the substantia nigra. Other mesencephalic DA neurons of the ventral tegmental area and retrorubral field are unaltered in their dopamine expression and histological organization. These data suggest that Pitx3-dependent gene expression is specifically required for the differentiation of DA progenitors within the mesencephalic DA system. M idbrain dopaminergic (DA) cells contribute to the control of voluntary movement, cognition, and emotional behavior. Degeneration of these cells results in Parkinson's disease, and aberrant dopamine neurotransmitter signaling is implicated in schizophrenia and addictive behavioral disorders (1-3). Within the midbrain there are three subgroups of DA neurons, the ventral tegmental area (VTA͞A10), substantia nigra (SN͞ A9), and retrorubral field (RRF͞A8), that together constitute the mesencephalic (mes) system (4). Those DA cells in the SN that innervate the striatum preferentially degenerate in Parkinson's disease, whereas other DA subgroups regulate emotional and reward behaviors.Transcription factors regulate the differentiation of midbrain DA neuron precursors. Two transcription factors have been shown to contribute to different aspects of mesDA neuronal differentiation. One of these, the orphan nuclear hormone receptor Nurr1, is required for maturation of mesDA neuron precursors. Mice harboring null alleles of Nurr1 do not express tyrosine hydroxylase (TH), which catalyzes the initial step of dopamine neurotransmitter biosynthesis (5-11). The other factor, LIM homeodomain transcription factor Lmx1b, contributes partially to the specification of mesDA neuronal progenitors beginning on embryonic day 12.5 in the mouse but is not essential for TH gene expression (12).A third transcription factor, the bicoid-related homeodomain-containing transcription factor Pitx3, which is also known as Ptx3, has been implicated in the development of DA neurons. Pitx3 gene expression is restricted to the developing eye and DA progenitor cells from embryonic day 11 throughout adult life in mice (13,14). In the brain, Pitx3 mRNA localizes specifically to the SN and VTA (14). A reduction in Pitx3 mRNA levels is observed in the ventral midbrain of Lmx1b knockout mice, 6-hydroxydopamine-lesioned rats, and Parkinson's patients (8,11,12,14). Yet, Pitx3 expression is maintained in the ventral midbrain of Nurr1 null mutant embryos (12). These data have been interpreted to suggest that Pitx3 contributes to the combinatorial code defined by multiple transcription factors that establish specification and differentiation of midbrain DA progenitors (12). Here we report that Pitx3 is essential for the development of neurons specific to the SN. The D...

Most cancers arise from oncogenic changes in the genomes of somatic cells, and while the cells may migrate by metastasis, they remain within that single individual. Natural transmission of cancer cells from one individual to another has been observed in two distinctive cases in mammals (Tasmanian devils1 and dogs2,3), but these are generally considered to be rare exceptions in nature. The discovery of transmissible cancer in soft-shell clams (Mya arenaria)4 suggested that this phenomenon might be more widespread. Here we analyzed disseminated neoplasia in mussels (Mytilus trossulus), cockles (Cerastoderma edule), and golden carpet shell clams (Polititapes aureus) and found that neoplasias in all three species are attributable to independent transmissible cancer lineages. In mussels and cockles, the cancer lineages are derived from their respective host species, but unexpectedly, cancer cells in P. aureus are all derived from Venerupis corrugata, a different species living in the same geographic area. No cases of disseminated neoplasia have thus far been found in V. corrugata from the same region. These findings show that transmission of cancer cells in the marine environment is common in multiple species, that it has originated many times, and that while most transmissible cancers were found spreading within the species of origin, cross-species transmission of cancer cells can occur.