BackgroundBrain tumor (BRAT) is a Drosophila member of the TRIM-NHL protein family. This family is conserved among metazoans and its members function as post-transcriptional regulators. BRAT was thought to be recruited to mRNAs indirectly through interaction with the RNA-binding protein Pumilio (PUM). However, it has recently been demonstrated that BRAT directly binds to RNA. The precise sequence recognized by BRAT, the extent of BRAT-mediated regulation, and the exact roles of PUM and BRAT in post-transcriptional regulation are unknown.ResultsGenome-wide identification of transcripts associated with BRAT or with PUM in Drosophila embryos shows that they bind largely non-overlapping sets of mRNAs. BRAT binds mRNAs that encode proteins associated with a variety of functions, many of which are distinct from those implemented by PUM-associated transcripts. Computational analysis of in vitro and in vivo data identified a novel RNA motif recognized by BRAT that confers BRAT-mediated regulation in tissue culture cells. The regulatory status of BRAT-associated mRNAs suggests a prominent role for BRAT in post-transcriptional regulation, including a previously unidentified role in transcript degradation. Transcriptomic analysis of embryos lacking functional BRAT reveals an important role in mediating the decay of hundreds of maternal mRNAs during the maternal-to-zygotic transition.ConclusionsOur results represent the first genome-wide analysis of the mRNAs associated with a TRIM-NHL protein and the first identification of an RNA motif bound by this protein family. BRAT is a prominent post-transcriptional regulator in the early embryo through mechanisms that are largely independent of PUM.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0659-4) contains supplementary material, which is available to authorized users.

SMAUG (SMG) is an RNA-binding protein that functions as a key component of a transcript degradationpathway that eliminates maternal mRNAs in the bulk cytoplasm of activated Drosophila melanogaster eggs. We previously showed that SMG destabilizes maternal Hsp83 mRNA by recruiting the CCR4-NOT deadenylase to trigger decay; however, the cis-acting elements through which this was accomplished were unknown. Here we show that Hsp83 transcript degradation is regulated by a major element, the Hsp83 mRNA instability element (HIE), which maps to a 615-nucleotide region of the open reading frame (ORF). The HIE is sufficient for association of a transgenic mRNA with SMG protein as well as for SMG-dependent destabilization. Although the Hsp83 mRNA is translated in the early embryo, we show that translation of the mRNA is not necessary for destabilization; indeed, the HIE functions even when located in an mRNA's 3 untranslated region. The Hsp83 mRNA contains eight predicted SMG recognition elements (SREs); all map to the ORF, and six reside within the HIE. Mutation of a single amino acid residue that is essential for SMG's interaction with SREs stabilizes endogenous Hsp83 transcripts. Furthermore, simultaneous mutation of all eight predicted SREs also results in transcript stabilization. A plausible model is that the multiple, widely distributed SREs in the ORF enable some SMG molecules to remain bound to the mRNA despite ribosome transit through any individual SRE. Thus, SMG can recruit the CCR4-NOT deadenylase to trigger Hsp83 mRNA degradation despite the fact that it is being translated.

BackgroundDuring the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole embryos. Here we report the first such analysis for primordial germ cells (PGCs), the progenitors of the germ-line stem cells.ResultsWe purified PGCs from Drosophila embryos, defined their proteome and transcriptome, and assessed the content, scale and dynamics of their MZT. Transcripts encoding proteins that implement particular types of biological functions group into nine distinct expression profiles, reflecting coordinate control at the transcriptional and posttranscriptional levels. mRNAs encoding germ-plasm components and cell-cell signaling molecules are rapidly degraded while new transcription produces mRNAs encoding the core transcriptional and protein synthetic machineries. The RNA-binding protein Smaug is essential for the PGC MZT, clearing transcripts encoding proteins that regulate stem cell behavior, transcriptional and posttranscriptional processes. Computational analyses suggest that Smaug and AU-rich element binding proteins function independently to control transcript elimination.ConclusionsThe scale of the MZT is similar in the soma and PGCs. However, the timing and content of their MZTs differ, reflecting the distinct developmental imperatives of these cell types. The PGC MZT is delayed relative to that in the soma, likely because relief of PGC-specific transcriptional silencing is required for zygotic genome activation as well as for efficient maternal transcript clearance.

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Eukaryotic transcriptional regulatory signals, defined as core and activator promoter elements, have yet to be identified in the earliest diverging group of eukaryotes, the primitive protozoans, which include the Trypanosomatidae family of parasites. The divergence within this family is highlighted by the apparent absence of the "universal" transcription factor TATA-binding protein. To understand gene expression in these protists, we have investigated spliced leader RNA gene transcription. The RNA product of this gene provides an m 7 G cap and a 39-nucleotide leader sequence to all cellular mRNAs via a trans-splicing reaction. Regulation of spliced leader RNA synthesis is controlled by a tripartite promoter located exclusively upstream from the transcription start site. Proteins PBP-1 and PBP-2 bind to two of the three promoter elements in the trypanosomatid Leptomonas seymouri. They represent the first trypanosome transcription factors with typical doublestranded DNA binding site recognition. These proteins ensure efficient transcription. However, accurate initiation is determined an initiator element with a a loose consensus of CYAC/AYR (؉1), which differs from that found in metazoan initiator elements as well as from that identified in one of the earliest diverging protozoans, Trichomonas vaginalis. Trypanosomes may utilize initiator element-protein interactions, and not TATA sequence-TATA-binding protein interactions, to direct proper transcription initiation by RNA polymerase II.Molecular studies of trypanosomatids, a ubiquitous and diverse family of protozoan pathogens, have revealed strikingly unusual mechanisms of mRNA synthesis. One central device is that two independent transcription events direct each mRNA produced in the trypanosome nucleus (for review, see Ref. 1). The protein-coding portion is transcribed as a single primary mRNA, often containing several open reading frames flanked by 5Ј-and 3Ј-untranslated regions. The capped 5Ј-end portion is transcribed as a short spliced leader (SL) 1 RNA. The two parts are fused in a trans-splicing reaction that yields a functional mRNA. During fusion, the 39 nt present on the 5Ј-end of the SL RNA (and referred to as the SL) are transferred to a region upstream from the coding region on the primary mRNA (2). Addition of the SL provides each mRNA with an m 7 G cap as well as four extensively methylated nucleotides, at positions 1-4 within the 39-nt SL RNA (3).The SL RNA is transcribed from a highly reiterated set of genes. In contrast to the long primary transcripts that form the bulk of the mature mRNA, each SL RNA has a discrete transcriptional start site. ␣-Amanitin studies show that it is very probable, though not proven, that the SL RNA gene is transcribed by RNA polymerase (pol) II. The primary SL RNA transcript and the transcript present in the trans-splicing spliceosome possess identical 5Ј-and 3Ј-ends, indicating that both transcription initiation and termination regulate the accumulation of SL RNA. SL RNA expression has been monitored using independe...

Excision repair cross complementing group 1 (ERCC1) and X-ray repair cross-complementing groups 1 (XRCC1) are DNA repair enzymes. Polymorphisms in DNA repair genes may be important factors affecting cancer susceptibility, prognosis and therapy outcome. The purpose of this study was to investigate the correlation of ERCC1 and XRCC1 polymorphisms with colorectal cancer (CRC) risk, and explore the effect of polymorphisms on event-free, overall survival and oxaliplatin-based therapy in CRC patients. Genotyping was examined with the iMLDR technique. An unconditional logistic regression model was used to estimate the association of certain polymorphisms with CRC risk. The Kaplan-Meier method, log-rank test and Cox regression model were employed to evaluate the effects of polymorphisms on survival analysis. Results showed that Trp/Trp genotype of XRCC1 Arg194Trp and AA genotype of ERCC1 rs2336219 have a significantly increased risk of CRC; Trp allele of XRCC1 Arg194Trp and CC genotype of ERCC1 rs735482 were associated with lower response to oxaliplatin-based chemotherapy, a shorter survival and a higher risk of relapse or metastasis. 194Trp/280Arg/399Arg haplotype was associated with a significant resistance, and the ERCC1 protein expression was statistically higher in tumours with rs735482 CC genotype than with AA genotype. Our studies indicate that XRCC1 and ERCC1 polymorphisms probably affect susceptibility, chemotherapy response and survival of CRC patients.

All trypanosome mRNAs have a spliced leader (SL).The SL RNA gene in Leptomonas seymouri is a member of the small nuclear RNA gene family. However, the SL RNA is required in stoichiometric amounts for transsplicing during mRNA formation. Expression of the SL RNA gene requires sequence elements at bp ؊60 to ؊70 and bp ؊30 to ؊40 upstream from the transcription initiation site. Using conventional and affinity chromatography, we have identified and characterized an ϳ122-kDa protein, promoter-binding protein (PBP) ؊1, that binds to double-strand DNA. The PBP-1-binding site is within the bp ؊60 to ؊70 element determined by DNase I footprinting. Therefore, PBP-1 is the first characterized double-strand DNA binding activity that interacts with a trypanosome gene promoter. A second protein, PBP-2, interacts with the PBP-1:DNA complex and its DNase I footprint extends to include the second promoter element (bp ؊30 to ؊40). An alteration of the spacing between the two promoter elements or mutation of the second element decreases PBP-2/PBP-1:DNA stability. Taken together, these data suggest that PBP-1 and PBP-2 are components of a transcription initiation complex that assembles within the SL RNA gene promoter.The Trypanosomatidae are an important family of flagellated, unicellular organisms that parasitize a diverse array of multicellular organisms. The disease-causing trypanosomes, found primarily in developing countries, inflict debilitating symptoms and eventual death on many thousands of people annually.A distinguishing feature of the protozoan family Trypanosomatidae is the presence of a capped, 39-nucleotide (nt) 1 RNA preceding the translational start site of every mRNA (reviewed in Ref. 1). This short RNA is derived from a 3-4-fold longer RNA, called the spliced leader (SL) RNA or Mini Exon Donor RNA. The 5Ј-end of the SL RNA fuses to a primary mRNA and the 3Ј-end is rapidly degraded. Although the trans-splicing of mRNA by an SL RNA occurs in several trematodes, nematodes, and euglenoids, only in trypanosomatids is addition of an SL RNA essential for the formation of every mRNA (2).The SL RNA genes are members of the small nuclear (sn) RNA class of eukaryotic genes (3-5). These genes encode short, nonpolyadenylated RNAs that participate in mRNA-processing reactions. In higher eukaryotes, in which snRNA genes have been extensively studied, snRNAs are synthesized from independent transcription units that contain promoter elements specific to this gene class (6, and reviewed in Refs. 7-9). The presence of common promoter elements was unexpected since some snRNA genes are transcribed by RNA polymerase II and others by RNA polymerase III. In trypanosomatids, the SL RNA genes appear to be transcribed by RNA polymerase II, whereas other snRNA genes, including the U2 snRNA, U6 snRNA, and U3 snRNA homolog (U-snRNA B) genes, are transcribed by RNA polymerase III (5, 10 -12).To characterize transcription of the SL RNA, we began by assessing the effects of mutations on a marked copy of an SL RNA gene. The marked gene was reintr...

Modulating the efficiency of translation plays an important role in a wide variety of cellular processes and is often mediated by trans-acting factors that interact with cis-acting sequences within the mRNA. Here we show that a cis-acting element, the Hsp83 degradation element (HDE), within the 3-untranslated region of the Drosophila Hsp83 mRNA functions as a translational enhancer. We show that this element is bound by a multiprotein complex, and we identify components using a novel affinity-based method called tandem RNA affinity purification tagging. Three proteins (DDP1, Hrp48, and poly(A)-binding protein) are components of the HDE-binding complex and function in translational enhancement. Our data support a model whereby the HDE is composed of several cis-acting subelements that represent binding sites for trans-acting factors, and the combined action of these trans-acting factors underlies the ability of the HDE to stimulate translation.Regulated translation plays an essential role in a wide variety of cellular processes. Although translational regulation is likely to function in virtually all eukaryotic cell types, these controls are particularly important in cells where transcriptional regulation is not an option. For example, maturation of mammalian red blood cells occurs after the nucleus is extruded and thus is driven by previously synthesized mRNAs. Similarly, in early metazoan embryos, the zygotic genome is transcriptionally silent, and maternally deposited mRNAs control early development. Translational regulation is also very important in large cells, such as neurons, where correct spatial and temporal expression of proteins cannot be achieved through transcriptional controls alone.Regulation of specific transcripts is often mediated by cisacting elements within the 5Ј-or 3Ј-untranslated region (UTR) 4 of an mRNA (1). These elements can act as binding sites for trans-acting factors that either directly or indirectly contact the translational machinery. Some of the best characterized mechanisms serve to repress protein expression, but mechanisms that stimulate protein production also exist. In principle, these positively acting events can be divided into two different classes. The first acts on transcripts that are translationally repressed. Translational stimulation is achieved by blocking the repressive mechanism (i.e. enhancement results from relief of repression). The second class of stimulatory events acts on mRNAs that are not repressed. In these cases, an mRNA is better able to recruit the basic translation machinery and is, therefore, expressed at a higher level. This latter type of mechanism is likely to be particularly important when a component of the translation machinery is limiting and, consequently, transcripts must compete for access to the translational apparatus.Many viral RNAs contain elements that aid in preferential expression in infected cells. For example, the 5Ј-UTR of the tobacco mosaic virus RNA contains a cis-acting element, ⍀, that is bound by Hsp101, which in turn recrui...