Connecting transcription to messenger RNA processing

Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae

Nuclear degradation of aberrant mRNAs in Saccharomyces cerevisiae is accomplished by the nuclear exosome and its cofactors TRAMP/CTEXT. Evidence from this investigation establishes a universal role of the Nrd1p-Nab3p-Sen1p (NNS) complex in the nuclear decay of all categories of aberrant mRNAs. In agreement with this, both nrd1-1 and nrd1-2 mutations impaired the decay of all classes of aberrant messages. This phenotype is similar to that displayed by GAL::RRP41 and rrp6-Δ mutant yeast strains. Remarkably, however, nrd1ΔCID mutation (lacking the C-terminal domain required for interaction of Nrd1p with RNAPII) only diminished the decay of aberrant messages with defects occurring during the early stage of mRNP biogenesis, without affecting other messages with defects generated later in the process. Co-transcriptional recruitment of Nrd1p on the aberrant mRNAs was vital for their concomitant decay. Strikingly, this recruitment on to mRNAs defective in the early phases of biogenesis is solely dependent upon RNAPII. In contrast, Nrd1p recruitment onto export-defective transcripts with defects occurring in the later stage of biogenesis is independent of RNAPII and dependent on the CF1A component, Pcf11p, which explains the observed characteristic phenotype of nrd1ΔCID mutation. Consistently, pcf11-2 mutation displayed a selective impairment in the degradation of only the export-defective messages.

Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow

Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs. The nuclear-localized regulatory mode was also reported for the plant miRNAs. However, evidence is still lacking to show the universality and conservation of the miRNA-mediated regulation in the plant nuclei. Here, we introduced a bioinformatics workflow for genome-wide investigation of miRNA-guided, cleavage-based regulation of the nascent nuclear transcripts. Facilitated by the tool package PmiRNTSA (Plant microRNA-mediated nascent transcript slicing analyzer), plant biologists could perform a comprehensive search for the miRNA slicing sites located within the introns or the exon-intron/intron-exon junctions of the target transcripts, which are supported by degradome sequencing data. The results enable the researchers to examine the co-transcriptional regulatory model of the miRNAs for a specific plant species. Moreover, a case study was performed to search for the slicing sites located within the exon-intron/intron-exon junctions in two model plants. A case study was performed to show the feasibility and reliability of our workflow. Together, we hope that this work could inspire much more innovative research efforts to expand the current understanding of the miRNA action modes in plants.

Nuclear mRNA Surveillance Mechanisms: Function and Links to Human Disease

Production of export-competent mRNAs involves transcription and a series of dynamic processing and modification events of pre-messenger RNAs in the nucleus. Mutations in the genes encoding the transcription and mRNP processing machinery and the complexities involved in the biogenesis events lead to the formation of aberrant messages. These faulty transcripts are promptly eliminated by the nuclear RNA exosome and its cofactors to safeguard the cells and organisms from genetic catastrophe. Mutations in the components of the core nuclear exosome and its cofactors lead to the tissue-specific dysfunction of exosomal activities, which are linked to diverse human diseases and disorders. In this article, we examine the structure and function of both the yeast and human RNA exosome complex and its cofactors, discuss the nature of the various altered amino acid residues implicated in these diseases with the speculative mechanisms of the mutation-induced disorders and project the frontier and prospective avenues of the future research in this field.

PAP Modulations in Daudi Cells and Molt-3 Cells Treated with Etoposide are Mutually Associated with Morphological Evidence of Apoptosis

Daudi (B-cell line) and Molt-3 (T-cell line) cells provide a model for the study of apoptosis, the induction of which is often accompanied by concominant modulations of proteins involved in mRNA maturation. One of these proteins is poly(A) polymerase (PAP), which is responsible for mRNA cleavage and polyadenylation. A number of recent reports also suggest involvement of mRNA maturation and stability in the induction of specific pathways of cell apoptosis. In this study we identified PAP activity levels and isoform modulations in two different cell lines (Daudi and Molt-3) and related them to DNA fragmentation (a hallmark of apoptosis) and cell cycle phase specificity in terms of the temporal sequence of events and the time that elapsed between administration of the apoptosis inducer (the widely used anticancer drug etoposide) and the observed effects. Treatment of both cell lines with 20 μg/mL etoposide induced apoptosis after four hours in Molt-3 cells and only after 24 hours in Daudi cells, as revealed by two independent methods. In Daudi cells the PAP activity levels and isoforms were downregulated prior to ΔΨm reduction, DNA fragmentation and the morphological changes of the nucleus, whereas in Molt-3 cells no PAP activity and isoform modulations were observed prior to the early hallmarks of apoptosis.

Transcriptome Analysis of Core Dinoflagellates Reveals a Universal Bias towards "GC" Rich Codons

Although dinoflagellates are a potential source of pharmaceuticals and natural products, the mechanisms for regulating and producing these compounds are largely unknown because of extensive post-transcriptional control of gene expression. One well-documented mechanism for controlling gene expression during translation is codon bias, whereby specific codons slow or even terminate protein synthesis. Approximately 10,000 annotatable genes from fifteen “core” dinoflagellate transcriptomes along a range of overall guanine and cytosine (GC) content were used for codonW analysis to determine the relative synonymous codon usage (RSCU) and the GC content at each codon position. GC bias in the analyzed dataset and at the third codon position varied from 51% and 54% to 66% and 88%, respectively. Codons poor in GC were observed to be universally absent, but bias was most pronounced for codons ending in uracil followed by adenine (UA). GC bias at the third codon position was able to explain low abundance codons as well as the low effective number of codons. Thus, we propose that a bias towards codons rich in GC bases is a universal feature of core dinoflagellates, possibly relating to their unique chromosome structure, and not likely a major mechanism for controlling gene expression.

Human p53 interacts with the elongating RNAPII complex and is required for the release of actinomycin D induced transcription blockage

The p53 tumour suppressor regulates the transcription initiation of selected genes by binding to specific DNA sequences at their promoters. Here we report a novel role of p53 in transcription elongation in human cells. Our data demonstrate that upon transcription elongation blockage, p53 is associated with genes that have not been reported as its direct targets. p53 could be co-immunoprecipitated with active forms of DNA-directed RNA polymerase II subunit 1 (RPB1), highlighting its association with the elongating RNA polymerase II. During a normal transcription cycle, p53 and RPB1 are localised at distinct regions of selected non-canonical p53 target genes and this pattern of localisation was changed upon blockage of transcription elongation. Additionally, transcription elongation blockage induced the proteasomal degradation of RPB1. Our results reveal a novel role of p53 in human cells during transcription elongation blockage that may facilitate the removal of RNA polymerase II from DNA.

Control of human papillomavirus gene expression by alternative splicing

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Alternative splicing is a key cellular mechanism controlling HPV gene expression.

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Many cellular SR proteins and hnRNPs have been identified that bind and control production of viral mRNAs.

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HPV16 E2 protein controls expression of SR proteins and has splicing-related functions.

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HPV16 infection through its regulatory effects on splicing factors may significantly alter cellular gene expression and cellular metabolism.

Human papillomaviruses possess circular double stranded DNA genomes of around 8 kb in size from which multiple mRNAs are synthesized during an infectious life cycle. Although at least three viral promoters are used to initiate transcription, viral mRNAs are largely the product of processing of pre-mRNAs by alternative splicing and polyadenylation. The HPV life cycle and viral gene expression are tightly linked to differentiation of the epithelium the virus infects: there is an orchestrated production of viral mRNAs and proteins. In this review we describe viral mRNA expression and the roles of the SR and hnRNP proteins that respectively positively and negatively regulate splicing. We discuss HPV regulation of splicing factors and detail the evidence that the papillomavirus E2 protein has splicing-related activities. We highlight the possibility that HPV-mediated control of splicing in differentiating epithelial cells may be necessary to accomplish the viral replication cycle.

Genomics Basics: DNA Structure, Gene Expression, Cloning, Genetic Mapping, and Molecular Tests

Genomics is the study of the structure and function of the human genome including genes and their surrounding DNA sequences. The over 3 billion base pairs of the human genome have now been sequenced and approximately 25 000 genes acknowledged. However, only 1% of the entire genome has been assigned to protein coding and decades more work is anticipated to define the functional relevance of noncoding DNA as well as the basis and consequences of sequence variations among individuals. For medical scientists, the focus remains on discovering both disease-causing and disease-susceptibility genes. For pharmaceutical companies, the opportunity to develop molecularly targeted therapy is not going unnoticed. For the practicing physician, the prospect of genomic medicine that incorporates molecular diagnosis and pathogenesis-targeted therapy requires basic understanding of terminology and concepts in molecular biology and the corresponding laboratory tests.

Human Papillomavirus E2 Regulates SRSF3 (SRp20) To Promote Capsid Protein Expression in Infected Differentiated Keratinocytes

The human papillomavirus (HPV) life cycle is tightly linked to differentiation of the infected epithelial cell, suggesting a sophisticated interplay between host cell metabolism and virus replication. Previously, we demonstrated in differentiated keratinocytes in vitro and in vivo that HPV type 16 (HPV16) infection caused increased levels of the cellular SR splicing factors (SRSFs) SRSF1 (ASF/SF2), SRSF2 (SC35), and SRSF3 (SRp20). Moreover, the viral E2 transcription and replication factor that is expressed at high levels in differentiating keratinocytes could bind and control activity of the SRSF1 gene promoter. Here, we show that the E2 proteins of HPV16 and HPV31 control the expression of SRSFs 1, 2, and 3 in a differentiation-dependent manner. E2 has the greatest transactivation effect on expression of SRSF3. Small interfering RNA depletion experiments in two different models of the HPV16 life cycle (W12E and NIKS16) and one model of the HPV31 life cycle (CIN612-9E) revealed that only SRSF3 contributed significantly to regulation of late events in the virus life cycle. Increased levels of SRSF3 are required for L1 mRNA and capsid protein expression. Capsid protein expression was regulated specifically by SRSF3 and appeared independent of other SRSFs. Taken together, these data suggest a significant role of the HPV E2 protein in regulating late events in the HPV life cycle through transcriptional regulation of SRSF3 expression.

IMPORTANCE

Human papillomavirus replication is accomplished in concert with differentiation of the infected epithelium. Virus capsid protein expression is confined to the upper epithelial layers so as to avoid immune detection. In this study, we demonstrate that the viral E2 transcription factor activates the promoter of the cellular SRSF3 RNA processing factor. SRSF3 is required for expression of the E4(^)L1 mRNA and so controls expression of the HPV L1 capsid protein. Thus, we reveal a new dimension of virus-host interaction crucial for production of infectious virus. SRSF proteins are known drug targets. Therefore, this study provides an excellent basis for developing strategies to regulate capsid protein production in the infected epithelium and the production of new virions.

Posttranscriptional adaptations of the vascular endothelium to hypoxia

PURPOSE OF REVIEW

Remarkable new advances have been made in the field of posttranscriptional gene regulation over recent years. These include the revelation of noncoding RNAs, such as microRNAs, antisense transcripts and their interactions with RNA-binding proteins (RBPs) in the context of both health and disease settings, such as hypoxia. In particular, these discoveries bear much relevance to the field of vascular biology, which historically has focused upon transcriptional processes. Thus, the contributions of these posttranscriptional gene regulatory mechanisms to vascular and endothelial biology represent a newer concept that warrants discussion.

RECENT FINDINGS

Recent studies have revealed two emerging themes that are critical to endothelial/vascular biology and function. First is the functional integration between the microRNA pathway and the cellular hypoxic response, which, in addition to specific microRNAs, involves key components of the microRNA biogenesis machinery. A key concept here is the regulation of a master transcriptional programme through posttranscriptional mechanisms. The second major theme involves the dynamic interactions between RBPs, microRNAs and antisense RNAs. The condition-dependent collaborations and competitions between these different classes of posttranscriptional regulators reveal a critical layer of control for gene expression.

SUMMARY

Taken together, these findings bear significant diagnostic and therapeutic implications for vascular disease.

Investigation of protein-RNA interactions by mass spectrometry--Techniques and applications

Protein-RNA complexes play many important roles in diverse cellular functions. They are involved in a wide variety of different processes in growth and differentiation at the various stages of the cell cycle. As their function and catalytic activity are directly coupled to the structural arrangement of their components--proteins and ribonucleic acids--the investigation of protein-RNA interactions is of great functional and structural importance. Here we discuss the most prominent examples of protein-RNA complexes and describe some frequently used purification strategies. We present various techniques and applications of mass spectrometry to study protein-RNA complexes. We discuss the analysis of intact complexes as well as proteomics-based and crosslinking-based approaches in which proteins are cleaved into smaller peptides. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.

Theory of the origin, evolution, and nature of life

Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

A model in vitro system for co-transcriptional splicing

A hallmark of metazoan RNA polymerase II transcripts is the presence of numerous small exons surrounded by large introns. Abundant evidence indicates that splicing to excise introns occurs co-transcriptionally, prior to release of the nascent transcript from RNAP II. Here, we established an efficient model system for co-transcriptional splicing in vitro. In this system, CMV-DNA constructs immobilized on beads generate RNAP II transcripts containing two exons and an intron. Consistent with previous work, our data indicate that elongating nascent transcripts are tethered to RNAP II on the immobilized DNA template. We show that nascent transcripts that reach full length, but are still attached to RNAP II, are efficiently spliced. When the nascent transcript is cleaved within the intron using RNase H, both the 5′ and 3′ cleavage fragments are detected in the bound fraction, where they undergo splicing. Together, our work establishes a system for co-transcriptional splicing in vitro, in which the spliceosome containing the 5′ and 3′ exons are tethered to RNAP II for splicing.

Heterogeneity in mammalian RNA 3' end formation

Precisely directed cleavage and polyadenylation of mRNA is a fundamental part of eukaryotic gene expression. Yet, 3' end heterogeneity has been documented for thousands of mammalian genes, and usage of one cleavage and polyadenylation signal over another has been shown to impact gene expression in many cases. Building upon the rich biochemical and genetic understanding of the 3' end formation, recent genomic studies have begun to suggest that widespread changes in mRNA cleavage and polyadenylation may be a part of large, dynamic gene regulatory programs. In this review, we begin with a modest overview of the studies that defined the mechanisms of mammalian 3' end formation, and then discuss how recent genomic studies intersect with these more traditional approaches, showing that both will be crucial for expanding our understanding of this facet of gene regulation.

A dual reporter approach to quantify defects in messenger RNA processing

Splicing and nuclear export are vital components of eukaryotic gene expression. Defects in splicing due to cis mutations are known to cause a number of human diseases. Here we present a dual reporter system that can be used to look at splicing or export deficiencies resulting from an insufficiency in components of the cotranscriptional machinery. The constructs use a bidirectional promoter to coexpress a test reporter and a control reporter. In the splicing construct, maximal expression of the test reporter is dependent on efficient splicing and splicing-related nuclear export, whereas the control reporter is an intronless complementary DNA expression cassette. The dual reporters allow a robust ratiometric output that is independent of cell number or transfection efficiency. Therefore, our construct is internally controlled and amenable to high-throughput analysis. As a counterscreen, we have a nonsplicing control construct in which neither reporter bears an intron. We demonstrate the sensitivity of our construct to defects in nuclear export by depleting UAP56 and NXF1, essential components of the cotranscriptional machinery.

Coupled transcription-splicing regulation of mutually exclusive splicing events at the 5' exons of protein 4.1R gene

The tightly regulated production of distinct erythrocyte protein 4.1R isoforms involves differential splicing of 3 mutually exclusive first exons (1A, 1B, 1C) to the alternative 3' splice sites (ss) of exon 2'/2. Here, we demonstrate that exon 1 and 2'/2 splicing diversity is regulated by a transcription-coupled splicing mechanism. We also implicate distinctive regulatory elements that promote the splicing of exon 1A to the distal 3' ss and exon 1B to the proximal 3' ss in murine erythroleukemia cells. A hybrid minigene driven by cytomegalovirus promoter mimicked 1B-promoter-driven splicing patterns but differed from 1A-promoter-driven splicing patterns, suggesting that promoter identity affects exon 2'/2 splicing. Furthermore, splicing factor SF2/ASF ultraviolet (UV) cross-linked to the exon 2'/2 junction CAGAGAA, a sequence that overlaps the distal U2AF(35)-binding 3' ss. Consequently, depletion of SF2/ASF allowed exon 1B to splice to the distal 3' ss but had no effect on exon 1A splicing. These findings identify for the first time that an SF2/ASF binding site also can serve as a 3' ss in a transcript-dependent manner. Taken together, our results suggest that 4.1R gene expression involves transcriptional regulation coupled with a complex splicing regulatory network.

Effects of the multiple polyadenylation signal AAUAAA on mRNA 3'-end formation and gene expression

Polyadenylation (poly(A)) of eukaryotic mRNA is a critical step for gene expression. In plants, poly(A) signals leading to the formation of polyadenosine tails after mRNAs include the far upstream elements, the AAUAAA-like signals, and the mRNA cleavage sites for poly(A). Multiple AAUAAA signals leading to alternative polyadenosine formation have been found in many genes, but the effects of each AAUAAA signal on gene expression remain to be uncovered. A DNA fragment, whose transcript contains two canonical AAUAAA signals from the 3'-untranslation region of endochitinase gene of tobacco (Nicotiana tabacum L. cv. W38), was mutated and constructed into the downstream of beta-glucuronidase (GUS) coding region. Transient expression of GUS gene from these constructs indicated that the distal AAUAAA signal from the stop codon was more important than the proximal one in stimulating gene expression. Also, the sequence rather than the distance between the stop codon and the AAUAAA signal region was critical for gene expression. Transgenic tobaccos with these constructs were also generated, and the position of the polyadenosine tail formation in this region was mapped. Results revealed that both AAUAAA signals were functional, and that polyadenosine tails of most transcripts were directed by the distal AAUAAA signal. Finally, the RNA stabilities of these variants in transgenic plants were measured. RNAs from the variants with the functional distal AAUAAA signal were more stable than those with the functional proximal one only. The possible secondary structure in this poly(A) signal region was predicted and discussed.

Species-specific cis-regulatory elements in the 3'-untranslated region direct alternative polyadenylation of bone morphogenetic protein 2 mRNA

BMP2 (bone morphogenetic protein 2) is a multifunctional member of the transforming growth factor-beta family of growth factors. Disruption of BMP2 signaling results in developmental defects, cancers, and other diseases. BMP2 mRNAs are alternatively polyadenylated, resulting in mRNAs with distinct 3'-untranslated regions. The longer mRNA contains additional putative binding sites for post-transcriptional regulatory factors, including micro-RNAs. We combined functional assays with computational analyses of emerging genome data to define site- and species-specific polyadenylation determinants. In all mouse and human cell lines tested, shorter mRNAs resulting from using the first polyadenylation signal (PA1) were more abundant than mRNAs from the second signal (PA2). However, the PA1/PA2 usage ratios were 2-3-fold higher in human than in mouse cells. Expression of human BMP2 constructs in mouse cells and mouse constructs in human cells showed that cis-regulatory elements direct species-specific 3' processing of BMP2 transcripts. A 72-nucleotide region downstream of PA2 in the mouse sequence contains two novel cis-acting elements previously hypothesized to regulate polyadenylation in a bioinformatics analysis. Mutations that humanized the mouse-specific elements lowered the affinity for cleavage stimulation factor CstF64 and significantly weakened the PA2 signal relative to the PA1 signal. Thus, we have experimentally defined for the first time cis-regulatory elements that control a species-specific difference in the 3'-end processing of BMP2 and potentially of other genes.

Human PARM-1 is a novel mucin-like, androgen-regulated gene exhibiting proliferative effects in prostate cancer cells

In this paper we characterize hPARM-1, the human ortholog of rat PARM-1 (prostatic androgen-repressed message-1) and demonstrate its role in prostate cancer. Immunofluorescence microscopy and ultrastructural analysis revealed the localization of hPARM-1 to Golgi, plasma membrane and the early endocytic pathway but not in lysosomes. Biochemical and deglycosylation studies showed hPARM-1 as a highly glycosylated, mucin-like type I transmembrane protein. Analysis of expression of hPARM-1 in various human tissues revealed its presence in most human tissues with especially high expression in heart, kidney and placenta. Androgen controls the expression of the gene as a marked 7-fold increase is seen in the androgen-dependent prostate cancer cell line, LNCaP on androgen stimulation. This is further supported by its decrease in expression in CWR22 xenograft upon castration. Moreover, ectopic expression of hPARM-1 in PC3 prostate cancer cells increased colony formation, suggesting a probable role in cell proliferation. These results suggest that hPARM-1 may have a role in normal biology of the prostate cell and in prostate cancer.

Regulation of heme oxygenase-1 mRNA deadenylation and turnover in NIH3T3 cells by nitrosative or alkylation stress

Background

Heme oxygenase-1 (HO-1) catalizes heme degradation, and is considered one of the most sensitive indicators of cellular stress. Previous work in human fibroblasts has shown that HO-1 expression is induced by NO, and that transcriptional induction is only partially responsible; instead, the HO-1 mRNA half-life is substantially increased in response to NO. The mechanism of this stabilization remains unknown.

Results

In NIH3T3 murine fibroblasts, NO exposure increased the half-life of the HO-1 transcript from ~1.6 h to 11 h, while treatments with CdCl₂, NaAsO₂ or H₂O₂ increased the half-life only up to 5 h. Although poly(A) tail shortening can be rate-limiting in mRNA degradation, the HO-1 mRNA deadenylation rate in NO-treated cells was ~65% of that in untreated controls. In untreated cells, HO-1 poly(A) removal proceeded until 30–50 nt remained, followed by rapid mRNA decay. In NO-treated cells, HO-1 deadenylation stopped with the mRNA retaining poly(A) tails 30–50 nt long. We hypothesize that NO treatment stops poly(A) tail shortening at the critical 30- to 50-nt length. This is not a general mechanism for the post-transcriptional regulation of HO-1 mRNA. Methyl methane sulfonate also stabilized HO-1 mRNA, but that was associated with an 8-fold decrease in the deadenylation rate compared to that of untreated cells. Another HO-1 inducer, CdCl₂, caused a strong increase in the mRNA level without affecting the HO-1 mRNA half-life.

Conclusion

The regulation of HO-1 mRNA levels in response to cellular stress can be induced by transcriptional and different post-transcriptional events that act independently, and vary depending on the stress inducer. While NO appears to stabilize HO-1 mRNA by preventing the final steps of deadenylation, methyl methane sulfonate achieves stabilization through the regulation of earlier stages of deadenylation.

Understanding stem cell differentiation through self-organization theory

The mechanism underling stem cells' key property, the ability to either divide into two replicate cells or a replicate and a differentiated daughter, still is not understood. We tested a hypothesis that stem cell asymmetric division/differentiation is spontaneously created by the coupling of processes within each daughter and the resulting biochemical feedbacks via the exchange of molecules between them during mitotic division. We developed a mathematical/biochemical model that accounts for dynamic processes accompanying division, including signaling initiation and transcriptional, translational and post-translational (TTP) reactions. Analysis of this model shows that it could explain how stem cells make the decision to divide symmetrically or asymmetrically under different microenvironmental conditions. The analysis also reveals that a stem cell can be induced externally to transition to an alternative state that does not have the potentiality to have the option to divide symmetrically or asymmetrically. With this model, we initiated a search of large databases of transcriptional regulatory network (TRN), protein-protein interaction, and cell signaling pathways. We found 12 subnetworks (motifs) that could support human stem cell asymmetric division. A prime example of the discoveries made possible by this tool, two groups of the genes in the genetic model are revealed to be strongly over-represented in a database of cancer-related genes.

Polyadenylation site choice in yeast is affected by competition between Npl3 and polyadenylation factor CFI

Multiple steps in mRNA processing and transcription are coupled. Notably, the processing of mRNA 3' ends is linked to transcription termination by RNA polymerase II. Previously, we found that the yeast hnRNP protein Npl3 can negatively regulate 3' end mRNA formation and termination at the GAL1 gene. Here we show that overexpression of the Hrp1 or Rna14 subunits of the CF IA polyadenylation factor increases recognition of a weakened polyadenylation site. Genetic interactions of mutant alleles of NPL3 or HRP1 with RNA15 also indicate antagonism between these factors. Npl3 competes with Rna15 for binding to a polyadenylation precursor and inhibits cleavage and polyadenylation in vitro. These results suggest that an important function of hnRNP proteins is to ensure the fidelity of mRNA processing. Our results support a model in which balanced competition of Npl3 with mRNA processing factors may promote recognition of proper polyadenylation sites while suppressing cryptic sites.

Mechanisms controlling production of membrane and secreted immunoglobulin during B cell development

The immunoglobulin gene which encodes both membrane-associated and secreted proteins through alternative RNA processing reactions has been a model system used for over 25 yr to better understand the regulatory mechanisms governing alternative RNA processing. This gene contains competing cleavage-polyadenylation and RNA splicing reactions and the relative use of the two pathways is differentially regulated between B cells and plasma cells. General cleavage-polyadenylation and RNA splicing reactions are both altered during B cell maturation to affect immunoglobulin expression. However, the specific factors involved in this regulation have yet to be identified clearly. As transcriptional regulators stimulate the developmental RNA processing switch, microarray analysis is a promising approach to identify candidate regulators of this complex RNA processing mechanism.

Deletion of the nuclear exosome component RRP6 leads to continued accumulation of the histone mRNA HTB1 in S-phase of the cell cycle in Saccharomyces cerevisiae

The nuclear exosome, a macromolecular complex of 3' to 5' exonucleases, is required for the post-transcriptional processing of a variety of RNAs including rRNAs and snoRNAs. Additionally, this complex forms part of a nuclear surveillance network where it acts to degrade any aberrantly processed mRNAs in the nucleus. The exosome complex has been implicated in the biogenesis pathway of general messenger RNAs through its interaction with the 3'-end processing machinery. During the cell cycle, yeast histone mRNAs accumulate in the S-phase and are rapidly degraded as cells enter the G2-phase. To determine if the exosome contributes to the cyclic turnover of yeast histone mRNAs, we examined the pattern of accumulation of 'HTB1' mRNA during the cell cycle in a deletion strain of 'RRP6', a component of the nuclear exosome. Our results show that cells lacking Rrp6p continue to accumulate HTB1 mRNA as the cell cycle proceeds. This continued accumulation appears to result from a delay in exit from S-phase in rrp6 cells. The accumulation of HTB1 mRNA in rrp6 cells is influenced by the interaction of the nuclear exosome with the 3'-end processing machinery although there is no evidence for differential regulation of histone mRNA 3'-end processing during the yeast cell cycle.

Specific trans-acting proteins interact with auxiliary RNA polyadenylation elements in the COX-2 3'-UTR

Two cyclooxygenase (COX) enzymes, COX-1 and COX-2, are present in human cells. While COX-1 is constitutively expressed, COX-2 is inducible and up-regulated in response to many signals. Since increased transcriptional activity accounts for only part of COX-2 up-regulation, we chose to explore other RNA processing mechanisms in the regulation of this gene. Previously, we showed that COX-2 is regulated by alternative polyadenylation, and that the COX-2 proximal polyadenylation signal contains auxiliary upstream sequence elements (USEs) that are very important in efficient polyadenylation. To explore trans-acting protein factors interacting with these cis-acting RNA elements, we performed pull-down assays with HeLa nuclear extract and biotinylated RNA oligonucleotides representing COX-2 USEs. We identified PSF, p54(nrb), PTB, and U1A as proteins specifically bound to the COX-2 USEs. We further explored their participation in polyadenylation using MS2 phage coat protein-MS2 RNA binding site tethering assays, and found that tethering any of these four proteins to the COX-2 USE mutant RNA can compensate for these cis-acting elements. Finally, we suggest that these proteins (p54(nrb), PTB, PSF, and U1A) may interact as a complex since immunoprecipitations of the transfected MS2 fusion proteins coprecipitate the other proteins.

Temporal and spatial control of gene expression in early embryos of farm animals

A gradual transition from oocyte-derived mRNA and proteins to full embryonic transcription characterises early embryonic development. Messenger RNAs and proteins of maternal origin are accumulated into the oocyte throughout its growth inthe ovary. Upon fertilisation, sev eral mechanisms ar e activated that controlthe appropriate use of such material and prepare for the synthesis of new products. The present review will describe some of the mechanisms active in early embryos of domestic species. Data will be presented on the control of gene expression by the 3' untranslated regions and their interaction with specialised sequences at the 5' cap end. The process of RNA sorting and localisation, initially described in different cell types and in oocytes of lower species, will also be discussed, particularly in relation to its possible role in regulating early pig development. Finally, specific genes involved in the activation of cattle embryonic transcription will be described. This brief overview will provide some suggestions on how these different mechanisms may be integrated and cooperate to ensure the correct initiation of embryonic development.

Knock-down of 25 kDa subunit of cleavage factor Im in Hela cells alters alternative polyadenylation within 3'-UTRs

Alternative polyadenylation leads to mRNAs with variable 3′ ends. Since a 3′-untranslated region (3′-UTR) often contains cis elements that impact stability or localization of mRNA or translation, selection of poly(A) sites in a 3′-UTR is regulated in mammalian cells. However, the molecular basis for alternative poly(A) site selection within a 3′-UTR has been unclear. Here we show involvement of cleavage factor Im (CFIm) in poly(A) site selection within a 3′-UTR. CFIm is a heterodimeric 3′ end-processing complex, which functions to assemble other processing factors on pre-mRNA in vitro. We knocked down 25 kDa subunit of CFIm (CFIm25) in HeLa cells and analyzed alternative poly(A) site selection of TIMP-2, syndecan2, ERCC6 and DHFR genes by northern blotting. We observed changes in the distribution of mRNAs in CFIm25 depleted cells, suggesting a role for CFIm in alternative poly(A) site selection. Furthermore, tissue specific analysis demonstrated that the CFIm25 gene gave rise to 1.1, 2.0 and 4.6 kb mRNAs. The 4.6 kb mRNA was ubiquitously expressed, while the 1.1 and 2.0 kb mRNAs were expressed in a tissue specific manner. We found three likely poly(A) sites in the CFIm25 3′-UTR, suggesting alternative polyadenylation. Our results indicate that alternative poly(A) site selection is a well-regulated process in vivo.

Multiple features contribute to the use of the immunoglobulin M secretion-specific poly(A) signal but are not required for developmental regulation

The secretory-specific poly(A) signal (mus) of the immunoglobulin mu gene plays a central role in regulating alternative RNA processing to produce RNAs that encode membrane-associated and secreted immunoglobulins. This poly(A) signal is in direct competition with a splice reaction, and regulation requires that these two reaction efficiencies be balanced. The mus poly(A) signal has several unique sequence features that may contribute to its strength and regulation. Site-directed mutations and small internal deletions made in the intact mu gene show that an extensive AU/A-rich sequence surrounding AAUAAA enhances signal use and that, of the two potential downstream GU-rich elements, both of which appear suboptimally located, only the proximal GU-rich sequence contributes substantially to use of this signal. A GU-rich sequence placed at a more standard location did not improve mus poly(A) signal use. All mu genes tested that contained modified mus poly(A) signals were developmentally regulated, indicating that the GU-rich sequences, the sequences between them previously identified as suboptimal U1A binding sites, and an upstream suboptimal U1A site do not contribute to mu mRNA processing regulation. Expression of wild-type and modified mu genes in HeLa cells overexpressing U1A also failed to demonstrate that U1A contributes to mus poly(A) signal regulation.

Homologous gene sequences mediate transcription-domain formation

The organisation of transcription in the mammalian nucleus is a topic of particular interest because of its relevance to gene regulation. RNA polymerase II transcription occurs at hundreds of sites throughout the nucleoplasm. Recent data indicate that coordinately regulated genes can localise to shared transcription sites. Other transcribed sequences have also been shown to cluster in the nucleus. The ribosomal RNA genes cluster in the nucleoli. Similarly, transiently transfected plasmids and dsDNA viruses form transcription domains (TDs) containing multiple templates. Intriguingly, plasmids expressing beta-globin gene sequences recruit the endogenous beta-globin loci to their TDs. In light of this observation, we have investigated plasmid TDs as a model for gene recruitment. We find that TD formation is dependent on the presence of homologous gene sequences. Plasmids containing non-homologous gene sequences form separate TDs, independent of homology in the backbone or promoter sequences. TD formation is also favoured by low plasmid concentrations. This effect is sequence-specific and high concentrations of one plasmid do not disrupt domain formation by non-homologous plasmids in the same cell. We conclude that recruitment into TDs is an active process that is driven by homologies between transcribed sequences and becomes saturated at high copy numbers.

RNA folding during transcription

The evolution of RNA sequence needs to satisfy three requirements: folding, structure, and function. Studies on folding during transcription are related directly to folding in the cell. Understanding RNA folding during transcription requires the elucidation of structure formation and structural changes of the RNA, and the consideration of intrinsic properties of the RNA polymerase and other proteins that interact with the RNA. This review summarizes the research progress in this area and outlines the enormous challenges facing this field. Significant advancement requires the development of new experimental methods and theoretical considerations in all aspects of transcription and RNA folding.

Pause sites promote transcriptional termination of mammalian RNA polymerase II

Polymerase II (Pol II) transcriptional termination depends on two independent genetic elements: poly(A) signals and downstream terminator sequences. The latter may either promote cotranscriptional RNA cleavage or pause elongating Pol II. We demonstrate that the previously characterized MAZ4 pause element promotes Pol II termination downstream of a poly(A) signal, dependent on both the proximity of the pause site and poly(A) signal and the strength of the poly(A) signal. The 5'-->3' exonuclease Xrn2 facilitates this pause-dependent termination by degrading the 3' product of poly(A) site cleavage. The human beta-actin gene also possesses poly(A) site proximal pause sequences, which like MAZ4 are G rich and promote transcriptional termination. Xrn2 depletion causes an increase in both steady-state RNA and Pol II levels downstream of the beta-actin poly(A) site. Taken together, we provide new insights into the mechanism of pause site-mediated termination and establish a general role for the 5'-->3' exonuclease Xrn2 in Pol II termination.

A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear targeting by human TFIIS

The three structural domains of transcription elongation factor TFIIS are conserved from yeast to human. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified previously in other transcription factors. We found this conserved sequence, the LW motif, in another three human proteins that are predominantly nuclear localized. We investigated two examples to determine whether the LW motif is actually a dedicated nuclear targeting signal. However, in one of the newly identified proteins, hIWS1 (human Iws1), a region containing classic nuclear localization signals (NLS) rather than the LW motif was necessary and sufficient for nuclear targeting in HeLa cells. In contrast, human TFIIS does not possess an NLS and only constructs containing the LW motif were efficiently targeted to nuclei. Moreover, mutations in the motif could cause cytoplasmic accumulation of TFIIS and enabled a structure/function assay for the domain based on the efficiency of nuclear targeting. Finally, GST pull-down assays showed that the LW motif is part of a protein-binding domain. We suggest that the targeting role the LW motif plays in TFIIS arises from its more general function as a protein interaction domain, enabling TFIIS to bind a carrier protein(s) that accomplishes nuclear import.

A nuclear surveillance pathway for mRNAs with defective polyadenylation

The pap1-5 mutation in poly(A) polymerase causes rapid depletion of mRNAs at restrictive temperatures. Residual mRNAs are polyadenylated, indicating that Pap1-5p retains at least partial activity. In pap1-5 strains lacking Rrp6p, a nucleus-specific component of the exosome complex of 3'-5' exonucleases, accumulation of poly(A)+ mRNA was largely restored and growth was improved. The catalytically inactive mutant Rrp6-1p did not increase growth of the pap1-5 strain and conferred much less mRNA stabilization than rrp6delta. This may indicate that the major function of Rrp6p is in RNA surveillance. Inactivation of core exosome components, Rrp41p and Mtr3p, or the nuclear RNA helicase Mtr4p gave different phenotypes, with accumulation of deadenylated and 3'-truncated mRNAs. We speculate that slowed mRNA polyadenylation in the pap1-5 strain is detected by a surveillance activity of Rrp6p, triggering rapid deadenylation and exosome-mediated degradation. In wild-type strains, assembly of the cleavage and polyadenylation complex might be suboptimal at cryptic polyadenylation sites, causing slowed polyadenylation.

Connections between mRNA 3' end processing and transcription termination

Discoveries within the last few years have revealed that the multiple steps in gene expression are remarkably integrated. There have recently been several advances in deciphering how mRNA 3' end processing is linked with transcription elongation and termination. It has been known for quite a long time that transcription termination is somehow intertwined with polyadenylation, but it is still unclear exactly how these two processes influence each other. Some recent reports are shedding light on these connections.

Tsix transcription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation

X-chromosome inactivation (XCI) is highly dynamic during early mouse embryogenesis and strictly depends on the Xist noncoding RNA. The regulation of Xist and its antisense partner Tsix remains however poorly understood. We provide here the first evidence of transcriptional control of Xist expression. We show that RNA polymerase II (RNAPolII) preinitiation complex recruitment and H3 Lys 4 (H3-K4) methylation at the Xist promoter form the basis of the Xist expression profiles that drives both imprinted and random XCI. In embryonic stem (ES) cells, which are derived from the inner cell mass where imprinted XCI is reversed and both Xs are active, we show that Xist is repressed at the level of preinitiation complex (PIC) recruitment. We further demonstrate that Tsix, although highly transcribed in ES cells, is not itself responsible for the transcriptional down-regulation of Xist. Rather, Tsix induces efficient H3-K4 methylation over the entire Xist/Tsix unit. We suggest that chromatin remodeling of the Xist locus induced by biallelic Tsix transcription renders both Xist loci epigenetically equivalent and equally competent for transcription. In this model, Tsix, by resetting the epigenetic state of the Xist/Tsix locus, mediates the transition from imprinted to random XCI.

[Alternative mRNA splicing, pathology and molecular therapeutics]

Pre-mRNA splicing operates towards at least 95 % of the transcript pool. It is subjected to a large number of variations, collectively regrouped under the term of alternative mRNA splicing, which occurs, on average, 6 to 8 times per pre-mRNA molecule. Consequently, many more proteins may be encoded from a single gene, which may satisfy a physiological need, or mark a pathological adaptation. The identification of mutations in sequences required for splicing, both constitutive and alternative, or for their control, has permitted to determine the causes of qualitative or quantitative variations in transcript levels associated with inherited diseases or cancer development. A number of molecular approaches have been undertaken to try to compensate for the effect of deleterious splicing mutations and to restore, at least in part, sufficient amounts of either the normal or a surrogate transcript. These include overexpression of splicing proteins, improvement of their activity by post-translational modification, splice-site increased or decreased usage, and RNA-mediated trans-splicing. Using such approaches, phenotypic improvements have been obtained in animal models, carrying new hopes for the development of therapeutic strategies aimed at correcting both inherited and acquired diseases that involve pre-mRNA splicing defects.

Negative transcriptional modulation and silencing of the bi-exonic Rnf35 gene in the preimplantation embryo. Binding of the CCAAT-displacement protein/Cux to the untranslated exon 1 sequence

Previous works have indicated promiscuous transcription from the zygotic genome immediately after fertilization. The mouse Rnf35 gene is bi-exonic in structure and is transcribed in the preimplantation embryo until it is permanently silenced at the blastocyst stage of development. We have previously shown that Rnf35 transcription is positively regulated by the nuclear factor Y. Using the uniquely permissive Chinese hamster ovary-K1 cell line in transient transfection assays, we demonstrate in this work that the Rnf35 promoter was negatively modulated by a cis-cognate repressor element, designated as the downstream exon 1 repressor, or DER, residing between +72 and +95 in the untranslated exon 1 of the Rnf35 gene. Simultaneous mutagenesis of the two half-sections, DER1 and DER2, of the DER sequence was required for derepression suggesting participation of multiple proteins in the DER-dependent transcriptional repression. Electrophoretic mobility shift assays demonstrated that the 3'-half of DER (DER2) was targeted by the repressor CCAAT-displacement protein (CDP)/Cux. Chromatin immunoprecipitation experiments further demonstrated in vivo CDP-DER association in the blastocyst and the 8.5 day embryo. Furthermore, the DER-dependent repression was partially relieved in vivo in co-transfection with an antisense CDP construct. Transcription of the Cdp gene was shown to first occur between the eight-cell and the blastocyst stages, correlating and possibly explaining the onset of Rnf35 silencing at the blastocyst stage. Taken together, our results suggest that the evolutionarily acquired exon 1 of Rnf35, and possibly exon 1 of other similarly structured bi-exonic early embryonic genes, contributes to transcriptional modulation and silencing in the developing mouse embryo.

Translational regulation during oogenesis and early development: the cap-poly(A) tail relationship

Metazoans rely on the regulated translation of select maternal mRNAs to control oocyte maturation and the initial stages of embryogenesis. These transcripts usually remain silent until their translation is temporally and spatially required during early development. Different translational regulatory mechanisms, varying from cytoplasmic polyadenylation to localization of maternal mRNAs, have evolved to assure coordinated initiation of development. A common feature of these mechanisms is that they share a few key trans-acting factors. Increasing evidence suggest that ubiquitous conserved mRNA-binding factors, including the eukaryotic translation initiation factor 4E (eIF4E) and the cytoplasmic polyadenylation element binding protein (CPEB), interact with cell-specific molecules to accomplish the correct level of translational activity necessary for normal development. Here we review how capping and polyadenylation of mRNAs modulate interaction with multiple regulatory factors, thus controlling translation during oogenesis and early development.

Structural Analysis of the Genes for Human Arylamine N-Acetyltransferases and Characterisation of Alternative Transcripts

Arylamine N-acetyltransferases are polymorphic drug-metabolising enzymes. The human isoforms, NAT1 and NAT2, are encoded by two genes with intronless coding regions. Human NAT1 protein is found in many tissues, unlike NAT2 which is present predominantly in the intestine and liver. We describe the exon-intron structure of the human NAT genes by analysing data from genomic databases. Comparison of expressed sequence tags, matching NAT gene sequences, with the sequence of human chromosome 8 implied the presence of 8 non-coding exons located 51.5, 51.4, 12.3, 11.9, 10.8, 9.6, 5.2 and 2.6 kb upstream of the single coding exon of the NAT1 gene. A number of expressed sequence tags also indicated transcription initiation from the upstream region adjacent to the NAT1 coding exon, consistent with earlier studies. The NAT2 gene consists of one previously described non-coding and one coding exon, located 8.6 kb apart. These findings were also confirmed by RT-PCR, using cDNA from heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Alternatively spliced NAT1 transcripts were found in all tissues. Transcription of the NAT2 gene was also detected in these tissues and was demonstrated to start either from the non-coding exon or from immediately upstream of the coding exon. Comparison of the RT-PCR products provided an initial estimate of the relative amounts of the different NAT transcripts expressed in each tissue. Finally, both expressed sequence tag analysis and RT-PCR demonstrated the presence of two differentially utilised polyadenylation signals for NAT1 and NAT2, located about 0.2 and 0.3 kb downstream of the coding region of each gene.

Protein and RNA Dynamics Play Key Roles in Determining the Specific Recognition of GU-rich Polyadenylation Regulatory Elements by Human Cstf-64 Protein

The N-terminal domain of the 64 kDa subunit of the cleavage stimulation factor (CstF-64) recognizes GU-rich elements within the 3'-untranslated region of eukaryotic mRNAs. This interaction is essential for mRNA 3' end processing and transcription termination, and its strength affects the efficiency of utilization of different polyadenylation sites. The structure of the RNA-binding N-terminal domain of CstF-64 showed how the N-terminal RNA recognition motif of CstF-64 recognizes GU-rich RNAs. However, it is still perplexing how this protein can bind selectively to RNAs that are rich in G and U residues regardless of their detailed sequence composition, yet discriminate effectively against non-GU-RNAs. We investigated by NMR the dynamics of the CstF-64 RNA-binding domain, both free and bound to two GU-rich RNA sequences that represent polyadenylation regulatory elements. While the free protein displays the motional properties typical of a well-folded protein domain and is uniformly rigid, the protein-RNA interface acquires significant mobility on the micro- to millisecond time-scale once GU-rich RNAs binds to it. These motional features, we propose, are intrinsic to the functional requirement to bind all GU-rich sequences and yet to discriminate against non-GU-rich RNAs. This behavior may be a general mechanism by which some RNA-binding proteins are able to bind to classes of sequences, as opposed to a well-defined sequence or consensus.

Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs

BACKGROUND

Cyclin-dependent kinases (CDKs) are a large family of proteins that function in a variety of key regulatory pathways in eukaryotic cells, including control over the cell cycle and gene transcription. Among the most important and broadly studied of these roles is reversible phosphorylation of the C-terminal domain (CTD) of RNA polymerase II, part of a complex array of CTD/protein interactions that coordinate the RNAP II transcription cycle. The RNAP CTD is strongly conserved in some groups of eukaryotes, but highly degenerate or absent in others; the reasons for these differences in stabilizing selection on CTD structure are not clear. Given the importance of reversible phosphorylation for CTD-based transcription, the distribution and evolutionary history of CDKs may be a key to understanding differences in constraints on CTD structure; however, the origins and evolutionary relationships of CTD kinases have not been investigated thoroughly. Moreover, although the functions of most CDKs are reasonably well studied in mammals and yeasts, very little is known from most other eukaryotes.

RESULTS

Here we identify 123 CDK family members from animals, plants, yeasts, and four protists from which genome sequences have been completed, and 10 additional CDKs from incomplete genome sequences of organisms with known CTD sequences. Comparative genomic and phylogenetic analyses suggest that cell-cycle CDKs are present in all organisms sampled in this study. In contrast, no clear orthologs of transcription-related CDKs are identified in the most putatively ancestral eukaryotes, Trypanosoma or Giardia. Kinases involved in CTD phosphorylation, CDK7, CDK8 and CDK9, all are recovered as well-supported and distinct orthologous families, but their relationships to each other and other CDKs are not well-resolved. Significantly, clear orthologs of CDK7 and CDK8 are restricted to only those organisms belonging to groups in which the RNAP II CTD is strongly conserved.

CONCLUSIONS

The apparent origins of CDK7 and CDK8, or at least their conservation as clearly recognizable orthologous families, correlate with strong stabilizing selection on RNAP II CTD structure. This suggests co-evolution of the CTD and these CTD-directed CDKs. This observation is consistent with the hypothesis that CDK7 and CDK8 originated at about the same time that the CTD was canalized as the staging platform RNAP II transcription. Alternatively, extensive CTD phosphorylation may occur in only a subset of eukaryotes and, when present, this interaction results in greater stabilizing selection on both CTD and CDK sequences. Overall, our results suggest that transcription-related kinases originated after cell-cycle related CDKs, and became more evolutionarily and functionally diverse as transcriptional complexity increased.

Conservation of Bmp2 post-transcriptional regulatory mechanisms

Bone morphogenetic protein (BMP) orthologs from diverse species like flies and humans are functionally interchangeable and play key roles in fundamental processes such as dorso-ventral axis formation in metazoans. Because both transcriptional and post-transcriptional mechanisms play central roles in modulating developmental protein levels, we have analyzed the 3'-untranslated region (3'UTR) of the Bmp 2 gene. This 3'UTR is unusually long and is alternatively polyadenylated. Mouse, human, and dog mRNAs are 83-87% identical within this region. A 265-nucleotide sequence, conserved between mammals, birds, frogs, and fish, is present in Bmp2 but not Bmp4. The ability of AmphiBMP2/4, a chordate ortholog to Bmp2 and Bmp4, to align with this sequence suggests that its function may have been lost in Bmp4. Activation of reporter genes by the conserved region acts by a post-transcriptional mechanism. Mouse, human, chick, and zebrafish Bmp2 synthetic RNAs decay rapidly in extracts from cells not expressing Bmp2. In contrast, these RNAs are relatively stable in extracts from Bmp2-expressing cells. Thus, Bmp2 RNA half-lives in vitro correlate with natural Bmp2 mRNA levels. The fact that non-murine RNAs interact appropriately with the mouse decay machinery suggests that the function of these cis-regulatory regions has been conserved for 450 million years since the fish and tetrapod lineages diverged. Overall, our results suggest that the Bmp2 3'UTR contains essential regulatory elements that act post-transcriptionally.

Stress response in yeast mRNA export factor: reversible changes in Rat8p localization are caused by ethanol stress but not heat shock

Ethanol stress (10% v/v) causes selective mRNA export in Saccharomyces cerevisiae in a similar manner to heat shock (42 degrees C). Bulk poly(A)(+) mRNA accumulates in the nucleus, whereas heat shock protein mRNA is exported under such conditions. Here we investigated the effects of stress on mRNA export factors. In cells treated with ethanol stress, the DEAD box protein Rat8p showed a rapid and reversible change in its localization, accumulating in the nucleus. This change correlated closely with the blocking of bulk poly(A)(+) mRNA export caused by ethanol stress. We also found that the nuclear accumulation of Rat8p is caused by a defect in the Xpo1p/Crm1p exportin. Intriguingly, the localization of Rat8p did not change in heat shocked cells, suggesting that the mechanisms blocking bulk poly(A)(+) mRNA export differ for heat shock and ethanol stress. These results suggest that changes in the localization of Rat8p contribute to the selective export of mRNA in ethanol stressed cells, and also indicate differences in mRNA export between the heat shock response and ethanol stress response.

Gle2p is essential to induce adaptation of the export of bulk poly(A)+ mRNA to heat shock in Saccharomyces cerevisiae

The export of bulk poly(A)(+) mRNA is blocked under heat-shocked (42 degrees C) conditions in Saccharomyces cerevisiae. We found that an mRNA export factor Gle2p rapidly dissociated from the nuclear envelope and diffused into the cytoplasm at 42 degrees C. However, in exponential phase cells pretreated with mild heat stress (37 degrees C for 1 h), Gle2p did not dissociate at 42 degrees C, and the export of bulk poly(A)(+) mRNA continued. Cells in stationary phase also continued with the export of bulk poly(A)(+) mRNA at 42 degrees C without the dissociation of Gle2p from the nuclear envelope. The dissociation of Gle2p was caused by increased membrane fluidity and correlated closely with blocking of the export of bulk poly(A)(+) mRNA. Furthermore, the mutants gle2Delta and rip1Delta could not induce such an adaptation of the export of bulk poly(A)(+) mRNA to heat shock. Our findings indicate that Gle2p plays a crucial role in mRNA export especially under heat-shocked conditions. Our findings also indicate that the nuclear pore complexes that Gle2p constitutes need to be stabilized for the adaptation and that the increased membrane integrity caused by treatment with mild heat stress or by survival in stationary phase is likely to contribute to the stabilization of the association between Gle2p and the nuclear pore complexes.

Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II

Capping of the 5' ends of nascent RNA polymerase II transcripts is the first pre-mRNA processing event in all eukaryotic cells. Capping enzyme (CE) is recruited to transcription complexes soon after initiation by the phosphorylation of Ser-5 of the carboxyl-terminal domain of the largest subunit of RNA polymerase II. Here, we analyze the role of CE in promoter clearance and its functional interactions with different factors that are involved in promoter clearance. FCP1-mediated dephosphorylation of the carboxyl-terminal domain results in a drastic decrease in cotranscriptional capping efficiency but is reversed by the presence of DRB sensitivity-inducing factor (DSIF). These results suggest involvement of DSIF in CE recruitment. Importantly, CE relieves transcriptional repression by the negative elongation factor, indicating a critical role of CE in the elongation checkpoint control mechanism during promoter clearance. This functional interaction between CE and the negative elongation factor documents a dynamic role of CE in promoter clearance beyond its catalytic activities.

Transcription factories: quantitative studies of nanostructures in the mammalian nucleus

Transcription by the three nuclear RNA polymerases is carried out in transcription factories. This conclusion has been drawn from estimates of the total number of nascent transcripts or active polymerase molecules and the number of transcription sites within a cell. Here we summarise the variety of methods used to determine these parameters, discuss their associated problems and outline future prospects.

Post-transcription cleavage generates the 3' end of F17R transcripts in vaccinia virus

Most vaccinia virus intermediate and late mRNAs possess 3' ends that are extremely heterogeneous in sequence. However, late mRNAs encoding the cowpox A-type inclusion protein (ATI), the second largest subunit of the RNA polymerase, and the late telomeric transcripts possess homogeneous 3' ends. In the case of the ATI mRNA, it has been shown that the homogeneous 3' end is generated by a post-transcriptional endoribonucleolytic cleavage event. We have determined that the F17R gene also produces homogeneous transcripts generated by a post-transcriptional cleavage event. Mapping of in vivo mRNA shows that the major 3' end of the F17R transcript maps 1262 nt downstream of the F17R translational start site. In vitro transcripts spanning the in vivo 3' end are cleaved in an in vitro reaction using extracts from virus infected cells, and the site of cleavage is the same both in vivo and in vitro. Cleavage is not observed using extract from cells infected in the presence of hydroxyurea; therefore, the cleavage factor is either virus-coded or virus-induced during the post-replicative phase of virus replication. The cis-acting sequence responsible for cleavage is orientation specific and the factor responsible for cleavage activity has biochemical properties similar to the factor required for cleavage of ATI transcripts. Partially purified cleavage factor generates cleavage products of expected size when either the ATI or F17R substrates are used in vitro, strongly suggesting that cleavage of both transcripts is mediated by the same factor.