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To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2007.05.028 Byline: Corinna Giorgi (1), Gene W. Yeo (2), Martha E. Stone (3), Donald B. Katz (3), Christopher Burge (4), Gina Turrigiano (5), Melissa J. Moore (1) Abstract: Proper neuronal function and several forms of synaptic plasticity are highly dependent on precise control of mRNA translation, particularly in dendrites. We find that eIF4AIII, a core exon junction complex (EJC) component loaded onto mRNAs by pre-mRNA splicing, is associated with neuronal mRNA granules and dendritic mRNAs. eIF4AIII knockdown markedly increases both synaptic strength and GLUR1 AMPA receptor abundance at synapses. eIF4AIII depletion also increases ARC, a protein required for maintenance of long-term potentiation; arc mRNA, one of the most abundant in dendrites, is a natural target for nonsense-mediated decay (NMD). Numerous new NMD candidates, some with potential to affect synaptic activity, were also identified computationally. Two models are presented for how translation-dependent decay pathways such as NMD might advantageously function as critical brakes for protein synthesis in cells such as neurons that are highly dependent on spatially and temporally restricted protein expression. Author Affiliation: (1) Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02454, USA (2) Crick-Jacobs Center for Computational and Theoretical Biology Salk Institute, La Jolla, CA 92037, USA (3) Department of Psychology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02454, USA (4) Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA (5) Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02454, USA Article History: Received 12 July 2006; Revised 23 December 2006; Accepted 9 May 2007 Article Note: (miscellaneous) Published: July 12, 2007

Recent work indicates that the posttranscriptional control of eukaryotic gene expression is much more elaborate and extensive than previously thought, with essentially every step of messenger RNA (mRNA) metabolism being subject to regulation in an mRNA-specific manner. Thus, a comprehensive understanding of eukaryotic gene expression requires an appreciation for how the lives of mRNAs are influenced by a wide array of diverse regulatory mechanisms., Many written accounts of eukaryotic gene expression might start something like this: 'Messenger RNAs (mRNAs) are the central conduits in the flow of information from DNA to protein. In eukaryotes, [...]

The U1 small nuclear ribonucleoprotein particle U1C protein has a zinc finger-like structure (C2H2 motif) at its N terminus, which is conserved from yeast to humans. Mutations of amino acid L13 within this domain rescue the essential function of the helicase protein Prp28p. Prp28p has been implicated in unwinding the 5' splice site (5'ss)-U1 small nuclear RNA (snRNA) base-pairing, to allow replacement of U1 snRNA with U6 snRNA during spliceosome assembly. The L13 phenotype has therefore been interpreted to indicate that WT U 1C contributes to 5'ss-U1 snRNA stabilization by binding to the RNA duplex. We show here that an L13 mutant extract cannot form stable base-pairing at room temperature but is permissive for U1-5'ss base-pairing at low temperature. This phenotype is similar to that of a U1C-depleted extract, indicating that the U1C L13 mutation is a strong loss-of-function mutation. The two mutant extracts are unlike a WT extract, which undergoes stable pairing at room temperature but little or no pairing at low temperature. Taken together with previous results and the failure to observe a direct interaction of U1C with the U1-5'ss duplex, the data suggest that U1C contributes indirectly to stable U1-5'ss base-pairing under permissive conditions. A model is proposed to account for the L13 results.

Although it has been known since the late 1970s that intron-containing and intronless versions of otherwise identical genes can exhibit dramatically different expression profiles, the underlying molecular mechanisms have only lately come to light. This review summarizes recent progress in our understanding of how introns and the act of their removal by the spliceosome can influence and enhance almost every step of mRNA metabolism. A rudimentary understanding of these effects can prove invaluable to researchers interested in optimizing transgene expression in eukaryotic systems.

The author reviews the publications on the mechanisms and regulation of nuclear RNA decay. The topics of interest include RNA turnover in mammalian cells, the nuclear decay pathways and the interplay between the RNA processing and decay machineries.

A tri-partite assay for studying exon ligation by the ai5gamma group II intron is discussed. Introns of the group self-splice using a 2-step mechanism and the second part has been studied using the novel assay. Novel information about the extent to which domain 6 can be modified without losing accurate exon ligation has been gained. A subset of interactions involving nucleotides flanking the 3' splice site that contribute to active site binding has been further explained.

Evidence for stable association of proteins at exon-exon junctions is discussed relative to pre-mRNA splicing. The splicing has been shown to change mRNP composition. Several proteins that associate with mRNA exon-exon junctions only as a result of splicing were found through use of a novel in vitro crosslinking approach.

Intron excision is an essential step in eukaryotic gene expression, but the molecular mechanisms by which the spliceosome accurately identifies splice sites in nuclear precursors to messenger RNAs (pre-mRNAs) are not well understood. A bimolecular assay for the second step of splicing has now revealed that exon ligation by the human spliceosome does not require covalent attachment of a 3' splice site to the branch site. Furthermore, accurate definition of the 3' splice site in this system is independent of either a covalently attached polypyrimidine tract or specific 3' exon sequences. Rather, in this system 3' splice site selection apparently occurs with a 5' → 3' directionality., Introns in nuclear pre-mRNAs are removed by the spliceosome, a 60S complex composed of the pre-mRNA, four small nuclear RNAs (snRNAs) (U1, U2, U4-U6, and U5), and numerous associated proteins [...]

The exchange of a 3'-5'- for 2'-5' bond in the first step of lariat formation and the exchange of one 3'-5' phosphodiester for another in the second step of exon ligation are the two different reactions for subtracting the introns from nuclear precursors to messenger RNAs (pre-mRNAs) by the spliceosome. A study conducted to detect the stereochemical course for each step, utilizing the splicing substrate containing phosphothioate, showed that both steps occur as a single 'in-line' Sn2 nucleophilic substitution reaction, similar to the mechanism of group I self splicing introns. The reaction sites for second step of spliceosomal processing is similar to that of group I self splicing introns.

The article discusses autoimmunity in the case of a genetic degree from the example of the delivery of functional dystrophin immunity in the case of patients with DuchenneEs muscular dystrophy, an x-linked, genetically inherited disease affecting newborn boys. The value of careful and critical observation in early-phase clinical studies of gene therapy aimed at altering gene expression is highlighted.

A simple and efficient method for synthesizing long, site-specifically modified RNA molecules was developed whereby segments of RNA were joined with the use of bacteriophage T4 DNA ligase. A single hydrogen or O-methyl group was substituted for the 2'-hydroxyl group at either splice site of a nuclear pre-messenger RNA substrate. Splicing of the modified pre-messenger RNA's in vitro revealed that, although a 2'-hydroxyl is not absolutely required at either splice site, the 2'-hydroxyl at the 3' splice site is important for the second step of splicing. These results are compared to previous studies of analogous 2'-hydroxyl groups in the self-splicing Tetrahymena group I intron., The precise removal of intervening sequences, or introns, by the process called splicing is a fundamental step in the maturation of most eukaryotic pre-mRNA's. Excision of these sequences takes place [...]

A study was done on the role of mercuric ion reductase (merA) and cysteine in the bacterial mercury detoxification pathway. It was shown that merA mutations lead to a disruption of the Hg(II) detoxification pathway in vivo. In addition, it was found that Cys558 participates in the formation of the reducible complex with Hg(II). Cys558 and Cys559 were further found to play a role in efficient scavenging.

An essential step in eukaryotic gene expression is the removal of introns from nascent transcripts by premRNA splicing. The means by which splicing affects downstream mRNA metabolism is by altering the implement of bound proteins that, together with the mRNA comprise the mRNP.

Research has been conducted on pre-mRNA splicing which presents a deposition of proton nucleotides unstream of exon-exon junctions on spliced mRNA. The authors have investigated the mechanism and timing of exon junction complex assembly, and have discussed the results.

In most eukaryotic introns the 3' splice site is defined by a surprisingly short AG consensus found a variable distance downstream of the branch site. Exactly how the spliceosome determines which AG to use, however, is not well understood. Previously we showed that when the branch site and 3' splice site AG are supplied by separate RNA molecules, there is a strong preference for use of the 5'-most AG in the 3' splice site-containing RNA. Here we show that this apparent 5' [right arrow] 3' directionality holds even when this RNA contains four tandem repeats of a 6-nt sequence containing AG. Exactly the same pattern of 3' splice site choice was observed when the same tandem repeats were incorporated into a full-length splicing substrate. When the 3' splice site AG is supplied by a separate RNA, that RNA must be linear with an unobstructed 5' end. Similarly, the branch-containing RNA must be truncated immediately 3' to the polypyrimidine tract. A model is presented that incorporates these observations and reconciles previously proposed mechanisms for 3' splice site selection.

Two of the hottest topics in eukaryotic gene expression research involve absolute nonsense: nonsense-mediated mRNA decay (NMD) and nonsense-associated altered splicing (NAS). 'Nonsense' in this case refers to a type [...]

For researchers trying to elucidate how one protein activity or intermolecular interaction contributes to a complex metabolic pathway, a specific chemical inhibitor can be an invaluable tool. Yet, in living [...]

Introns have been considered examples of 'junk DNA,' a description for chromosomal sequences having no apparent function. This view was shattered by results of a cloning project aimed at sequencing the mouse UHG. UHG was found to be an example of an 'inside-out' gene wherein only introns encode function. The UHG structure is not believed to be unique, so further research could reveal other conserved intronic sequences.

In vitro formation of RNA which catalyzes bond forming reactions and the formation of a self-alkylating ribozyme shows that it is possible that in the beginning of evolution all reactions were catalyzed by RNA. The polyribonucleotides served as both the proteins and nucleic acids. RNA's with modified sugars and bases could have catalyzed the synthesis of active nucleosides.