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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

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.

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 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.

Abstract: Single‐molecule fluorescence in situ hybridization (smFISH) provides direct access to the spatial relationship between nucleic acids and specific subcellular locations. The ability to precisely localize a messenger RNA can reveal key information about its regulation. Although smFISH is well established in cell culture or thin sections, the utility of smFISH is hindered in thick tissue sections due to the poor probe penetration of fixed tissue, the inaccessibility of target mRNAs for probe hybridization, high background fluorescence, spherical aberration along the optical axis, and the lack of methods for image segmentation of organelles. Studying mRNA localization in 50 µm thick Drosophila larval muscle sections, these obstacles are overcome using sample‐specific optimization of smFISH, particle identification based on maximum likelihood testing, and 3D multiple‐organelle segmentation. The latter allows independent thresholds to be assigned to different regions of interest within an image stack. This approach therefore facilitates accurate measurement of mRNA location in thick tissues. [ABSTRACT FROM AUTHOR]

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.

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.

Summary Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remain controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae . We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ∼590 nt, and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs. [ABSTRACT FROM AUTHOR]

Throughout their lifetimes, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Since the discovery of the first mRNP component more than 40 years ago, what is known as the mRNA interactome now comprises >1,000 proteins. These proteins bind mRNAs in myriad ways with varying affinities and stoichiometries, with many assembling onto nascent RNAs in a highly ordered process during transcription and precursor mRNA (pre-mRNA) processing. The nonrandom distribution of major mRNP proteins observed in transcriptome-wide studies leads us to propose that mRNPs are organized into three major domains loosely corresponding to 5′ untranslated regions (UTRs), open reading frames, and 3′ UTRs. Moving from the nucleus to the cytoplasm, mRNPs undergo extensive remodeling as they are first acted upon by the nuclear pore complex and then by the ribosome. When not being actively translated, cytoplasmic mRNPs can assemble into large multi-mRNP assemblies or be permanently disassembled and degraded. In this review, we aim to give the reader a thorough understanding of past and current eukaryotic mRNP research. [ABSTRACT FROM AUTHOR]

The article discusses the testing of connectivity in RNA that contains innumerable nucleotides by a SeqZip methodology. It is mentioned that the long range exons connectivity information is needed in individual RNA molecules. The author finds that the SeqZip methodology makes use of RNA templated DNA-DNA litigation to establish connectivity between long distance sequences in a single RNA molecule. It is mentioned that tests are done to characterize exon diversity of Drosophila melanogaster.

CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exons. For example, CRISPR-mediated editing of β-catenin exon 3, which encodes an autoinhibitory domain, induces partial skipping of the in-frame exon and nuclear accumulation of β-catenin. A single sgRNA can induce small insertions or deletions that partially alter splicing or unexpected larger deletions that remove exons. Exon skipping adds to the unexpected outcomes that must be accounted for, and perhaps taken advantage of, in CRISPR experiments. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1237-8) contains supplementary material, which is available to authorized users.