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https://www.readbyqxmd.com/read/28096519/the-nuclear-poly-a-binding-protein-of-mammals-but-not-of-fission-yeast-participates-in-mrna-polyadenylation
#1
Uwe Kühn, Juliane Buschmann, Elmar Wahle
The nuclear poly(A) binding protein (PABPN1) has been suggested, on the basis of biochemical evidence, to play a role in mRNA polyadenylation by strongly increasing the processivity of poly(A) polymerase. While experiments in metazoans have tended to support such a role, the results were not unequivocal, and genetic data show that the S. pombe orthologue of PABPN1, Pab2, is not involved in mRNA polyadenylation. The specific model that PABPN1 increases the rate of poly(A) tail elongation has never been examined in vivo...
January 17, 2017: RNA
https://www.readbyqxmd.com/read/28096518/structural-basis-for-guanidine-sensing-by-the-ykkc-family-of-riboswitches
#2
Robert A Battaglia, Ian R Price, Ailong Ke
Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.04 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. The riboswitch folds into a boot-shaped structure, with a co-axially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel...
January 17, 2017: RNA
https://www.readbyqxmd.com/read/28096517/the-nucleoside-analog-clitocine-is-a-potent-and-efficacious-readthrough-agent
#3
Westley J Friesen, Christopher R Trotta, Yuki Tomizawa, Jin Zhuo, Briana Johnson, Jairo Sierra, Bijoyita Roy, Marla Weetall, Jean Hedrick, Josephine Sheedy, James Takasugi, Young-Choon Moon, Suresh Babu, Ramil Baiazitov, John D Leszyk, Thomas W Davis, Stuart W Peltz, Ellen M Welch
Nonsense mutations resulting in a premature stop codon in an open reading frame occur in critical tumor suppressor genes in a large number of the most common forms of cancers and are known to cause or contribute to the progression of disease. Low molecular weight compounds that induce readthrough of nonsense mutations offer a new means of treating patients with genetic disorders or cancers resulting from nonsense mutations. We have identified the nucleoside analog clitocine as a potent and efficacious suppressor of nonsense mutations...
January 17, 2017: RNA
https://www.readbyqxmd.com/read/28069890/apobec1-complementation-factor-a1cf-is-not-required-for-c-to-u-rna-editing-in-vivo
#4
Elizabeth M Snyder, Christopher McCarty, Adrienne Mehalow, Karen Svenson, Stephen Murray, Ron Korstanje, Robert E Braun
Editing of the human and murine ApoB mRNA by APOBEC1, the catalytic enzyme of the protein complex that catalyzes C-to-U RNA editing, creates an internal stop codon within the APOB coding sequence, generating two protein isoforms. It has been long held that APOBEC1-mediated editing activity is dependent on the RNA binding protein A1CF. The importance of A1CF in adult tissues has been unclear as a previously reported null allele displays embryonic lethality. This work aimed to address the function of A1CF in adult mouse tissues using a conditional A1cf allele...
January 9, 2017: RNA
https://www.readbyqxmd.com/read/28069889/thermodynamic-stabilities-of-three-way-junction-nanomotifs-in-prohead-rna
#5
Alyssa C Hill, Susan J Schroeder
The thermodynamic stabilities of four natural prohead or packaging RNA (pRNA) three-way junction (3WJ) nanomotifs and seven phi29 pRNA 3WJ deletion mutant nanomotifs were investigated using UV optical melting on a three-component RNA system. Our data reveal that some pRNA 3WJs are more stable than the phi29 pRNA 3WJ. The stability of the 3WJ contributes to the unique self-assembly properties of pRNA. Thus, ultrastable pRNA 3WJ motifs suggest new scaffolds for pRNA-based nanotechnology. We present data demonstrating that pRNA 3WJs differentially respond to the presence of metal ions...
January 9, 2017: RNA
https://www.readbyqxmd.com/read/28069888/human-non-coding-rna-886-nc886-adopts-two-structurally-distinct-conformers-that-are-functionally-opposing-regulators-of-pkr
#6
Brenda M Calderon, Graeme L Conn
The double-stranded RNA (dsRNA)-activated protein kinase (PKR) senses dsRNA produced during viral infection and halts cellular protein synthesis to block viral replication. How basal PKR activity is controlled in the absence of infection was unclear until the recent identification of a potential endogenous regulator, the cellular non-coding RNA 886 (nc886). However, nc886 adopts two distinct conformations for which the structural details and potential functional differences remain unclear. Here, we isolated and separately dissected the function of form of nc886 to more clearly define the molecular mechanism of nc886-mediated PKR inhibition...
January 9, 2017: RNA
https://www.readbyqxmd.com/read/28062594/survey-of-800-datasets-from-human-tissue-and-body-fluid-reveals-xenomirs-are-likely-artifacts
#7
Wenjing Kang, Claus Heiner Bang-Bertelsen, Anja Holm, Anna Houben, Anne Holt Müller, Thomas Thymann, Flemming Pociot, Xavier Estivill, Marc Riemer Friedländer
miRNAs are small 22 nucleotide RNAs that can post-transcriptionally regulate gene expression. It has been proposed that dietary plant miRNAs can enter the human bloodstream and regulate host transcripts, however these findings have been widely disputed. We here conduct the first comprehensive meta-study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing datasets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%), however the abundances are low, comprising 0...
January 6, 2017: RNA
https://www.readbyqxmd.com/read/28057857/a-central-role-of-cwc25-in-spliceosome-dynamics-during-catalytic-phase-of-pre-mrna-splicing
#8
Chi-Kang Tseng, Che-Sheng Chung, Hsin-Chou Chen, Soo-Chen Cheng
Splicing of precursor mRNA occurs via two consecutive steps of transesterification reaction; both require ATP and several proteins. Despite the energy requirement in the catalytic phase, incubation of the purified spliceosome under proper ionic conditions can elicit competitive reversible transesterification, debranching and spliced-exon-reopening reactions without necessity for ATP or other factors, suggesting that small changes in the conformational state of the spliceosome can lead to disparate chemical consequences for the substrate...
January 5, 2017: RNA
https://www.readbyqxmd.com/read/28053272/trans-generational-function-of-tetrahymena-piwi-protein-twi8p-at-distinctive-non-coding-rna-loci
#9
Brian M Farley, Kathleen Collins
Trans-generational transmission of genome-regulatory epigenetic information can determine phenotypes in the progeny of sexual reproduction. Sequence specificity of trans-generational regulation derives from small RNAs assembled into Piwi-protein complexes. Known targets of trans-generational regulation are primarily transposons and transposon-derived sequences. Here, we extend the scope of Piwi-mediated trans-generational regulation to include unique non-coding RNA loci. Ciliates such as Tetrahymena have a phenotypically silent germline micronucleus and an expressed somatic macronucleus, which is differentiated anew from a germline genome copy in sexual reproduction...
January 4, 2017: RNA
https://www.readbyqxmd.com/read/28053271/mutations-of-exosc3-rrp40p-associated-with-neurological-diseases-impact-ribosomal-rna-processing-functions-of-the-exosome-in-s-cerevisiae
#10
Abigail Gillespie, Jason Gabunilas, Joanna C Jen, Guillaume F Chanfreau
The RNA exosome is a conserved multiprotein complex that achieves a large number of processive and degradative functions in eukaryotic cells. Recently, mutations have been mapped to one of the subunits of the exosome, EXOSC3 (yeast Rrp40p), which result in pontocerebellar hypoplasia with motor neuron degeneration in human patients. However the molecular impact of these mutations in the pathology of these diseases is not well understood. To investigate the molecular consequences of mutations in EXOSC3 that lead to neurological diseases, we analyzed the effect of three of the mutations which affect conserved residues of EXOSC3/Rrp40p (G31A, G191C and W238R; G8A, G148C and W195R, respectively in human and yeast) in S...
January 4, 2017: RNA
https://www.readbyqxmd.com/read/28031482/involvement-of-fission-yeast-pdc2-in-rna-degradation-and-p-body-function
#11
Chun-Yu Wang, Yi-Ting Wang, Wan-Yi Hsiao, Shao-Win Wang
In this study we identified Pdc2, the fission yeast ortholog of human Pat1b protein, which forms complex with Lsm1-7 and plays a role in coupling deadenylation and decapping. The involvement of Pdc2 in RNA degradation and P-body function were also determined. We found that Pdc2 interacts with Dcp2 and is required for decapping in vivo. Although not absolutely essential for P-bodies assembly, over-expression of Pdc2 enhanced P-body formation even in the absence of Pdc1, the fission yeast functional homologue of human Edc4 protein, indicating that Pdc2 also plays a role in P-body formation...
December 28, 2016: RNA
https://www.readbyqxmd.com/read/28031481/xenopus-piwi-proteins-interact-with-a-broad-proportion-of-the-oocyte-transcriptome
#12
James A Toombs, Yuliya A Sytnikova, Gung-Wei Chirn, Ignatius Ang, Nelson C Lau, Michael D Blower
Piwi proteins utilize small RNAs (piRNAs) to recognize and repress target transcripts such as transposable elements (TE). However, the extensive diversity in piRNA sequences also suggests that Piwi/piRNA complexes interact with many transcripts beyond TEs. To examine the extent of Piwi interaction with target RNAs, we used Ribonucleoprotein-Immunoprecipitation (RIP) and Cross-linking and Immunoprecipitation (CLIP) to identify thousands of transcripts that associate with the Piwi proteins XIWI and XILI (Piwi-protein-Associated Transcripts, PATs) from early stage oocytes of X...
December 28, 2016: RNA
https://www.readbyqxmd.com/read/28003516/linking-maternal-and-somatic-5s-rrna-types-with-different-sequence-specific-non-ltr-retrotransposons
#13
Mauro D Locati, Johanna F B Pagano, Wim A Ensink, Marina van Olst, Selina van Leeuwen, Ulrike Nehrdich, Kongju Zhu, Herman P Spaink, Geneviève Girard, Han Rauwerda, Martijs J Jonker, Rob J Dekker, Timo M Breit
5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo and adult tissue, identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions...
December 21, 2016: RNA
https://www.readbyqxmd.com/read/28003515/conserved-binding-of-gcac-motifs-by-mec-8-couch-potato-and-the-rbpms-protein-family
#14
Heddy Soufari, Cameron D Mackereth
Precise regulation of mRNA processing, translation, localization and stability relies on specific interactions with RNA-binding proteins whose biological function and target preference are dictated by their preferred RNA motifs. The RBPMS family of RNA-binding proteins is defined by a conserved RNA recognition motif (RRM) domain found in metazoan RBPMS/Hermes and RBPMS2, Drosophila couch potato, and MEC-8 from C. elegans. In order to determine the parameters of RNA sequence recognition by the RBPMS family, we have first used the N-terminal domain from MEC-8 in binding assays and have demonstrated a preference for two GCAC motifs optimally separated by greater than six nucleotides...
December 21, 2016: RNA
https://www.readbyqxmd.com/read/28003514/s-cerevisiae-trm140-has-two-recognition-modes-for-3-methylcytidine-modification-of-the-anticodon-loop-of-trna-substrates
#15
Lu Han, Erin Marcus, Sonia D'Silva, Eric M Phizicky
The 3-methylcytidine (m3C) modification is ubiquitous in eukaryotic tRNA, widely found at C32 in the anticodon loop of tRNAThr, tRNASer, and some tRNAArg species, as well as in the variable loop (V-loop) of certain tRNASer species. In the yeast Saccharomyces cerevisiae, formation of m3C32 requires Trm140 for six tRNA substrates, including three tRNAThr species and three tRNASer species, whereas in Schizosacchomyces pombe, two Trm140 homologs are employed, one for tRNAThr and one for tRNASer. The occurrence of a single Trm140 homolog is conserved broadly among Ascomycota, whereas multiple Trm140-related homologs are found in metazoans and other fungi...
December 21, 2016: RNA
https://www.readbyqxmd.com/read/27999116/revisiting-gnra-and-uncg-folds-u-turns-versus-z-turns-in-rna-hairpin-loops
#16
Luigi D'Ascenzo, Filip Leonarski, Quentin Vicens, Pascal Auffinger
When thinking about RNA three-dimensional structures, coming across GNRA and UNCG tetraloops is perceived as a boon since their folds have been extensively described. Nevertheless, analyzing loop conformations within RNA and RNP structures led us to uncover several instances of GNRA and UNCG loops that do not fold as expected. We noticed that when a GNRA does not assume its "natural" fold, it adopts the one we typically associate with a UNCG sequence. The same folding interconversion occurs for loops with UNCG sequences, for instance within tRNA anticodon loops...
December 20, 2016: RNA
https://www.readbyqxmd.com/read/27994090/a-common-class-of-transcripts-with-5-intron-depletion-distinct-early-coding-sequence-features-and-n1-methyladenosine-modification
#17
Can Cenik, Hon Nian Chua, Guramrit Singh, Abdalla Akef, Michael P Snyder, Alexander F Palazzo, Melissa J Moore, Frederick P Roth
Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region...
December 19, 2016: RNA
https://www.readbyqxmd.com/read/27974622/the-conserved-snare-sec-22-localizes-to-late-endosomes-and-negatively-regulates-rna-interference-in-caenorhabditis-elegans
#18
Yani Zhao, Benjamin T Holmgren, Andrea Hinas
Small RNA pathways, including RNA interference (RNAi), play crucial roles in regulation of gene expression. Initially considered to be cytoplasmic, these processes have later been demonstrated to associate with membranes. For example, maturation of late endosomes/multivesicular bodies (MVBs) is required for efficient RNAi whereas fusion of MVBs to lysosomes appears to reduce silencing efficiency. SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) mediate membrane fusion and are thus at the core of membrane trafficking...
December 14, 2016: RNA
https://www.readbyqxmd.com/read/27974621/characterization-of-a-tutase-nuclease-complex-required-for-drosophila-gametogenesis
#19
Ching-Jung Lin, Jiayu Wen, Fernando Bejarano, Fuqu Hu, Diane Bortolamiol-Becet, Lijuan Kan, Piero Sanfilippo, Shu Kondo, Eric C Lai
Post-transcriptional regulatory strategies that involve coupling between terminal uridyltransferase (TUTase) and exoribonuclease enzymes have recently been characterized in diverse species. Of note, the 3' exoribonuclease Dis3L2 has received substantial attention as a factor that metabolizes uridylated substrates in contexts such as general mRNA degradation, turnover of specific miRNAs, and quality control of non-coding RNAs. To date, most studies of Dis3L2 have focused on fungi and mammalian cells. Here, we introduce Drosophila as a system that permits analysis of molecular mechanisms as well as the ability to interrogate organismal phenotypes...
December 14, 2016: RNA
https://www.readbyqxmd.com/read/27974620/will-the-circle-be-unbroken-specific-mutations-in-the-yeast-sm-protein-ring-expose-a-requirement-for-assembly-factor-brr1-a-homolog-of-gemin2
#20
Beate Schwer, Allen J Roth, Stewart Shuman
A seven-subunit Sm protein ring assembles around specific U-rich RNA segments of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP crystal structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights to structure-function relationships of the SmD1 and SmD2 subunits. Of sixteen conserved amino acids comprising their RNA-binding sites or inter-subunit interfaces, only Arg88 in SmD1 and Arg97 in SmD2 were essential for growth. Tests for genetic interactions with non-Sm splicing factors identified benign mutations of SmD1 (N37A, R88K, R93A) and SmD2 (R49A, N66A, R97K, D99A) that were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and/or Msl1...
December 14, 2016: RNA
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