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Spliceosome

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https://www.readbyqxmd.com/read/28723644/fir-haplodeficiency-promotes-splicing-to-pyruvate-kinase-m2-in-mice-thymic-lymphoma-tissues-revealed-by-six-plex-tandem-mass-tag-quantitative-proteomic-analysis
#1
Asako Kimura, Kouichi Kitamura, Guzhanuer Ailiken, Mamoru Satoh, Toshinari Minamoto, Nobuko Tanaka, Fumio Nomura, Kazuyuki Matsushita
The switch of pyruvate kinase (PK) M1 to PKM2 is pivotal for glucose metabolism in cancers. The PKM1/M2 shift is controlled by the alternative splicing of two mutually exclusive exons in the PKM gene. PKM1 is expressed in differentiated tissues, whereas PKM2 is expressed in cancer tissues. This study revealed that the haplodeficiency of FUSE-binding protein (FBP)-interacting repressor (FIR), a transcriptional repressor of the c-myc gene, contributed to the splicing of PKM1 to PKM2 in mice thymic lymphoma and/or T-cell type acute lymphoblastic leukemia (T-ALL) using six-plex tandem mass tag (TMT) quantitative proteomic analysis...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28719341/label-free-quantitative-proteomics-analysis-on-the-cisplatin-resistance-in-ovarian-cancer-cells
#2
F Wang, Y Zhu, S Fang, S Li, S Liu
Quantitative proteomics has been made great progress in recent years. Label free quantitative proteomics analysis based on the mass spectrometry is widely used. Using this technique, we determined the differentially expressed proteins in the cisplatin-sensitive ovarian cancer cells COC1 and cisplatin-resistant cells COC1/DDP before and after the application of cisplatin. Using the GO analysis, we classified those proteins into different subgroups bases on their cellular component, biological process, and molecular function...
May 20, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28712727/error-prone-splicing-controlled-by-the-ubiquitin-relative-hub1
#3
Ramazan Karaduman, Sittinan Chanarat, Boris Pfander, Stefan Jentsch
Accurate pre-mRNA splicing is needed for correct gene expression and relies on faithful splice site recognition. Here, we show that the ubiquitin-like protein Hub1 binds to the DEAD-box helicase Prp5, a key regulator of early spliceosome assembly, and stimulates its ATPase activity thereby enhancing splicing and relaxing fidelity. High Hub1 levels enhance splicing efficiency but also cause missplicing by tolerating suboptimal splice sites and branchpoint sequences. Notably, Prp5 itself is regulated by a Hub1-dependent negative feedback loop...
July 11, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28701519/nineteen-complex-related-factor-prp45-is-required-for-the-early-stages-of-cotranscriptional-spliceosome-assembly
#4
Martina Hálová, Ondřej Gahura, Martin Převorovský, Zdeněk Cit, Marian Novotný, Anna Valentová, Kateřina Abrhámová, František Půta, Petr Folk
Splicing in S. cerevisiae has been shown to proceed cotranscriptionally, but the nature of the coupling remains a subject of debate. Here, we examine the effect of nineteen complex-related splicing factor Prp45 (a homolog of SNW1/SKIP) on cotranscriptional splicing. RNA-sequencing and RT-qPCR showed elevated pre-mRNA levels but only limited reduction of spliced mRNAs in cells expressing C-terminally truncated Prp45, Prp45(1-169). Assays with a series of reporters containing the AMA1 intron with regulatable splicing confirmed decreased splicing efficiency and showed the leakage of unspliced RNAs in prp45(1-169) cells...
July 12, 2017: RNA
https://www.readbyqxmd.com/read/28695491/identification-and-characterization-of-the-chinese-giant-salamander-andrias-davidianus-mirnas-by-deep-sequencing-and-predication-of-their-targets
#5
Yong Huang, You Bing Yang, Xiao Chan Gao, Hong Tao Ren, Xi Hong Sun
MicroRNAs (miRNAs) are non-coding small RNA of approximately 22 nt in length. They are considered as key regulators for gene expression at the post-transcriptional level and play an important role in the regulation of many fundamental biological processes. Andrias davidianus, as one of the largest amphibian on earth, may represent the transitional type of animal from aquatic to terrestrial life, but so far, no miRNA has been identified in the species. In this study, Illumina deep sequencing was used for high-throughput analysis of miRNAs in a pooled small RNA library isolated from eight tissues sample of A...
August 2017: 3 Biotech
https://www.readbyqxmd.com/read/28686815/re2o7-mediated-dehydrative-cyclization-reactions-total-synthesis-of-herboxidiene-and-its-12-desmethyl-analog
#6
Paul Floreancig, Tyler Rohrs, Qi Qin
Re2O7 catalysis effects efficient and stereoselective dehydrative cyclization reactions from monoallylic diols, with stereocontrol arising from thermodynamic equilibration. This method was applied to a rapid synthesis of the spliceosome inhibitor herboxidiene. The route was also utilized for the synthesis of an analog that highlights the importance of a single methyl group in biasing the conformation in the acyclic region of the molecule.
July 7, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28677323/caloric-restriction-impacts-plasma-micrornas-in-rhesus-monkeys
#7
Augusto Schneider, Joseph M Dhahbi, Hani Atamna, Josef P Clark, Ricki J Colman, Rozalyn M Anderson
Caloric restriction (CR) is one of the most robust interventions shown to delay aging in diverse species, including rhesus monkeys (Macaca mulatta). Identification of factors involved in CR brings a promise of translatability to human health and aging. Here, we show that CR induced a profound change in abundance of circulating microRNAs (miRNAs) linked to growth and insulin signaling pathway, suggesting that miRNAs are involved in CR's mechanisms of action in primates. Deep sequencing of plasma RNA extracts enriched for short species revealed a total of 243 unique species of miRNAs including 47 novel species...
July 5, 2017: Aging Cell
https://www.readbyqxmd.com/read/28669867/radical-probing-of-spliceosome-assembly
#8
Charnpal S Grewal, Oliver A Kent, Andrew M MacMillan
Here we describe the synthesis and use of a directed hydroxyl radical probe, tethered to a pre-mRNA substrate, to map the structure of this substrate during the spliceosome assembly process. These studies indicate an early organization and proximation of conserved pre-mRNA sequences during spliceosome assembly. This methodology may be adapted to the synthesis of a wide variety of modified RNAs for use as probes of RNA structure and RNA-protein interaction.
June 29, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28668587/studying-structure-and-function-of-spliceosomal-helicases
#9
REVIEW
Ralf Ficner, Achim Dickmanns, Piotr Neumann
The splicing of eukaryotic precursor mRNAs requires the activity of at least three DEAD-box helicases, one Ski2-like helicase and four DEAH-box helicases. High resolution structures for five of these spliceosomal helicases were obtained by means of X-ray crystallography. Additional low resolution structural information could be derived from single particle cryo electron microscopy and small angle X-ray scattering. The functional characterization includes biochemical methods to measure the ATPase and helicase activities...
June 28, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28666385/human-ribosomal-protein-es1-is-engaged-in-cellular-events-related-to-processing-and-functioning-of-u11-snrna
#10
Alexander V Gopanenko, Alexey A Malygin, Alexey E Tupikin, Pavel P Laktionov, Marsel R Kabilov, Galina G Karpova
Ribosomal proteins are involved in many cellular processes through interactions with various RNAs. Here, applying the photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation approach to HEK293 cells overproducing ribosomal protein (rp) eS1, we determined the products of RNU5A-1 and RNU11 genes encoding U5 and U11 snRNAs as the RNA partners of ribosome-unbound rp eS1. U11 pre-snRNA-associated rp eS1 was revealed in the cytoplasm and nucleus where rp eS1-bound U11/U12 di-snRNP was also found...
June 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28666123/splicing-correcting-therapy-for-sma
#11
Lili Wan, Gideon Dreyfuss
Spinal muscular atrophy (SMA) is caused by deficiency of SMN protein, which is crucial for spliceosome subunits biogenesis. Most SMA patients have SMN1 deletions, leaving SMN2 as sole SMN source; however, a C→T substitution converts an exonic-splicing enhancer (ESE) to a silencer (ESS), causing frequent exon7 skipping in SMN2 pre-mRNA and yielding a truncated protein. Antisense treatment to SMN2 intron7-splicing silencer (ISS) improves SMN expression and motor function. To view this Bench to Bedside, open or download the PDF...
June 29, 2017: Cell
https://www.readbyqxmd.com/read/28663330/gene-of-the-month-prpf31
#12
REVIEW
Anna M Rose, Rong Luo, Utsav K Radia, Shomi S Bhattacharya
Pre-mRNA splicing is an essential process in eukaryotic cells where the transcribed intronic sequences are removed, prior to translation into protein. PRPF31 is a ubiquitously expressed splicing factor, which aids in the assembly of the macromolecular spliceosome. Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa (adRP), a form of retinal degeneration that causes progressive visual impairment. Interestingly, mutations in PRPF31 are non-penetrant, with some mutation carriers being phenotypically unaffected...
June 29, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28659141/isvase-identification-of-sequence-variant-associated-with-splicing-event-using-rna-seq-data
#13
Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Jun Yu, Songnian Hu
BACKGROUND: Exon recognition and splicing precisely and efficiently by spliceosome is the key to generate mature mRNAs. About one third or a half of disease-related mutations affect RNA splicing. Software PVAAS has been developed to identify variants associated with aberrant splicing by directly using RNA-seq data. However, it bases on the assumption that annotated splicing site is normal splicing, which is not true in fact. RESULTS: We develop the ISVASE, a tool for specifically identifying sequence variants associated with splicing events (SVASE) by using RNA-seq data...
June 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28655759/rbm25-is-a-global-splicing-factor-promoting-inclusion-of-alternatively-spliced-exons-and-is-itself-regulated-by-lysine-mono-methylation
#14
Scott M Carlson, Cameron M Soulette, Ze Yang, Joshua E Elias, Angela N Brooks, Or Gozani
In eukaryotes, pre-mRNA splicing removes non-coding intron sequences to produce mature mRNA. This removal is controlled in part by RNA-binding proteins that regulate alternative splicing decisions through interactions with the splicing machinery. RNA binding motif protein 25 (RBM25) is a putative splicing factor strongly conserved across eukaryotic lineages. However, the role of RBM25 in global splicing regulation and its cellular functions are unknown. Here we show that RBM25 is required for viability of multiple human cell lines, suggesting that it could play a key role in pre-mRNA splicing...
June 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28655105/-sensitivity-of-alternative-spliceosomes-of-l-type-pml-rar%C3%AE-fusion-gene-to-ato
#15
F Xue, Y H Tan, F G Ren, Y F Zhang, X H Chen, Z F Xu, J M Chang, J Xu, F Gao, J Li, B Yin, H X Liu, H W Wang
No abstract text is available yet for this article.
June 14, 2017: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/28654215/the-fgsrp1-sr-protein-gene-is-important-for-plant-infection-and-pre-mrna-processing-in-fusarium-graminearum
#16
Yimei Zhang, Xuli Gao, Manli Sun, Huiquan Liu, Jin-Rong Xu
The versatile functions of SR (serine/arginine-rich) proteins in pre-mRNA splicing and processing are modulated by reversible phosphorylation. Previous studies showed that FgPrp4, the only protein kinase among spliceosome components, is important for intron splicing and the FgSrp1 SR protein is phosphorylated at five conserved sites in Fusarium graminearum. In this study, we showed that the Fgsrp1 deletion mutant rarely produced conidia and caused only limited symptoms on wheat heads and corn silks. Deletion of FgSRP1 also reduced ascospore ejection and deoxynivalenol (DON) production...
June 27, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28648680/reversibly-constraining-spliceosome-substrate-complexes-by-engineering-disulfide-crosslinks
#17
Patrick McCarthy, Erin Garside, Yonatan Meschede-Krasa, Andrew MacMillan, Daniel Pomeranz Krummel
The spliceosome is a highly dynamic mega-Dalton enzyme, formed in part by assembly of U snRNPs onto its pre-mRNA substrate transcripts. Early steps in spliceosome assembly are challenging to study biochemically and structurally due to compositional and conformational dynamics. We detail an approach to covalently and reversibly constrain or trap non-covalent pre-mRNA/protein spliceosome complexes. This approach involves engineering a single disulfide bond between a thiol-bearing cysteine sidechain and a proximal backbone phosphate of the pre-mRNA, site-specifically modified with an N-thioalkyl moiety...
June 22, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28648679/structure-determination-of-group-ii-introns
#18
REVIEW
Timothy Wiryaman, Navtej Toor
Group II introns are self-splicing catalytic RNAs that are able to excise themselves from pre-mRNAs using a mechanism identical to that utilized by the spliceosome. Both structural and phylogenetic data support the hypothesis that group II introns and the spliceosome share a common ancestor. Structures of group II introns have given insight into the active site required for the catalysis of RNA splicing. This review outlines crucial aspects of the structure determination of group II introns such as sample preparation and data processing...
June 23, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28642865/spinal-muscular-atrophy-from-defective-chaperoning-of-snrnp-assembly-to-neuromuscular-dysfunction
#19
REVIEW
Maia Lanfranco, Neville Vassallo, Ruben J Cauchi
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder that results from decreased levels of the survival motor neuron (SMN) protein. SMN is part of a multiprotein complex that also includes Gemins 2-8 and Unrip. The SMN-Gemins complex cooperates with the protein arginine methyltransferase 5 (PRMT5) complex, whose constituents include WD45, PRMT5 and pICln. Both complexes function as molecular chaperones, interacting with and assisting in the assembly of an Sm protein core onto small nuclear RNAs (snRNAs) to generate small nuclear ribonucleoproteins (snRNPs), which are the operating components of the spliceosome...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28637748/impaired-spliceosomal-usnrnp-assembly-leads-to-sm-mrna-down-regulation-and-sm-protein-degradation
#20
Archana Bairavasundaram Prusty, Rajyalakshmi Meduri, Bhupesh Kumar Prusty, Jens Vanselow, Andreas Schlosser, Utz Fischer
Specialized assembly factors facilitate the formation of many macromolecular complexes in vivo. The formation of Sm core structures of spliceosomal U-rich small nuclear ribonucleoprotein particles (UsnRNPs) requires assembly factors united in protein arginine methyltransferase 5 (PRMT5) and survival motor neuron (SMN) complexes. We demonstrate that perturbations of this assembly machinery trigger complex cellular responses that prevent aggregation of unassembled Sm proteins. Inactivation of the SMN complex results in the initial tailback of Sm proteins on the PRMT5 complex, followed by down-regulation of their encoding mRNAs...
June 21, 2017: Journal of Cell Biology
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