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https://www.readbyqxmd.com/read/28193846/protein-4-1r-exon-16-3-splice-site-activation-requires-coordination-among-tia1-pcbp1-and-rbm39-during-terminal-erythropoiesis
#1
Shu-Ching Huang, Henry S Zhang, Brian Yu, Ellen McMahon, Dan T Nguyen, Faye H Yu, Alexander C Ou, Jennie Park Ou, Edward J Benz
Exon 16 of protein 4.1R encodes a spectrin/actin-binding peptide critical for erythrocyte membrane stability. Its expression during erythroid differentiation is regulated by alternative pre-mRNA splicing. A UUUUCCCCCC-motif situated between the branch point and the 3' splice site is crucial for inclusion. We show that the "UUUU" region and the last 3 C's in this motif are necessary for the binding of splicing factors TIA1 and Pcbp1, and that these proteins appear to act in a collaborative manner to enhance exon 16 inclusion...
February 13, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28157704/overlooked-fancd2-variant-encodes-a-promising-portent-tumor-suppressor-and-alternative-polyadenylation-contributes-to-its-expression
#2
Bing Hang, Yihang Shen, Piyan Zhang, Panneerselvam Jayabal, Raymond Che, Jun Zhang, Herbert Yu, Peiwen Fei
Fanconi Anemia (FA) complementation group D2 protein (FANCD2) is the center of the FA tumor suppressor pathway, which has become an important field of investigation in human aging and cancer. Here we report an overlooked central player in the FA pathway, FANCD2 variant 2 (FANCD2-V2), which appears to perform more potent tumor suppressor-function compared to the known variant of FANCD2, namely, FANCD2-V1. Detailed analysis of the FANCD2 gene structure indicated a proximal and distal polyadenylation site (PAS), associated with V2 and V1 transcripts accordingly...
February 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28103691/sudemycin-k-a-synthetic-antitumor-splicing-inhibitor-variant-with-improved-activity-and-versatile-chemistry
#3
Kamil Makowski, Luisa Vigevani, Fernando Albericio, Juan Valcárcel, Mercedes Álvarez
Important links exist between the process of pre-mRNA splicing and cancer, as illustrated by the frequent mutation of splicing factors in tumors and the emergence of various families of antitumor drugs that target components of the splicing machinery, notably SF3B1, a protein subunit of spliceosomal U2 small nuclear ribonucleoprotein particle (snRNP). Sudemycins are synthetic compounds that harbor a pharmacophore common to various classes of splicing inhibitors. Here, we describe the synthesis and functional characterization of novel sudemycin analogues that functionally probe key chemical groups within this pharmacophore...
20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28102758/p-tefb-finding-its-ways-to-release-promoter-proximally-paused-rna-polymerase-ii
#4
You Li, Min Liu, Lin-Feng Chen, Ruichuan Chen
The release of a paused Pol II depends on the recruitment of P-TEFb. Recent studies showed that both active P-TEFb and inactive P-TEFb (7SK snRNP) can be recruited to the promoter regions of global genes by different mechanisms. Here, we summarize the recent advances on these distinct recruitment mechanisms.
January 19, 2017: Transcription
https://www.readbyqxmd.com/read/28088760/usp15-regulates-dynamic-protein-protein-interactions-of-the-spliceosome-through-deubiquitination-of-prp31
#5
Tanuza Das, Joon Kyu Park, Jinyoung Park, Eunji Kim, Michael Rape, Eunice EunKyeong Kim, Eun Joo Song
Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified with K63-linked ubiquitin chains by the PRP19 complex and deubiquitinated by USP15 and its substrate targeting factor SART3. USP15(SART3) makes a complex with USP4 and this ternary complex serves as a platform to deubiquitinate PRP31 and PRP3...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28087715/sf3b1-hsh155-heat-motif-mutations-affect-interaction-with-the-spliceosomal-atpase-prp5-resulting-in-altered-branch-site-selectivity-in-pre-mrna-splicing
#6
Qing Tang, Susana Rodriguez-Santiago, Jing Wang, Jia Pu, Andrea Yuste, Varun Gupta, Alberto Moldón, Yong-Zhen Xu, Charles C Query
Mutations in the U2 snRNP component SF3B1 are prominent in myelodysplastic syndromes (MDSs) and other cancers and have been shown recently to alter branch site (BS) or 3' splice site selection in splicing. However, the molecular mechanism of altered splicing is not known. We show here that hsh155 mutant alleles in Saccharomyces cerevisiae, counterparts of SF3B1 mutations frequently found in cancers, specifically change splicing of suboptimal BS pre-mRNA substrates. We found that Hsh155p interacts directly with Prp5p, the first ATPase that acts during spliceosome assembly, and localized the interacting regions to HEAT (Huntingtin, EF3, PP2A, and TOR1) motifs in SF3B1 associated with disease mutations...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28076346/cryo-em-structure-of-a-human-spliceosome-activated-for-step-2-of-splicing
#7
Karl Bertram, Dmitry E Agafonov, Wen-Ti Liu, Olexandr Dybkov, Cindy L Will, Klaus Hartmuth, Henning Urlaub, Berthold Kastner, Holger Stark, Reinhard Lu Hrmann
Spliceosome rearrangements facilitated by RNA helicase Prp16 before catalytic step 2 of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after Prp16 action (C*). The architecture of the catalytic U2-U6 RNP core of the human C* spliceosome is highly similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated (by ~20 Å) from the catalytic centre, and its position close to the U6 snRNA ACAGA box is stabilised by interactions with the Prp8 RNase H-like and Prp17 WD40 domains...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28062854/sf3b1-mutations-associated-with-myelodysplastic-syndromes-alter-the-fidelity-of-branchsite-selection-in-yeast
#8
Tucker J Carrocci, Douglas M Zoerner, Joshua C Paulson, Aaron A Hoskins
RNA and protein components of the spliceosome work together to identify the 5' splice site, the 3' splice site, and the branchsite (BS) of nascent pre-mRNA. SF3b1 plays a key role in recruiting the U2 snRNP to the BS. Mutations in human SF3b1 have been linked to many diseases such as myelodysplasia (MDS) and cancer. We have used SF3b1 mutations associated with MDS to interrogate the role of the yeast ortholog, Hsh155, in BS selection and splicing. These alleles change how the spliceosome recognizes the BS and alter splicing when nonconsensus nucleotides are present at the -2, -1 and +1 positions relative to the branchpoint adenosine...
January 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28059623/coordinating-cell-cycle-regulated-histone-gene-expression-through-assembly-and-function-of-the-histone-locus-body
#9
Robert J Duronio, William F Marzluff
Metazoan replication-dependent (RD) histone genes encode the only known cellular mRNAs that are not polyadenylated. These mRNAs end instead in a conserved stem-loop, which is formed by an endonucleolytic cleavage of the pre-mRNA. The genes for all 5 histone proteins are clustered in all metazoans and coordinately regulated with high levels of expression during S phase. Production of histone mRNAs occurs in a nuclear body called the Histone Locus Body (HLB), a subdomain of the nucleus defined by a concentration of factors necessary for histone gene transcription and pre-mRNA processing...
January 6, 2017: RNA Biology
https://www.readbyqxmd.com/read/28054357/linking-amyotrophic-lateral-sclerosis-and-spinal-muscular-atrophy-through-rna-transcriptome-homeostasis-a-genomics-perspective
#10
REVIEW
Margarida Gama-Carvalho, Marina L Garcia-Vaquero, Francisco R Pinto, Florence Besse, Joachim Weis, Aaron Voigt, Jörg B Schulz, Javier De Las Rivas
In this review we present our most recent understanding of key biomolecular processes that underlie two motor neuron degenerative disorders, Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA). We focus on the role of four multifunctional proteins involved in RNA metabolism (TDP-43, FUS, SMN and Senataxin) that play a causal role in these diseases. Recent results have led to a novel scenario of intricate connections between these four proteins, bringing transcriptome homeostasis into the spotlight as a common theme in motor neuron degeneration...
January 5, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28045380/structure-and-conformational-plasticity-of-the-u6-small-nuclear-ribonucleoprotein-core
#11
Eric J Montemayor, Allison L Didychuk, Honghong Liao, Panzhou Hu, David A Brow, Samuel E Butcher
U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayor et al...
January 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28031290/retraction-notice-the-smn-structure-reveals-its-crucial-role-in-snrnp-assembly
#12
Chenda O Seng, Craig Magee, Philip J Young, Christian L Lorson, James P Allen
No abstract text is available yet for this article.
December 27, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/27991914/the-spliceosome-u2-snrnp-factors-promote-genome-stability-through-distinct-mechanisms-transcription-of-repair-factors-and-r-loop-processing
#13
M Tanikawa, K Sanjiv, T Helleday, P Herr, O Mortusewicz
Recent whole-exome sequencing of malignancies have detected recurrent somatic mutations in U2 small nuclear ribonucleoprotein complex (snRNP) components of the spliceosome. These factors have also been identified as novel players in the DNA-damage response (DDR) in several genome-wide screens and proteomic analysis. Although accumulating evidence implies that the spliceosome has an important role in genome stability and is an emerging hallmark of cancer, its precise role in DNA repair still remains elusive...
December 19, 2016: Oncogenesis
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
#14
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
https://www.readbyqxmd.com/read/27907902/active-5-splice-sites-regulate-the-biogenesis-efficiency-of-arabidopsis-micrornas-derived-from-intron-containing-genes
#15
Katarzyna Knop, Agata Stepien, Maria Barciszewska-Pacak, Michal Taube, Dawid Bielewicz, Michal Michalak, Jan W Borst, Artur Jarmolowski, Zofia Szweykowska-Kulinska
Arabidopsis, miR402 that is encoded within the first intron of a protein-coding gene At1g77230, is induced by heat stress. Its upregulation correlates with splicing inhibition and intronic proximal polyA site selection. It suggests that miR402 is not processed from an intron, but rather from a shorter transcript after selection of the proximal polyA site within this intron. Recently, introns and active 5' splice sites (5'ss') have been shown to stimulate the accumulation of miRNAs encoded within the first exons of intron-containing MIR genes...
October 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899032/proteomic-profiling-of-the-spinal-cord-in-als-decreased-atp5d-levels-suggest-synaptic-dysfunction-in-als-pathogenesis
#16
Jooyeon Engelen-Lee, Anna M Blokhuis, Wim G M Spliet, R Jeroen Pasterkamp, Eleonora Aronica, Jeroen A A Demmers, Roel Broekhuizen, Giovanni Nardo, Niels Bovenschen, Leonard H Van Den Berg
BACKGROUND: We aimed to gain new insights into the pathogenesis of sporadic ALS (sALS) through a comprehensive proteomic analysis. METHODS: Protein profiles of the anterior and posterior horn in post-mortem spinal cord samples of 10 ALS patients and 10 controls were analysed using 2D-differential gel electrophoresis. The identified protein spots with statistically significant level changes and a spot ratio >2.0 were analysed by LC-MS/MS. RESULTS: In the posterior horn only 3 proteins were differentially expressed...
November 29, 2016: Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration
https://www.readbyqxmd.com/read/27894420/structural-basis-for-the-recognition-of-spliceosomal-smn-b-b-proteins-by-the-rbm5-ocre-domain-in-splicing-regulation
#17
André Mourão, Sophie Bonnal, Komal Soni, Lisa Warner, Rémy Bordonné, Juan Valcárcel, Michael Sattler
The multi-domain splicing factor RBM5 regulates the balance between antagonistic isoforms of the apoptosis-control genes FAS/CD95, Caspase-2 and AID. An OCRE (OCtamer REpeat of aromatic residues) domain found in RBM5 is important for alternative splicing regulation and mediates interactions with components of the U4/U6.U5 tri-snRNP. We show that the RBM5 OCRE domain adopts a unique β-sheet fold. NMR and biochemical experiments demonstrate that the OCRE domain directly binds to the proline-rich C-terminal tail of the essential snRNP core proteins SmN/B/B'...
November 29, 2016: ELife
https://www.readbyqxmd.com/read/27882870/large-scale-remodeling-of-a-repressed-exon-ribonucleoprotein-to-an-exon-definition-complex-active-for-splicing
#18
Somsakul Pop Wongpalee, Ajay Vashisht, Shalini Sharma, Darryl Chui, James A Wohlschlegel, Douglas L Black
Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition...
November 24, 2016: ELife
https://www.readbyqxmd.com/read/27881601/structural-basis-for-snrna-recognition-by-the-double-wd40-repeat-domain-of-gemin5
#19
Wenxing Jin, Yi Wang, Chao-Pei Liu, Na Yang, Mingliang Jin, Yao Cong, Mingzhu Wang, Rui-Ming Xu
Assembly of the spliceosomal small nuclear ribonucleoparticle (snRNP) core requires the participation of the multisubunit SMN (survival of motor neuron) complex, which contains SMN and several Gemin proteins. The SMN and Gemin2 subunits directly bind Sm proteins, and Gemin5 is required for snRNP biogenesis and has been implicated in snRNA recognition. The RNA sequence required for snRNP assembly includes the Sm site and an adjacent 3' stem-loop, but a precise understanding of Gemin5's RNA-binding specificity is lacking...
November 1, 2016: Genes & Development
https://www.readbyqxmd.com/read/27881600/structural-insights-into-gemin5-guided-selection-of-pre-snrnas-for-snrnp-assembly
#20
Chao Xu, Hideaki Ishikawa, Keiichi Izumikawa, Li Li, Hao He, Yuko Nobe, Yoshio Yamauchi, Hanief M Shahjee, Xian-Hui Wu, Yi-Tao Yu, Toshiaki Isobe, Nobuhiro Takahashi, Jinrong Min
In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)4-6G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m(7)G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays...
November 1, 2016: Genes & Development
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