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https://www.readbyqxmd.com/read/27907902/active-5-splice-sites-regulate-the-biogenesis-efficiency-of-arabidopsis-micrornas-derived-from-intron-containing-genes
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/27880071/interplay-of-cis-and-trans-regulatory-mechanisms-in-the-spliceosomal-rna-helicase-brr2
#7
Eva Absmeier, Christian Becke, Jan Wollenhaupt, Karine F Santos, Markus C Wahl
RNA helicase Brr2 is implicated in multiple phases of pre-mRNA splicing and thus requires tight regulation. Brr2 can be auto-inhibited via a large N-terminal region folding back onto its helicase core and auto-activated by a catalytically inactive C-terminal helicase cassette. Furthermore, it can be regulated in trans by the Jab1 domain of the Prp8 protein, which can inhibit Brr2 by intermittently inserting a C-terminal tail in the enzyme's RNA-binding tunnel or activate the helicase after removal of this tail...
November 23, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27863087/posttranscriptional-coordination-of-splicing-and-mirna-biogenesis-in-plants
#8
REVIEW
Agata Stepien, Katarzyna Knop, Jakub Dolata, Michal Taube, Mateusz Bajczyk, Maria Barciszewska-Pacak, Andrzej Pacak, Artur Jarmolowski, Zofia Szweykowska-Kulinska
MicroRNAs (miRNAs) are short, single-stranded, noncoding RNAs that play a crucial role in basic physiological and morphological processes and in response to various stresses in eukaryotic organisms. However, the miRNA biogenesis, which is based on the action of complex protein machinery, varies between plants and animals, with the differences largely concerning the location of the process, the protein composition of the microprocessor, the mechanism of miRNA action on mRNA target, and the miRNA gene ( MIR ) structure...
November 9, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27858508/activation-of-transcription-enforces-the-formation-of-distinct-nuclear-bodies-in-zebrafish-embryos
#9
Patricia Heyn, Hanna Salmonowicz, Jonathan Rodenfels, Karla M Neugebauer
Nuclear bodies are cellular compartments that lack lipid bilayers and harbor specific RNAs and proteins. Recent proposals that nuclear bodies form through liquid-liquid phase separation leave the question of how different nuclear bodies maintain their distinct identities unanswered. Here we investigate Cajal bodies (CBs), histone locus bodies (HLBs) and nucleoli - involved in assembly of the splicing machinery, histone mRNA 3' end processing, and rRNA processing, respectively - in the embryos of the zebrafish, Danio rerio...
November 18, 2016: RNA Biology
https://www.readbyqxmd.com/read/27792457/functions-and-regulation-of-the-brr2-rna-helicase-during-splicing
#10
Eva Absmeier, Karine F Santos, Markus C Wahl
Pre-mRNA splicing entails the stepwise assembly of an inactive spliceosome, its catalytic activation, splicing catalysis and spliceosome disassembly. Transitions in this reaction cycle are accompanied by compositional and conformational rearrangements of the underlying RNA-protein interaction networks, which are driven and controlled by eight conserved superfamily 2 RNA helicases. The Ski2-like helicase, Brr2, provides the key remodeling activity during spliceosome activation and is additionally implicated in the catalytic and disassembly phases of splicing, indicating that Brr2 needs to be tightly regulated during splicing...
October 28, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27754875/global-analysis-of-pre-mrna-subcellular-localization-following-splicing-inhibition-by-spliceostatin-a
#11
Rei Yoshimoto, Daisuke Kaida, Masaaki Furuno, A Maxwell Burroughs, Shohei Noma, Harukazu Suzuki, Yumi Kawamura, Yoshihide Hayashizaki, Akila Mayeda, Minoru Yoshida
Spliceostatin A (SSA) is a methyl ketal derivative of FR901464, a potent antitumor compound isolated from a culture broth of Pseudomonas sp. no. 2663. These compounds selectively bind to the essential spliceosome component SF3b, a subcomplex of the U2 snRNP, to inhibit pre-mRNA splicing. However, the mechanism of SSA's antitumor activity is unknown. It is noteworthy that SSA causes accumulation of a truncated form of the CDK inhibitor protein p27 translated from CDKN1B pre-mRNA, which is involved in SSA-induced cell-cycle arrest...
October 17, 2016: RNA
https://www.readbyqxmd.com/read/27720643/molecular-architecture-of-sf3b-and-structural-consequences-of-its-cancer-related-mutations
#12
Constantin Cretu, Jana Schmitzová, Almudena Ponce-Salvatierra, Olexandr Dybkov, Evelina I De Laurentiis, Kundan Sharma, Cindy L Will, Henning Urlaub, Reinhard Lührmann, Vladimir Pena
SF3b is a heptameric protein complex of the U2 small nuclear ribonucleoprotein (snRNP) that is essential for pre-mRNA splicing. Mutations in the largest SF3b subunit, SF3B1/SF3b155, are linked to cancer and lead to alternative branch site (BS) selection. Here we report the crystal structure of a human SF3b core complex, revealing how the distinctive conformation of SF3b155's HEAT domain is maintained by multiple contacts with SF3b130, SF3b10, and SF3b14b. Protein-protein crosslinking enabled the localization of the BS-binding proteins p14 and U2AF65 within SF3b155's HEAT-repeat superhelix, which together with SF3b14b forms a composite RNA-binding platform...
October 20, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27715441/specific-genomic-cues-regulate-cajal-body-assembly
#13
Iain A Sawyer, Gordon L Hager, Miroslav Dundr
The assembly of specialized sub-nuclear microenvironments known as nuclear bodies (NBs) is important for promoting efficient nuclear function. In particular, the Cajal body (CB), a prominent NB that facilitates spliceosomal snRNP biogenesis, assembles in response to genomic cues. Here, we detail the factors that regulate CB assembly and structural maintenance. These include the importance of transcription at nucleating gene loci, the grouping of these genes on human chromosomes 1, 6 and 17, as well as cell cycle and biochemical regulation of CB protein function...
October 7, 2016: RNA Biology
https://www.readbyqxmd.com/read/27683728/interaction-between-rna-helicase-root-initiation-defective-1-and-gametophytic-factor-1-is-involved-in-female-gametophyte-development-in-arabidopsis
#14
Dong Zi Zhu, Xue Fang Zhao, Chang Zhen Liu, Fang Fang Ma, Fang Wang, Xin-Qi Gao, Xian Sheng Zhang
ROOT INITIATION DEFECTIVE 1 (RID1) is an Arabidopsis DEAH/RHA RNA helicase. It functions in hypocotyl de-differentiation, de novo meristem formation, and cell specification of the mature female gametophyte (FG). However, it is unclear how RID1 regulates FG development. In this study, we observed that mutations to RID1 disrupted the developmental synchrony and retarded the progression of FG development. RID1 exhibited RNA helicase activity, with a preference for unwinding double-stranded RNA in the 3' to 5' direction...
October 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27683217/stoichiometries-of-u2af35-u2af65-and-u2-snrnp-reveal-new-early-spliceosome-assembly-pathways
#15
Li Chen, Robert Weinmeister, Jana Kralovicova, Lucy P Eperon, Igor Vorechovsky, Andrew J Hudson, Ian C Eperon
The selection of 3' splice sites (3'ss) is an essential early step in mammalian RNA splicing reactions, but the processes involved are unknown. We have used single molecule methods to test whether the major components implicated in selection, the proteins U2AF35 and U2AF65 and the U2 snRNP, are able to recognize alternative candidate sites or are restricted to one pre-specified site. In the presence of adenosine triphosphate (ATP), all three components bind in a 1:1 stoichiometry with a 3'ss. Pre-mRNA molecules with two alternative 3'ss can be bound concurrently by two molecules of U2AF or two U2 snRNPs, so none of the components are restricted...
September 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27679741/ddx6-transfers-p-tefb-kinase-to-the-af4-af4n-aff1-super-elongation-complex
#16
Fabian Mück, Silvia Bracharz, Rolf Marschalek
AF4/AFF1 and AF5/AFF4 are both backbones for the assembly of "super elongation complexes" (SECs) that exert 2 distinct functions after the recruitment of P-TEFb from the 7SK snRNP: (1) initiation and elongation of RNA polymerase II gene transcription, and (2) modification of transcribed gene regions by distinct histone methylation patterns. In this study we aimed to investigate one of the initial steps, namely how P-TEFb is transferred from 7SK snRNPs to the SECs. In particular, we were interested in the role of DDX6 that we have recently identified as part of the AF4 complex...
2016: American Journal of Blood Research
https://www.readbyqxmd.com/read/27679474/hlarp7-c-terminal-domain-contains-an-xrrm-that-binds-the-3-hairpin-of-7sk-rna
#17
Catherine D Eichhorn, Rahul Chug, Juli Feigon
The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal La module binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear...
November 16, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27662573/a-broad-set-of-chromatin-factors-influences-splicing
#18
Eric Allemand, Michael P Myers, Jose Garcia-Bernardo, Annick Harel-Bellan, Adrian R Krainer, Christian Muchardt
Several studies propose an influence of chromatin on pre-mRNA splicing, but it is still unclear how widespread and how direct this phenomenon is. We find here that when assembled in vivo, the U2 snRNP co-purifies with a subset of chromatin-proteins, including histones and remodeling complexes like SWI/SNF. Yet, an unbiased RNAi screen revealed that the outcome of splicing is influenced by a much larger variety of chromatin factors not all associating with the spliceosome. The availability of this broad range of chromatin factors impacting splicing further unveiled their very context specific effect, resulting in either inclusion or skipping, depending on the exon under scrutiny...
September 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27659333/deletion-of-snurf-snrpn-u1b-and-u1b-upstream-exons-in-a-child-with-developmental-delay-and-excessive-weight
#19
Costas Koufaris, Angelos Alexandrou, Ioannis Papaevripidou, Ioanna Alexandrou, Violetta Christophidou-Anastasiadou, Carolina Sismani
Prader-Willi syndrome is a rare syndrome characterized by hypotonia, developmental delay and excessive appetite. This syndrome is caused by the loss of function of paternally-expressed genes located in an imprinting centre in 15q11-q13. Here, we report the case of a patient who was referred to us with Prader-Willi syndrome-like symptoms including obesity and developmental delay. Examination of this patient revealed that he was a carrier of a paternally inherited deletion that affected the U1B and U1B* upstream exons of the SNURF-SNRNP gene within the 15q11-q13 imprinted region...
September 2016: Journal of Genetics
https://www.readbyqxmd.com/read/27648855/smn-a-chaperone-for-nuclear-rnp-social-occasions
#20
Amanda C Raimer, Kelsey M Gray, A Gregory Matera
Survival Motor Neuron (SMN) protein localizes to both the nucleus and the cytoplasm. Cytoplasmic SMN is diffusely localized in large oligomeric complexes with core member proteins, called Gemins. Biochemical and cell biological studies have demonstrated that the SMN complex is required for the cytoplasmic assembly and nuclear transport of Sm-class ribonucleoproteins (RNPs). Nuclear SMN accumulates with spliceosomal small nuclear (sn)RNPs in Cajal bodies, sub-domains involved in multiple facets of snRNP maturation...
September 20, 2016: RNA Biology
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