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https://www.readbyqxmd.com/read/29030393/fanconi-anemia-fancd2-and-fanci-proteins-regulate-the-nuclear-dynamics-of-splicing-factors
#1
María Moriel-Carretero, Sara Ovejero, Marie Gérus-Durand, Dimos Vryzas, Angelos Constantinou
Proteins disabled in the cancer-prone disorder Fanconi anemia (FA) ensure the maintenance of chromosomal stability during DNA replication. FA proteins regulate replication dynamics, coordinate replication-coupled repair of interstrand DNA cross-links, and mitigate conflicts between replication and transcription. Here we show that FANCI and FANCD2 associate with splicing factor 3B1 (SF3B1), a key spliceosomal protein of the U2 small nuclear ribonucleoprotein (U2 snRNP). FANCI is in close proximity to SF3B1 in the nucleoplasm of interphase and mitotic cells...
October 13, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/29027900/rna-polymerase-ii-stalling-at-pre-mrna-splice-sites-is-enforced-by-ubiquitination-of-the-catalytic-subunit
#2
Laura Milligan, Camille Sayou, Alex Tuck, Tatsiana Auchynnikava, Jane Ea Reid, Ross Alexander, Flavia de Lima Alves, Robin Allshire, Christos Spanos, Juri Rappsilber, Jean D Beggs, Grzegorz Kudla, David Tollervey
Numerous links exist between co-transcriptional RNA processing and the transcribing RNAPII. In particular, pre-mRNA splicing was reported to be associated with slowed RNAPII elongation. Here, we identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. Ubiquitination was increased in the absence of the Bre5-Ubp3 ubiquitin protease complex. Bre5 binds RNA in vivo, with a preference for exon 2 regions of intron-containing pre-mRNAs and poly(A) proximal sites. Ubiquitinated RNAPII showed similar enrichment...
October 13, 2017: ELife
https://www.readbyqxmd.com/read/28967883/3-2-%C3%A3-resolution-structure-of-the-90s-preribosome-before-a1-pre-rrna-cleavage
#3
Jingdong Cheng, Nikola Kellner, Otto Berninghausen, Ed Hurt, Roland Beckmann
The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors...
November 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28961236/transcriptome-analysis-of-hypoxic-cancer-cells-uncovers-intron-retention-in-eif2b5-as-a-mechanism-to-inhibit-translation
#4
Lauren K Brady, Hejia Wang, Caleb M Radens, Yue Bi, Milan Radovich, Amit Maity, Cristina Ivan, Mircea Ivan, Yoseph Barash, Constantinos Koumenis
Cells adjust to hypoxic stress within the tumor microenvironment by downregulating energy-consuming processes including translation. To delineate mechanisms of cellular adaptation to hypoxia, we performed RNA-Seq of normoxic and hypoxic head and neck cancer cells. These data revealed a significant down regulation of genes known to regulate RNA processing and splicing. Exon-level analyses classified > 1,000 mRNAs as alternatively spliced under hypoxia and uncovered a unique retained intron (RI) in the master regulator of translation initiation, EIF2B5...
September 2017: PLoS Biology
https://www.readbyqxmd.com/read/28934475/in-vivo-probing-of-nascent-rna-structures-reveals-principles-of-cotranscriptional-folding
#5
Danny Incarnato, Edoardo Morandi, Francesca Anselmi, Lisa M Simon, Giulia Basile, Salvatore Oliviero
Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates' secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5'-halves of long-range helices get sequestered into transient non-native interactions until their 3' counterparts have been transcribed...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28923949/cytosine-deamination-and-base-excision-repair-cause-r-loop-induced-cag-repeat-fragility-and-instability-in-saccharomyces-cerevisiae
#6
Xiaofeng A Su, Catherine H Freudenreich
CAG/CTG repeats are structure-forming repetitive DNA sequences, and expansion beyond a threshold of ∼35 CAG repeats is the cause of several human diseases. Expanded CAG repeats are prone to breakage, and repair of the breaks can cause repeat contractions and expansions. In this study, we found that cotranscriptional R-loops formed at a CAG-70 repeat inserted into a yeast chromosome. R-loops were further elevated upon deletion of yeast RNaseH genes and caused repeat fragility. A significant increase in CAG repeat contractions was also observed, consistent with previous human cell studies...
October 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28730434/cotranscriptional-production-of-chemically-modified-rna-nanoparticles
#7
Maria L Kireeva, Kirill A Afonin, Bruce A Shapiro, Mikhail Kashlev
RNA nanoparticles consisting of multiple RNA strands of different sequences forming various three-dimensional structures emerge as promising carriers of siRNAs, RNA aptamers, and ribozymes. In vitro transcription of a mixture of dsDNA templates encoding all the subunits of the RNA nanoparticle may result in cotranscriptional self-assembly of the nanoparticle. Based on our experience with production of RNA nanorings, RNA nanocubes, and RNA three-way junctions, we propose a strategy for optimization of the cotranscriptional production of chemically modified ribonuclease-resistant RNA nanoparticles...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28721856/repeat-induced-point-mutation-and-other-genome-defense-mechanisms-in-fungi
#8
Eugene Gladyshev
Transposable elements have colonized the genomes of nearly all organisms, including fungi. Although transposable elements may sometimes provide beneficial functions to their hosts their overall impact is considered deleterious. As a result, the activity of transposable elements needs to be counterbalanced by the host genome defenses. In fungi, the primary genome defense mechanisms include repeat-induced point mutation (RIP) and methylation induced premeiotically, meiotic silencing by unpaired DNA, sex-induced silencing, cosuppression (also known as somatic quelling), and cotranscriptional RNA surveillance...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28701519/nineteen-complex-related-factor-prp45-is-required-for-the-early-stages-of-cotranscriptional-spliceosome-assembly
#9
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...
October 2017: RNA
https://www.readbyqxmd.com/read/28698297/disrupted-prenatal-rna-processing-and-myogenesis-in-congenital-myotonic-dystrophy
#10
James D Thomas, Łukasz J Sznajder, Olgert Bardhi, Faaiq N Aslam, Zacharias P Anastasiadis, Marina M Scotti, Ichizo Nishino, Masayuki Nakamori, Eric T Wang, Maurice S Swanson
Myotonic dystrophy type 1 (DM1) is a CTG microsatellite expansion (CTG(exp)) disorder caused by expression of CUG(exp) RNAs. These mutant RNAs alter the activities of RNA processing factors, including MBNL proteins, leading to re-expression of fetal isoforms in adult tissues and DM1 pathology. While this pathogenesis model accounts for adult-onset disease, the molecular basis of congenital DM (CDM) is unknown. Here, we test the hypothesis that disruption of developmentally regulated RNA alternative processing pathways contributes to CDM disease...
June 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28693387/the-flc-locus-a-platform-for-discoveries-in-epigenetics-and-adaptation
#11
Charles Whittaker, Caroline Dean
Our understanding of the detailed molecular mechanisms underpinning adaptation is still poor. One example for which mechanistic understanding of regulation has converged with studies of life history variation is Arabidopsis thaliana FLOWERING LOCUS C (FLC). FLC determines the need for plants to overwinter and their ability to respond to prolonged cold in a process termed vernalization. This review highlights how molecular analysis of vernalization pathways has revealed important insight into antisense-mediated chromatin silencing mechanisms that regulate FLC...
October 6, 2017: Annual Review of Cell and Developmental Biology
https://www.readbyqxmd.com/read/28581511/rna-fate-determination-through-cotranscriptional-adenosine-methylation-and-microprocessor-binding
#12
Philip Knuckles, Sarah H Carl, Michael Musheev, Christof Niehrs, Alice Wenger, Marc Bühler
Eukaryotic gene expression is heavily regulated at the transcriptional and post-transcriptional levels. An additional layer of regulation occurs co-transcriptionally through processing and decay of nascent transcripts physically associated with chromatin. This process involves RNA interference (RNAi) machinery and is well documented in yeast, but little is known about its conservation in mammals. Here we show that Dgcr8 and Drosha physically associate with chromatin in murine embryonic stem cells (mES), specifically with a subset of transcribed coding and noncoding genes...
July 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28446598/the-histone-variant-h2a-z-promotes-efficient-cotranscriptional-splicing-in-s-cerevisiae
#13
Lauren T Neves, Stephen Douglass, Roberto Spreafico, Srivats Venkataramanan, Tracy L Kress, Tracy L Johnson
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28446597/the-histone-variant-h2a-z-promotes-splicing-of-weak-introns
#14
Kelly E Nissen, Christina M Homer, Colm J Ryan, Michael Shales, Nevan J Krogan, Kristin L Patrick, Christine Guthrie
Multiple lines of evidence implicate chromatin in the regulation of premessenger RNA (pre-mRNA) splicing. However, the influence of chromatin factors on cotranscriptional splice site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe Using epistatic miniarray profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28423325/rapid-genome-wide-recruitment-of-rna-polymerase-ii-drives-transcription-splicing-and-translation-events-during-t-cell-responses
#15
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, N Henriette Uhlenhaut, Matthias Heinig, Caroline C Friedel, Elke Glasmacher
Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28399446/enzyme-mediated-tagging-of-rna
#16
REVIEW
Lea Anhäuser, Andrea Rentmeister
RNA molecules can play diverse roles in the cell owing to their secondary structure dynamics and various binding modes. Studying localization and dynamics of RNA in vitro or in cells requires tagging with suitable reporter molecules-fluorophores being the most prominent ones. Enzymatic RNA labeling approaches are currently emerging as valuable alternatives to purely chemical synthesis and to binding- or hybridization-based RNA-imaging approaches. Different classes of enzymes allow for cotranscriptional or posttranscriptional installation of small functional groups in RNA...
April 8, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28398514/distributed-biotin-streptavidin-transcription-roadblocks-for-mapping-cotranscriptional-rna-folding
#17
Eric J Strobel, Kyle E Watters, Yuri Nedialkov, Irina Artsimovitch, Julius B Lucks
RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks...
July 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28301768/theory-and-modeling-of-rna-structure-and-interactions-with-metal-ions-and-small-molecules
#18
REVIEW
Li-Zhen Sun, Dong Zhang, Shi-Jie Chen
In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion-RNA and ligand-RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data-directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal ion-dependent RNA stabilities...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28283057/super-enhancer-mediated-rna-processing-revealed-by-integrative-microrna-network-analysis
#19
Hiroshi I Suzuki, Richard A Young, Phillip A Sharp
Super-enhancers are an emerging subclass of regulatory regions controlling cell identity and disease genes. However, their biological function and impact on miRNA networks are unclear. Here, we report that super-enhancers drive the biogenesis of master miRNAs crucial for cell identity by enhancing both transcription and Drosha/DGCR8-mediated primary miRNA (pri-miRNA) processing. Super-enhancers, together with broad H3K4me3 domains, shape a tissue-specific and evolutionarily conserved atlas of miRNA expression and function...
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28148777/sabotaging-of-the-oxidative-stress-response-by-an-oncogenic-noncoding-rna
#20
Nitin Mahajan, Hua-Jun Wu, Richard L Bennett, Catalina Troche, Jonathan D Licht, Jason D Weber, Leonard B Maggi, Michael H Tomasson
Overexpression of the multiple myeloma set domain (MMSET) Wolf-Hirschhorn syndrome candidate 1 gene, which contains an orphan box H/ACA class small nucleolar RNA, ACA11, in an intron, is associated with several cancer types, including multiple myeloma (MM). ACA11 and MMSET are overexpressed cotranscriptionally as a result of the t(4;14) chromosomal translocation in a subset of patients with MM. RNA sequencing of CD138(+) tumor cells from t(4;14)-positive and -negative MM patient bone marrow samples revealed an enhanced oxidative phosphorylation mRNA signature...
February 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
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