keyword
MENU ▼
Read by QxMD icon Read
search

exon junction complexes

keyword
https://www.readbyqxmd.com/read/28283335/discovery-of-selective-atp-competitive-eif4a3-inhibitors
#1
Masahiro Ito, Misa Iwatani, Yusuke Kamada, Satoshi Sogabe, Shoichi Nakao, Toshio Tanaka, Tomohiro Kawamoto, Samuel Aparicio, Atsushi Nakanishi, Yasuhiro Imaeda
Eukaryotic initiation factor 4A3 (eIF4A3), an ATP-dependent RNA helicase, is a core component of exon junction complex (EJC). EJC has a variety of roles in RNA metabolism such as translation, surveillance, and localization of spliced RNA. It is worthwhile to identify selective eIF4A3 inhibitors with a view to investigating the functions of eIF4A3 and EJC further to clarify the roles of the ATPase and helicase activities in cells. Our chemical optimization of hit compound 2 culminated in the discovery of ATP-competitive eIF4A3 inhibitor 18 with submicromolar ATPase inhibitory activity and excellent selectivity over other helicases...
February 20, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28273136/dux4-induced-dsrna-and-myc-mrna-stabilization-activate-apoptotic-pathways-in-human-cell-models-of-facioscapulohumeral-dystrophy
#2
Sean C Shadle, Jun Wen Zhong, Amy E Campbell, Melissa L Conerly, Sujatha Jagannathan, Chao-Jen Wong, Timothy D Morello, Silvère M van der Maarel, Stephen J Tapscott
Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of DUX4 in skeletal muscle cells. DUX4 is a transcription factor that activates genes normally associated with stem cell biology and its mis-expression in FSHD cells results in apoptosis. To identify genes and pathways necessary for DUX4-mediated apoptosis, we performed an siRNA screen in an RD rhabdomyosarcoma cell line with an inducible DUX4 transgene. Our screen identified components of the MYC-mediated apoptotic pathway and the double-stranded RNA (dsRNA) innate immune response pathway as mediators of DUX4-induced apoptosis...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28192756/scn1a-clinical-spectrum-includes-the-self-limited-focal-epilepsies-of-childhood
#3
Sara Kivity, Karen L Oliver, Zaid Afawi, John A Damiano, Todor Arsov, Melanie Bahlo, Samuel F Berkovic
INTRODUCTION: Amongst autosomal dominant genetic epilepsy with febrile seizures plus (GEFS+) families, SCN1A variants are the most common genetic cause. Initially regarded as a generalized form of epilepsy, the GEFS+ spectrum is now known to include some focal epilepsies, but it is generally not conceptualized as extending to the self-limited focal epilepsies of childhood, such as Panayiotopoulos syndrome. There are, however, three reports of SCN1A variants in Panayiotopoulos syndrome...
February 4, 2017: Epilepsy Research
https://www.readbyqxmd.com/read/28166730/transcriptome-analysis-reveals-the-complexity-of-alternative-splicing-regulation-in-the-fungus-verticillium-dahliae
#4
Lirong Jin, Guanglin Li, Dazhao Yu, Wei Huang, Chao Cheng, Shengjie Liao, Qijia Wu, Yi Zhang
BACKGROUND: Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. RESULTS: This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, using two different strains and multiple methods for cDNA library preparations. We identified alternatively spliced mRNA isoforms in over a half of the multi-exonic fungal genes...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28062664/mapping-eqtls-with-rna-seq-reveals-novel-susceptibility-genes-non-coding-rnas-and-alternative-splicing-events-in-systemic-lupus-erythematosus
#5
Christopher A Odhams, Andrea Cortini, Lingyan Chen, Amy L Roberts, Ana Viñuela, Alfonso Buil, Kerrin S Small, Emmanouil T Dermitzakis, David L Morris, Timothy J Vyse, Deborah S Cunninghame Graham
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines...
January 5, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28008720/the-exon-junction-complex-a-lifelong-guardian-of-mrna-fate
#6
REVIEW
Lauren A Woodward, Justin W Mabin, Pooja Gangras, Guramrit Singh
During messenger RNA (mRNA) biogenesis and processing in the nucleus, many proteins are imprinted on mRNAs assembling them into messenger ribonucleoproteins (mRNPs). Some of these proteins remain stably bound within mRNPs and have a long-lasting impact on their fate. One of the best-studied examples is the exon junction complex (EJC), a multiprotein complex deposited primarily 24 nucleotides upstream of exon-exon junctions as a consequence of pre-mRNA splicing. The EJC maintains a stable, sequence-independent, hold on the mRNA until its removal during translation in the cytoplasm...
December 23, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27994090/a-common-class-of-transcripts-with-5-intron-depletion-distinct-early-coding-sequence-features-and-n-1-methyladenosine-modification
#7
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...
March 2017: RNA
https://www.readbyqxmd.com/read/27980089/structure-of-a-yeast-step-ii-catalytically-activated-spliceosome
#8
Chuangye Yan, Ruixue Wan, Rui Bai, Gaoxingyu Huang, Yigong Shi
Each cycle of precursor messenger RNA (pre-mRNA) splicing comprises two sequential reactions, first freeing the 5' exon and generating an intron lariat-3' exon and then ligating the two exons and releasing the intron lariat. The second reaction is executed by the step II catalytically activated spliceosome (known as the C* complex). Here, we present the cryo-electron microscopy structure of a C* complex from Saccharomyces cerevisiae at an average resolution of 4.0 angstroms. Compared with the preceding spliceosomal complex (C complex), the lariat junction has been translocated by 15 to 20 angstroms to vacate space for the incoming 3'-exon sequences...
January 13, 2017: Science
https://www.readbyqxmd.com/read/27941783/simulation-based-comprehensive-benchmarking-of-rna-seq-aligners
#9
Giacomo Baruzzo, Katharina E Hayer, Eun Ji Kim, Barbara Di Camillo, Garret A FitzGerald, Gregory R Grant
Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated...
December 12, 2016: Nature Methods
https://www.readbyqxmd.com/read/27929060/export-of-pirna-precursors-by-ejc-triggers-assembly-of-cytoplasmic-yb-body-in-drosophila
#10
Cynthia Dennis, Emilie Brasset, Arpita Sarkar, Chantal Vaury
PIWI-interacting RNAs (piRNAs) are effectors of transposable element (TE) silencing in the reproductive apparatus. In Drosophila ovarian somatic cells, piRNAs arise from longer single-stranded RNA precursors that are processed in the cytoplasm presumably within the Yb-bodies. piRNA precursors encoded by the flamenco (flam) piRNA cluster accumulate in a single focus away from their sites of transcription. In this study, we identify the exportin complex containing Nxf1 and Nxt1 as required for flam precursor nuclear export...
December 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27927164/the-role-of-nucleotide-composition-in-premature-termination-codon-recognition
#11
Fouad Zahdeh, Liran Carmel
BACKGROUND: It is not fully understood how a termination codon is recognized as premature (PTC) by the nonsense-mediated decay (NMD) machinery. This is particularly true for transcripts lacking an exon junction complex (EJC) along their 3' untranslated region (3'UTR), and thus degrade through the EJC-independent NMD pathway. RESULTS: Here, we analyzed data of transcript stability change following NMD repression and identified over 200 EJC-independent NMD-targets...
December 7, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27917290/functional-analysis-of-alternative-splicing-of-the-flowering-locus-t-orthologous-gene-in-chrysanthemum-morifolium
#12
Yachao Mao, Jing Sun, Peipei Cao, Rong Zhang, Qike Fu, Sumei Chen, Fadi Chen, Jiafu Jiang
As the junction of floral development pathways, the FLOWERING LOCUS T (FT) protein called 'florigen' plays an important role in the process of plant flowering through signal integration. We isolated four transcripts encoding different isoforms of a FT orthologous gene CmFTL1, from Chrysanthemum morifolium cultivar 'Jimba'. Sequence alignments suggested that the four transcripts are related to the intron 1. Expression analysis showed that four alternative splicing (AS) forms of CmFTL1 varied depending on the developmental stage of the flower...
2016: Horticulture Research
https://www.readbyqxmd.com/read/27879206/exon-junction-complex-proteins-bind-nascent-transcripts-independently-of-pre-mrna-splicing-in-drosophila-melanogaster
#13
Subhendu Roy Choudhury, Anand K Singh, Tina McLeod, Marco Blanchette, Boyun Jang, Paul Badenhorst, Aditi Kanhere, Saverio Brogna
Although it is currently understood that the exon junction complex (EJC) is recruited on spliced mRNA by a specific interaction between its central protein, eIF4AIII, and splicing factor CWC22, we found that eIF4AIII and the other EJC core proteins Y14 and MAGO bind the nascent transcripts of not only intron-containing but also intronless genes on Drosophila polytene chromosomes. Additionally, Y14 ChIP-seq demonstrates that association with transcribed genes is also splicing-independent in Drosophila S2 cells...
November 23, 2016: ELife
https://www.readbyqxmd.com/read/27874031/harnessing-short-poly-a-binding-protein-interacting-peptides-for-the-suppression-of-nonsense-mediated-mrna-decay
#14
Tobias Fatscher, Niels H Gehring
Nonsense-mediated mRNA decay (NMD) is a cellular process that eliminates messenger RNA (mRNA) substrates with premature translation termination codons (PTCs). In addition, NMD regulates the expression of a number of physiological mRNAs, for example transcripts containing long 3' UTRs. Current models implicate the interaction between cytoplasmic poly(A)-binding protein (PABPC1) and translation termination in NMD. Accordingly, PABPC1 present within close proximity of a termination codon antagonizes NMD. Here, we use reporter mRNAs with different NMD-inducing 3' UTRs to establish a general NMD-inhibiting property of PABPC1...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27867087/a-quantitative-immunoassay-for-lung-cancer-biomarker-ciz1b-in-patient-plasma
#15
Dawn Coverley, Gillian Higgins, Daniel West, Oliver T Jackson, Adam Dowle, Aidan Haslam, Eve Ainscough, Rebecca Chalkley, John White
OBJECTIVES: Non-invasive tests for early detection of lung cancer are an important unmet clinical need. CIZ1b plasma biomarker can discriminate stage 1 lung cancer from within high-risk groups with clinically useful accuracy, with ROC AUCs in excess of 0.9 for two independent retrospective cohorts, and could therefore meet this need. Our aim was to characterise the native state of the biomarker and develop a quantitative immunoassay. DESIGN AND METHODS: Selective denaturation, preparative electrophoresis and mass spectrometry of human plasma were used to characterise the biomarker and interaction partners...
November 17, 2016: Clinical Biochemistry
https://www.readbyqxmd.com/read/27854212/non-random-distribution-of-dmd-deletion-breakpoints-and-implication-of-double-strand-breaks-repair-and-replication-error-repair-mechanisms
#16
Isabelle Marey, Rabah Ben Yaou, Nathalie Deburgrave, Aurélie Vasson, Juliette Nectoux, France Leturcq, Bruno Eymard, Pascal Laforet, Anthony Behin, Tanya Stojkovic, Michèle Mayer, Vincent Tiffreau, Isabelle Desguerre, François Constant Boyer, Aleksandra Nadaj-Pakleza, Xavier Ferrer, Karim Wahbi, Henri-Marc Becane, Mireille Claustres, Jamel Chelly, Mireille Cossee
BACKGROUND: Dystrophinopathies are mostly caused by copy number variations, especially deletions, in the dystrophin gene (DMD). Despite the large size of the gene, deletions do not occur randomly but mainly in two hot spots, the main one involving exons 45 to 55. The underlying mechanisms are complex and implicate two main mechanisms: Non-homologous end joining (NHEJ) and micro-homology mediated replication-dependent recombination (MMRDR). OBJECTIVE: Our goals were to assess the distribution of intronic breakpoints (BPs) in the genomic sequence of the main hot spot of deletions within DMD gene and to search for specific sequences at or near to BPs that might promote BP occurrence or be associated with DNA break repair...
May 27, 2016: Journal of Neuromuscular Diseases
https://www.readbyqxmd.com/read/27798850/identification-and-molecular-characterization-of-cellular-factors-required-for-glucocorticoid-receptor-mediated-mrna-decay
#17
Ok Hyun Park, Joori Park, Mira Yu, Hyoung-Tae An, Jesang Ko, Yoon Ki Kim
Glucocorticoid (GC) receptor (GR) has been shown recently to bind a subset of mRNAs and elicit rapid mRNA degradation. However, the molecular details of GR-mediated mRNA decay (GMD) remain unclear. Here, we demonstrate that GMD triggers rapid degradation of target mRNAs in a translation-independent and exon junction complex-independent manner, confirming that GMD is mechanistically distinct from nonsense-mediated mRNA decay (NMD). Efficient GMD requires PNRC2 (proline-rich nuclear receptor coregulatory protein 2) binding, helicase ability, and ATM-mediated phosphorylation of UPF1 (upstream frameshift 1)...
September 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/27780844/mouse-models-of-casc3-reveal-developmental-functions-distinct-from-other-components-of-the-exon-junction-complex
#18
Hanqian Mao, Hannah E Brown, Debra L Silver
The exon junction complex (EJC) is a multiprotein complex integral to mRNA metabolism. Biochemistry and genetic studies have concluded that the EJC is composed of four core proteins, MAGOH, EIF4A3, RBM8A, and CASC3. Yet recent studies in Drosophila indicate divergent physiological functions for Barentsz, the mammalian Casc3 ortholog, raising the question as to whether CASC3 is a constitutive component of the EJC. This issue remains poorly understood, particularly in an in vivo mammalian context. We previously found that haploinsufficiency for Magoh, Eif4a3, or Rbm8a disrupts neuronal viability and neural progenitor proliferation, resulting in severe microcephaly...
January 2017: RNA
https://www.readbyqxmd.com/read/27684375/alternative-isoform-analysis-of-ttc8-expression-in-the-rat-pineal-gland-using-a-multi-platform-sequencing-approach-reveals-neural-regulation
#19
Stephen W Hartley, James C Mullikin, David C Klein, Morgan Park, Steven L Coon
Alternative isoform regulation (AIR) vastly increases transcriptome diversity and plays an important role in numerous biological processes and pathologies. However, the detection and analysis of isoform-level differential regulation is difficult, particularly in the face of complex and incompletely-annotated transcriptomes. Here we have used Illumina short-read/high-throughput RNA-Seq to identify 55 genes that exhibit neurally-regulated AIR in the pineal gland, and then used two other complementary experimental platforms to further study and characterize the Ttc8 gene, which is involved in Bardet-Biedl syndrome and non-syndromic retinitis pigmentosa...
2016: PloS One
https://www.readbyqxmd.com/read/27681125/the-splicing-history-of-an-mrna-affects-its-level-of-translation-and-sensitivity-to-cleavage-by-the-virion-host-shutoff-endonuclease-during-herpes-simplex-virus-infections
#20
Jouliana Sadek, G Sullivan Read
During lytic herpes simplex virus (HSV) infections, the virion host shutoff (Vhs) (UL41) endoribonuclease degrades many cellular and viral mRNAs. In uninfected cells, spliced mRNAs emerge into the cytoplasm bound by exon junction complexes (EJCs) and are translated several times more efficiently than unspliced mRNAs that have the same sequence but lack EJCs. Notably, most cellular mRNAs are spliced, whereas most HSV mRNAs are not. To examine the effect of splicing on gene expression during HSV infection, cells were transfected with plasmids harboring an unspliced renilla luciferase (RLuc) reporter mRNA or RLuc constructs with introns near the 5' or 3' end of the gene...
December 1, 2016: Journal of Virology
keyword
keyword
112658
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"