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https://www.readbyqxmd.com/read/27913849/targeted-next-generation-sequencing-reveals-mody-in-up-to-6-5-of-antibody-negative-diabetes-cases-listed-in-the-norwegian-childhood-diabetes-registry
#1
Bente B Johansson, Henrik U Irgens, Janne Molnes, Paweł Sztromwasser, Ingvild Aukrust, Petur B Juliusson, Oddmund Søvik, Shawn Levy, Torild Skrivarhaug, Geir Joner, Anders Molven, Stefan Johansson, Pål R Njølstad
AIMS/HYPOTHESIS: MODY can be wrongly diagnosed as type 1 diabetes in children. We aimed to find the prevalence of MODY in a nationwide population-based registry of childhood diabetes. METHODS: Using next-generation sequencing, we screened the HNF1A, HNF4A, HNF1B, GCK and INS genes in all 469 children (12.1%) negative for both GAD and IA-2 autoantibodies and 469 antibody-positive matched controls selected from the Norwegian Childhood Diabetes Registry (3882 children)...
December 2, 2016: Diabetologia
https://www.readbyqxmd.com/read/27913687/do-we-know-whether-potential-g-quadruplexes-actually-form-in-long-functional-rna-molecules
#2
REVIEW
Carika Weldon, Ian C Eperon, Cyril Dominguez
The roles of deoxyribonucleic acid (DNA) G-quadruplex structures in gene expression and telomere maintenance have been well characterized. Recent results suggest that such structures could also play pivotal roles in ribonucleic acid (RNA) biology, such as splicing or translation regulation. However, it has been difficult to show that RNA G-quadruplexes (G4s) exist in specific long RNA sequences, such as precursor messenger RNA, in a functional or cellular context. Most current methods for identifying G4s involve the use of short, purified RNA sequences in vitro, in the absence of competition with secondary structures or protein binding...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913622/a-venom-serpin-splicing-isoform-of-the-endoparasitoid-wasp-pteromalus-puparum-suppresses-host-prophenoloxidase-cascade-by-forming-complexes-with-host-hemolymph-proteinases
#3
Zhichao Yan, Qi Fang, Yang Liu, Shan Xiao, Lei Yang, Fei Wang, Chunju An, John H Werren, Gongyin Ye
To ensure successful parasitism, parasitoid wasps inject venom along with their eggs into their hosts. The venom serves to suppress host immune responses, including melanization. Venom from Pteromalus puparum, a pupal endoparasitoid, inhibits melanization of host hemolymph in vitro in a dose-dependent manner. Using assay guided fractionation, a serpin splicing isoform with phenoloxidase (PO) inhibitory activity was identified as P. puparum serpin-1, venom isoform (PpS1V). This serpin gene has 16 predicted splicing isoforms that differ only in the C-terminal region...
December 2, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27913570/revisiting-the-human-polypeptide-galnac-t1-and-t13-paralogs
#4
María Florencia Festari, Felipe Trajtenberg, Nora Berois, Sergio Pantano, Leslie Revoredo, Yun Kong, Patricia Solari-Saquieres, Yoshiki Narimatsu, Teresa Freire, Sylvie Bay, Carlos Robello, Jean Bénard, Thomas A Gerken, Henrik Clausen, Eduardo Osinaga
Polypeptide GalNAc-transferases (GalNAc-Ts) constitute a family of 20 human glycosyltransferases (comprising 9 subfamilies), which initiate mucin-type O-glycosylation. The O-glycoproteome is thought to be differentially regulated via the different substrate specificities and expression patterns of each GalNAc-T isoforms. Here, we present a comprehensive in vitro analysis of the peptide substrate specificity of GalNAc-T13, showing that it essentially overlaps with the ubiquitous expressed GalNAc-T1 isoform found in the same subfamily as T13...
November 22, 2016: Glycobiology
https://www.readbyqxmd.com/read/27913434/a-study-of-tp53-rna-splicing-illustrates-pitfalls-of-rna-seq-methodology
#5
Sunali Mehta, Peter Tsai, Annette Lasham, Hamish Campbell, Roger Reddel, Antony Braithwaite, Cristin Print
TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to infer isoform abundance. In this study, we used deep RNA-seq, droplet digital PCR (ddPCR), and real-time quantitative reverse transcriptase PCR (RT-qPCR) from nine human cell lines and RNA-seq data available for tumors in The Cancer Genome Atlas to analyze TP53 splice variant expression...
October 20, 2016: Cancer Research
https://www.readbyqxmd.com/read/27913189/construction-and-analysis-of-a-human-testis-sperm-enriched-interaction-network-unraveling-the-ppp1cc2-interactome
#6
Joana Vieira Silva, Sooyeon Yoon, Pieter-Jan De Bock, Alexander V Goltsev, Kris Gevaert, José Fernando F Mendes, Margarida Fardilha
BACKGROUND: Phosphoprotein phosphatase 1 catalytic subunit gamma 2 (PPP1CC2), a PPP1CC tissue-specific alternative splice restricted to testicular germ cells and spermatozoa, is essential for spermatogenesis and spermatozoa motility. The key to understand PPP1CC2 regulation lies on the characterization of its interacting partners. METHODS: We construct a testis/sperm-enriched protein interaction network and analyzed the topological properties and biological context of the network...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27912093/direct-regulation-of-alternative-splicing-by-smad3-through-pcbp1-is-essential-to-the-tumor-promoting-role-of-tgf-%C3%AE
#7
Veenu Tripathi, Katherine M Sixt, Shaojian Gao, Xuan Xu, Jing Huang, Roberto Weigert, Ming Zhou, Ying E Zhang
No abstract text is available yet for this article.
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27911856/splicing-factor-ratio-as-an-index-of-epithelial-mesenchymal-transition-and-tumor-aggressiveness-in-breast-cancer
#8
Pietro Fici, Giulia Gallerani, Anne-Pierre Morel, Laura Mercatali, Toni Ibrahim, Emanuela Scarpi, Dino Amadori, Alain Puisieux, Michel Rigaud, Francesco Fabbri
Epithelial-to-mesenchymal transition (EMT) has been shown to be associated with tumor progression and metastasis. During this process in breast cancer, a crucial role is played by alternative splicing systems. To identify a new early prognostic marker of metastasis, we evaluated EMT-related gene expression in breast cell lines, and in primary tumor tissue from 31 patients with early breast cancer, focusing our attention on EMT-related splicing factors ESRP1, ESRP2 and RBFOX2. Results showed that the expression patterns of these genes were indicative of the onset of EMT in in-vitro models, but not in tissue samples...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27911835/two-crystal-structures-reveal-design-for-repurposing-the-c-ala-domain-of-human-alars
#9
Litao Sun, Youngzee Song, David Blocquel, Xiang-Lei Yang, Paul Schimmel
The 20 aminoacyl tRNA synthetases (aaRSs) couple each amino acid to their cognate tRNAs. During evolution, 19 aaRSs expanded by acquiring novel noncatalytic appended domains, which are absent from bacteria and many lower eukaryotes but confer extracellular and nuclear functions in higher organisms. AlaRS is the single exception, with an appended C-terminal domain (C-Ala) that is conserved from prokaryotes to humans but with a wide sequence divergence. In human cells, C-Ala is also a splice variant of AlaRS...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911724/control-of-hiv-1-gene-expression-by-sr-proteins
#10
REVIEW
Charlotte Mahiet, Chad M Swanson
Cellular proteins are required for all steps of human immunodeficiency virus type 1 (HIV-1) gene expression including transcription, splicing, 3'-end formation/polyadenylation, nuclear export and translation. SR proteins are a family of cellular RNA-binding proteins that regulate and functionally integrate multiple steps of gene expression. Specific SR proteins are best characterised for regulating HIV-1 RNA splicing by binding specific locations in the viral RNA, though recently they have also been shown to control transcription, 3'-end formation, and translation...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911701/the-contribution-of-intrinsically-disordered-regions-to-protein-function-cellular-complexity-and-human-disease
#11
REVIEW
M Madan Babu
In the 1960s, Christian Anfinsen postulated that the unique three-dimensional structure of a protein is determined by its amino acid sequence. This work laid the foundation for the sequence-structure-function paradigm, which states that the sequence of a protein determines its structure, and structure determines function. However, a class of polypeptide segments called intrinsically disordered regions does not conform to this postulate. In this review, I will first describe established and emerging ideas about how disordered regions contribute to protein function...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27910918/crescent-shaped-fabry-perot-fiber-cavity-for-ultra-sensitive-strain-measurement
#12
Ye Liu, D N Wang, W P Chen
Optical Fabry-Perot interferometer sensors based on inner air-cavity is featured with compact size, good robustness and high strain sensitivity, especially when an ultra-thin air-cavity is adopted. The typical shape of Fabry-Perot inner air-cavity with reflection mode of operation is elliptic, with minor axis along with and major axis perpendicular to the fiber length. The first reflection surface is diverging whereas the second one is converging. To increase the visibility of the output interference pattern, the length of major axis should be large for a given cavity length...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27909578/advances-in-analyzing-rna-diversity-in-eukaryotic-transcriptomes-peering-through-the-omics-lens
#13
REVIEW
Sushant Bangru, Auinash Kalsotra
Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants...
2016: F1000Research
https://www.readbyqxmd.com/read/27907902/active-5-splice-sites-regulate-the-biogenesis-efficiency-of-arabidopsis-micrornas-derived-from-intron-containing-genes
#14
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/27907216/correction-deciphering-transcriptome-and-complex-alternative-splicing-transcripts-in-mammary-gland-tissues-from-cows-naturally-infected-with-staphylococcus-aureus-mastitis
#15
Xiu Ge Wang, Zhi Hua Ju, Ming Hai Hou, Qiang Jiang, Chun Hong Yang, Yan Zhang, Yan Sun, Rong Ling Li, Chang Fa Wang, Ji Feng Zhong, Jin Ming Huang
[This corrects the article DOI: 10.1371/journal.pone.0159719.].
2016: PloS One
https://www.readbyqxmd.com/read/27907167/infusion-advancing-discovery-of-fusion-genes-and-chimeric-transcripts-from-deep-rna-sequencing-data
#16
Konstantin Okonechnikov, Aki Imai-Matsushima, Lukas Paul, Alexander Seitz, Thomas F Meyer, Fernando Garcia-Alcalde
Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind of analysis, however, is complicated by native trans-splicing events, the splicing-induced complexity of the transcriptome and biases and artefacts introduced in experiments and data analysis. There are a number of tools available for the detection of fusions from RNA-seq data; however, certain differences in specificity and sensitivity between commonly used approaches have been found...
2016: PloS One
https://www.readbyqxmd.com/read/27906336/in-line-optofluidic-refractive-index-sensing-in-a-side-channel-photonic-crystal-fiber
#17
Nan Zhang, Georges Humbert, Zhifang Wu, Kaiwei Li, Perry Ping Shum, Nancy Meng Ying Zhang, Ying Cui, Jean-Louis Auguste, Xuan Quyen Dinh, Lei Wei
An in-line optofluidic refractive index (RI) sensing platform is constructed by splicing a side-channel photonic crystal fiber (SC-PCF) with side-polished single mode fibers. A long-period grating (LPG) combined with an intermodal interference between LP<sub>01</sub> and LP<sub>11</sub> core modes is used for sensing the RI of the liquid in the side channel. The resonant dip shows a nonlinear wavelength shift with increasing RI over the measured range from 1.3330 to 1.3961. The RI response of this sensing platform for a low RI range of 1...
November 28, 2016: Optics Express
https://www.readbyqxmd.com/read/27906075/nuclear-bodies-reorganize-during-myogenesis-in-vitro-and-are-differentially-disrupted-by-expression-of-fshd-associated-dux4
#18
Sachiko Homma, Mary Lou Beermann, Bryant Yu, Frederick M Boyce, Jeffrey Boone Miller
BACKGROUND: Nuclear bodies, such as nucleoli, PML bodies, and SC35 speckles, are dynamic sub-nuclear structures that regulate multiple genetic and epigenetic processes. Additional regulation is provided by RNA/DNA handling proteins, notably TDP-43 and FUS, which have been linked to ALS pathology. Previous work showed that mouse cell line myotubes have fewer but larger nucleoli than myoblasts, and we had found that nuclear aggregation of TDP-43 in human myotubes was induced by expression of DUX4-FL, a transcription factor that is aberrantly expressed and causes pathology in facioscapulohumeral dystrophy (FSHD)...
December 1, 2016: Skeletal Muscle
https://www.readbyqxmd.com/read/27905398/structure-of-the-rbm7-zcchc8-core-of-the-next-complex-reveals-connections-to-splicing-factors
#19
Sebastian Falk, Ksenia Finogenova, Mireille Melko, Christian Benda, Søren Lykke-Andersen, Torben Heick Jensen, Elena Conti
The eukaryotic RNA exosome participates extensively in RNA processing and degradation. In human cells, three accessory factors (RBM7, ZCCHC8 and hMTR4) interact to form the nuclear exosome targeting (NEXT) complex, which directs a subset of non-coding RNAs for exosomal degradation. Here we elucidate how RBM7 is incorporated in the NEXT complex. We identify a proline-rich segment of ZCCHC8 as the interaction site for the RNA-recognition motif (RRM) of RBM7 and present the crystal structure of the corresponding complex at 2...
December 1, 2016: Nature Communications
https://www.readbyqxmd.com/read/27905109/a-lethal-neonatal-phenotype-of-mitochondrial-short-chain-enoyl-coa-hydratase-1-deficiency
#20
F Al Mutairi, H E Shamseldin, M Alfadhel, R J Rodenburg, F S Alkuraya
Short-chain enoyl-CoA hydratase (SCEH) is a mitochondrial enzyme involved in the oxidation of fatty acids and the catabolic pathway of valine and, to a lesser extent, isoleucine. Deficiency of this enzyme was recently shown to cause an early childhood Leigh syndrome phenotype. The few reported patients were compound heterozygotes for two missense or missense with truncating variants in ECHS1 that encodes SCEH. We describe two siblings with severe refractory lactic acidosis and death within the first 2 days of life...
October 13, 2016: Clinical Genetics
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