keyword
MENU ▼
Read by QxMD icon Read
search

link-RNA

keyword
https://www.readbyqxmd.com/read/29643409/intrinsically-disordered-n-termini-in-human-parechovirus-1-capsid-proteins-bind-encapsidated-rna
#1
Shabih Shakeel, James D Evans, Mark Hazelbaker, C Cheng Kao, Robert C Vaughan, Sarah J Butcher
Human parechoviruses (HPeV) are picornaviruses with a highly-ordered RNA genome contained within icosahedrally-symmetric capsids. Ordered RNA structures have recently been shown to interact with capsid proteins VP1 and VP3 and facilitate virus assembly in HPeV1. Using an assay that combines reversible cross-linking, RNA affinity purification and peptide mass fingerprinting (RCAP), we mapped the RNA-interacting regions of the capsid proteins from the whole HPeV1 virion in solution. The intrinsically-disordered N-termini of capsid proteins VP1 and VP3, and unexpectedly, VP0, were identified to interact with RNA...
April 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29610341/multiple-nuclear-replicating-viruses-require-the-stress-induced-protein-zc3h11a-for-efficient-growth
#2
Shady Younis, Wael Kamel, Tina Falkeborn, Hao Wang, Di Yu, Robert Daniels, Magnus Essand, Jorma Hinkula, Göran Akusjärvi, Leif Andersson
The zinc finger CCCH-type containing 11A ( ZC3H11A ) gene encodes a well-conserved zinc finger protein that may function in mRNA export as it has been shown to associate with the transcription export (TREX) complex in proteomic screens. Here, we report that ZC3H11A is a stress-induced nuclear protein with RNA-binding capacity that localizes to nuclear splicing speckles. During an adenovirus infection, the ZC3H11A protein and splicing factor SRSF2 relocalize to nuclear regions where viral DNA replication and transcription take place...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29505267/direct-selection-of-fluorescence-enhancing-rna-aptamers
#3
Michael Gotrik, Gurpreet Sekhon, Saumya Saurabh, Margaret Nakamoto, Michael Eisenstein, H Tom Soh
RNA aptamers that generate a strong fluorescence signal upon binding a nonfluorescent small-molecule dye offer a powerful means for the selective imaging of individual RNA species. Unfortunately, conventional in vitro discovery methods are not efficient at generating such fluorescence-enhancing aptamers, because they primarily exert selective pressure based on target affinity-a characteristic that correlates poorly with fluorescence enhancement. Thus, only a handful of fluorescence-enhancing aptamers have been reported to date...
March 14, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29440426/sting-dependent-translation-inhibition-restricts-rna-virus-replication
#4
Kate M Franz, William J Neidermyer, Yee-Joo Tan, Sean P J Whelan, Jonathan C Kagan
In mammalian cells, IFN responses that occur during RNA and DNA virus infections are activated by distinct signaling pathways. The RIG-I-like-receptors (RLRs) bind viral RNA and engage the adaptor MAVS (mitochondrial antiviral signaling) to promote IFN expression, whereas cGAS (cGMP-AMP synthase) binds viral DNA and activates an analogous pathway via the protein STING (stimulator of IFN genes). In this study, we confirm that STING is not necessary to induce IFN expression during RNA virus infection but also find that STING is required to restrict the replication of diverse RNA viruses...
February 27, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29374143/n6-methyladenosine-links-rna-metabolism-to-cancer-progression
#5
REVIEW
Dongjun Dai, Hanying Wang, Liyuan Zhu, Hongchuan Jin, Xian Wang
N6-methyladenosine (m6A) is the most abundant mRNA modification. With the development of antibody-based sequencing technologies and the findings of m6A-related "writers", "erasers", and "readers", the relationships between m6A and mRNA metabolism are emerging. The m6A modification influences almost every step of RNA metabolism that comprises mRNA processing, mRNA exporting from nucleus to cytoplasm, mRNA translation, mRNA decay, and the biogenesis of long-non-coding RNA (lncRNA) and microRNA (miRNA)...
January 26, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29185492/interaction-profiling-of-rna-binding-ubiquitin-ligases-reveals-a-link-between-posttranscriptional-regulation-and-the-ubiquitin-system
#6
Andrea Hildebrandt, Gregorio Alanis-Lobato, Andrea Voigt, Kathi Zarnack, Miguel A Andrade-Navarro, Petra Beli, Julian König
RNA-binding ubiquitin ligases (RBULs) have the potential to link RNA-mediated mechanisms to protein ubiquitylation. Despite this, the cellular functions, substrates and interaction partners of most RBULs remain poorly characterized. Affinity purification (AP) combined with quantitative mass spectrometry (MS)-based proteomics is a powerful approach for analyzing protein functions. Mapping the physiological interaction partners of RNA-binding proteins has been hampered by their intrinsic properties, in particular the existence of low-complexity regions, which are prone to engage in non-physiological interactions...
November 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29176620/cellular-microrna-networks-regulate-host-dependency-of-hepatitis-c-virus-infection
#7
Qisheng Li, Brianna Lowey, Catherine Sodroski, Siddharth Krishnamurthy, Hawwa Alao, Helen Cha, Stephan Chiu, Ramy El-Diwany, Marc G Ghany, T Jake Liang
Cellular microRNAs (miRNAs) have been shown to regulate hepatitis C virus (HCV) replication, yet a systematic interrogation of the repertoire of miRNAs impacting HCV life cycle is lacking. Here we apply integrative functional genomics strategies to elucidate global HCV-miRNA interactions. Through genome-wide miRNA mimic and hairpin inhibitor phenotypic screens, and miRNA-mRNA transcriptomics analyses, we identify three proviral and nine antiviral miRNAs that interact with HCV. These miRNAs are functionally linked to particular steps of HCV life cycle and related viral host dependencies...
November 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/29107839/efficient-one-pot-enzymatic-synthesis-of-dephospho-coenzyme-a
#8
Krishna Sapkota, Faqing Huang
Dephospho coenzyme A (depCoA) is the last intermediate for CoA biosynthesis, and it can be used as a transcription initiator to prepare CoA-linked RNA by in vitro transcription. However, commercially available depCoA is expensive. We hereby describe a simple and efficient enzymatic synthesis of depCoA in a single-step from commercially available and inexpensive oxidized pantethine (Ox-Pan) and ATP. A plasmid (pCoaDAa) was constructed to co-express and co-purify two enzymes pantothenate kinase (PanK/coaA) and phosphopantetheine adenylyltransferase (PPAT/coaD)...
February 2018: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29061892/the-origin-of-heredity-in-protocells
#9
Timothy West, Victor Sojo, Andrew Pomiankowski, Nick Lane
Here we develop a computational model that examines one of the first major biological innovations-the origin of heredity in simple protocells. The model assumes that the earliest protocells were autotrophic, producing organic matter from CO2 and H2 Carbon fixation was facilitated by geologically sustained proton gradients across fatty acid membranes, via iron-sulfur nanocrystals lodged within the membranes. Thermodynamic models suggest that organics formed this way should include amino acids and fatty acids...
December 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28622300/the-als-linked-e102q-mutation-in-sigma-receptor-1-leads-to-er-stress-mediated-defects-in-protein-homeostasis-and-dysregulation-of-rna-binding-proteins
#10
Alice Dreser, Jan Tilmann Vollrath, Antonio Sechi, Sonja Johann, Andreas Roos, Alfred Yamoah, Istvan Katona, Saeed Bohlega, Dominik Wiemuth, Yuemin Tian, Axel Schmidt, Jörg Vervoorts, Marc Dohmen, Cordian Beyer, Jasper Anink, Eleonora Aronica, Dirk Troost, Joachim Weis, Anand Goswami
Amyotrophic lateral sclerosis (ALS) is characterized by the selective degeneration of motor neurons (MNs) and their target muscles. Misfolded proteins which often form intracellular aggregates are a pathological hallmark of ALS. Disruption of the functional interplay between protein degradation (ubiquitin proteasome system and autophagy) and RNA-binding protein homeostasis has recently been suggested as an integrated model that merges several ALS-associated proteins into a common pathophysiological pathway...
October 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28539829/multifaceted-regulation-of-gene-expression-by-the-apoptosis-and-splicing-associated-protein-complex-and-its-components
#11
REVIEW
Bhagyashree Deka, Kusum Kumari Singh
The differential deposition of RNA-binding proteins (RBPs) on pre-mRNA mediates the processes of gene expression. One of the complexes containing RBPs that play a crucial part in RNA metabolism is the apoptosis-and splicing-associated protein (ASAP) complex. In this review, we present a summary of the structure of ASAP complex and its localization. Also, we discuss the findings by different groups on various functions of the subunits of the ASAP complex in RNA metabolism. The subunits of the ASAP complex are RNPS1, Acinus and SAP18...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28343865/regulatory-role-of-rna-chaperone-tdp-43-for-rna-misfolding-and-repeat-associated-translation-in-sca31
#12
Taro Ishiguro, Nozomu Sato, Morio Ueyama, Nobuhiro Fujikake, Chantal Sellier, Akemi Kanegami, Eiichi Tokuda, Bita Zamiri, Terence Gall-Duncan, Mila Mirceta, Yoshiaki Furukawa, Takanori Yokota, Keiji Wada, J Paul Taylor, Christopher E Pearson, Nicolas Charlet-Berguerand, Hidehiro Mizusawa, Yoshitaka Nagai, Kinya Ishikawa
Microsatellite expansion disorders are pathologically characterized by RNA foci formation and repeat-associated non-AUG (RAN) translation. However, their underlying pathomechanisms and regulation of RAN translation remain unknown. We report that expression of expanded UGGAA (UGGAAexp) repeats, responsible for spinocerebellar ataxia type 31 (SCA31) in Drosophila, causes neurodegeneration accompanied by accumulation of UGGAAexp RNA foci and translation of repeat-associated pentapeptide repeat (PPR) proteins, consistent with observations in SCA31 patient brains...
April 5, 2017: Neuron
https://www.readbyqxmd.com/read/28248320/non-coding-rna-the-cancer-link-rna-between-pip-3-and-akt
#13
COMMENT
Eytan Zlotorynski
No abstract text is available yet for this article.
April 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28178234/corrigendum-sra-and-set-domain-containing-proteins-link-rna-polymerase-v-occupancy-to-dna-methylation
#14
Lianna M Johnson, Jiamu Du, Christopher J Hale, Sylvain Bischof, Suhua Feng, Ramakrishna K Chodavarapu, Xuehua Zhong, Giuseppe Marson, Matteo Pellegrini, David J Segal, Dinshaw J Patel, Steven E Jacobsen
No abstract text is available yet for this article.
March 2, 2017: Nature
https://www.readbyqxmd.com/read/27888635/lncrnas-the-bridge-linking-rna-and-colorectal-cancer
#15
REVIEW
Yanfei Yang, Linjie Zhao, Lingzi Lei, Wayne Bond Lau, Bonnie Lau, Qilian Yang, Xiaobing Le, Huiliang Yang, Chenlu Wang, Zhongyue Luo, Yu Xuan, Yi Chen, Xiangbing Deng, Lian Xu, Min Feng, Tao Yi, Xia Zhao, Yuquan Wei, Shengtao Zhou
Long noncoding RNAs (lncRNAs) are transcribed by genomic regions (exceeding 200 nucleotides in length) that do not encode proteins. While the exquisite regulation of lncRNA transcription can provide signals of malignant transformation, lncRNAs control pleiotropic cancer phenotypes through interactions with other cellular molecules including DNA, protein, and RNA. Recent studies have demonstrated that dysregulation of lncRNAs is influential in proliferation, angiogenesis, metastasis, invasion, apoptosis, stemness, and genome instability in colorectal cancer (CRC), with consequent clinical implications...
February 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/27793055/personalized-anticancer-therapy-selection-using-molecular-landscape-topology-and-thermodynamics
#16
Edward A Rietman, Jacob G Scott, Jack A Tuszynski, Giannoula Lakka Klement
Personalized anticancer therapy requires continuous consolidation of emerging bioinformatics data into meaningful and accurate information streams. The use of novel mathematical and physical approaches, namely topology and thermodynamics can enable merging differing data types for improved accuracy in selecting therapeutic targets. We describe a method that uses chemical thermodynamics and two topology measures to link RNA-seq data from individual patients with academically curated protein-protein interaction networks to select clinically relevant targets for treatment of low-grade glioma (LGG)...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/27715485/constructive-edge-of-uridylation-induced-rna-degradation
#17
REVIEW
Ruslan Aphasizhev, Takuma Suematsu, Liye Zhang, Inna Aphasizheva
RNA uridylation is a significant transcriptome-shaping factor in protists, fungi, metazoans, and plants. The 3' U-additions are catalyzed by terminal uridyltransferases (TUTases), a diverse group of enzymes that along with non-canonical poly(A) polymerases form a distinct group in the superfamily of DNA polymerase β-like nucleotidyl transferases. Within and across studied organisms and subcellular compartments, TUTases differ in nucleotide triphosphate selectivity, interacting partners, and RNA targets. A general premise linking RNA uridylation to 3'-5' degradation received support from several studies of small RNAs and mRNA turnover...
November 2016: RNA Biology
https://www.readbyqxmd.com/read/27662868/uv-rna-immunoprecipitation-uv-rip-protocol-in-neurons
#18
Katie Schaukowitch, Jae-Yeol Joo, Tae-Kyung Kim
With the many advances in genome-wide sequencing, it has been discovered that much more of the genome is transcribed into RNA than previously appreciated. These nonprotein-coding RNAs (ncRNAs) come in many different forms, and they have been shown to have a variety of functions within the cell, influencing processes such as gene expression, mRNA splicing, and transport, just as a few examples. As we delve deeper into studying their mechanisms of action, it becomes important to understand how they play these roles, in particular by understanding what proteins these ncRNAs interact with...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27659976/rip-rna-immunoprecipitation
#19
Miriam Gagliardi, Maria R Matarazzo
The relevance of RNA-protein interactions in modulating mRNA and noncoding RNA function is increasingly appreciated and several methods have been recently developed to map them. The RNA immunoprecipitation (RIP) is a powerful method to study the physical association between individual proteins and RNA molecules in vivo. The basic principles of RIP are very similar to those of chromatin immunoprecipitation (ChIP), a largely used tool in the epigenetic field, but with some important caveats. The approach is based on the use of a specific antibody raised against the protein of interest to pull down the RNA-binding protein (RBP) and target-RNA complexes...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27579606/chimeric-rna-oligonucleotides-incorporating-triazole-linked-trinucleotides-synthesis-and-function-as-mrna-in-cell-free-translation-reactions
#20
Tomoko Fujino, Takeru Suzuki, Koudai Okada, Kanako Kogashi, Ken-Ichi Yasumoto, Kazuhiro Sogawa, Hiroyuki Isobe
A method for the synthesis of chimeric oligonucleotides was developed to incorporate purine nucleobases and multiple triazole linkers in natural, phosphate-linked structures of RNA. A solution-phase synthesis method for triazole-linked RNA oligomers via copper-catalyzed azide-alkyne cycloaddition reaction was optimized and tolerated purine nucleobases and protecting groups for further transformations. Three (TL)RNA trinucleotides with 5'-protected hydroxy and 3'-phosphoramidite groups were prepared, and one congener with a representative sequence was subjected to automated, solid-phase phosphoramidite synthesis...
October 7, 2016: Journal of Organic Chemistry
keyword
keyword
70198
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"