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https://www.readbyqxmd.com/read/28431233/a-compendium-of-rna-binding-proteins-that-regulate-microrna-biogenesis
#1
Thomas Treiber, Nora Treiber, Uwe Plessmann, Simone Harlander, Julia-Lisa Daiß, Norbert Eichner, Gerhard Lehmann, Kevin Schall, Henning Urlaub, Gunter Meister
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28410363/highly-accessible-au-rich-regions-in-3-untranslated-regions-are-hotspots-for-binding-of-regulatory-factors
#2
Mireya Plass, Simon H Rasmussen, Anders Krogh
Post-transcriptional regulation is regarded as one of the major processes involved in the regulation of gene expression. It is mainly performed by RNA binding proteins and microRNAs, which target RNAs and typically affect their stability. Recent efforts from the scientific community have aimed at understanding post-transcriptional regulation at a global scale by using high-throughput sequencing techniques such as cross-linking and immunoprecipitation (CLIP), which facilitates identification of binding sites of these regulatory factors...
April 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28404834/promotion-of-orange-fleshed-sweet-potato-increased-vitamin-a-intakes-and-reduced-the-odds-of-low-retinol-binding-protein-among-postpartum-kenyan-women
#3
Amy Webb Girard, Frederick Grant, Michelle Watkinson, Haile Selassie Okuku, Rose Wanjala, Donald Cole, Carol Levin, Jan Low
Background: Orange-fleshed sweet potato (OFSP) improves vitamin A (VA) status of young children; research with pregnant and lactating women is limited.Objective: We examined the effectiveness of the Mama SASHA (Sweetpotato Action for Security and Health in Africa) program to improve nutrition knowledge, diets, and nutritional status of pregnant and lactating women (PLW) in Western Kenya.Methods: Eight health facilities were allocated to the Mama SASHA intervention or comparison arms. PLW in intervention facilities received enhanced nutrition counseling at health clinics, were linked with community-based maternal support groups, and received vouchers for OFSP vine cuttings...
April 12, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28392367/six-gu-rich-6gur-fus-binding-motifs-detected-by-normalization-of-clip-seq-by-nascent-seq
#4
Jun-Ichi Takeda, Akio Masuda, Kinji Ohno
FUS, an RNA-binding protein (RBP), is mutated or abnormally regulated in neurodegenerative disorders. FUS regulates various aspects of RNA metabolisms. FUS-binding sites are rich in GU contents and are highly degenerative. FUS-binding motifs of GGU, GGUG, GUGGU and CGCGC have been previously reported. These motifs, however, are applicable to a small fraction of FUS-binding sites. As CLIP-seq tags are enriched in genes that are highly expressed, we normalized CLIP-seq tags by Nascent-seq tags or RNA-seq tags of mouse N2a cells...
April 6, 2017: Gene
https://www.readbyqxmd.com/read/28391211/p300-based-asynchronous-brain-computer-interface-for-environmental-control-system
#5
Eda Akman Aydin, Omer Faruk Bay, Inan Guler
An Asynchronous Brain Computer Interface (A-BCI) determines whether or not a subject is on control state, and produces control commands only in case of subject's being on control state. In this study, we propose a novel P300 based A-BCI algorithm that distinguishes control state and non-control state of users. Furthermore, A-BCI algorithm combined with a dynamic stopping function that enables users to select control command independent from a fixed number of intensification sequence. The proposed P300 based A-BCI algorithm uses classification patterns to determine control state and uses optimal operating point of receiver operating characteristics (ROC) curve for dynamic stopping function...
April 4, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28389532/rna-binding-proteins-with-prion-like-domains-in-health-and-disease
#6
REVIEW
Alice Ford Harrison, James Shorter
Approximately 70 human RNA-binding proteins (RBPs) contain a prion-like domain (PrLD). PrLDs are low-complexity domains that possess a similar amino acid composition to prion domains in yeast, which enable several proteins, including Sup35 and Rnq1, to form infectious conformers, termed prions. In humans, PrLDs contribute to RBP function and enable RBPs to undergo liquid-liquid phase transitions that underlie the biogenesis of various membraneless organelles. However, this activity appears to render RBPs prone to misfolding and aggregation connected to neurodegenerative disease...
April 7, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28388421/dead-box-rna-binding-protein-ddx5-not-a-black-box-during-reprogramming
#7
Christian M Nefzger, Jose M Polo
The role of RNA binding proteins (RBPs) during nuclear reprogramming is poorly characterized. In this issue of Cell Stem Cell,Li et al. (2017) show that DEAD-box RBP DDX5 acts as a reprogramming roadblock and give important mechanistic insights into the establishment of pluripotency by characterizing the intricate downstream events.
April 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28373441/expression-of-rna-binding-motif-protein-3-rbm3-and-cold-inducible-rna-binding-protein-cirp-is-associated-with-improved-clinical-outcome-in-patients-with-colon-cancer
#8
Ho Hee Jang, Hae Na Lee, So-Young Kim, Suntaek Hong, Won-Suk Lee
BACKGROUND: Recent studies have shown a potential role of RNA-binding proteins (RBPs) in a variety of biological pathways, including cancer progression, whilst their expression in various tumor types may be associated with patient prognosis. However, the role of the RBP family members has not been explored in colon cancer and their possible use as prognostic biomarkers is largely unknown. MATERIALS AND METHODS: To determine the prognostic role of three RBP genes: insulin-like growth factor-binding protein 2 (IGFBP2), RNA-binding motif protein 3 (RBM3), and cold-inducible RNA-binding protein (CIRP) in colon cancer...
April 2017: Anticancer Research
https://www.readbyqxmd.com/read/28369676/transcriptome-wide-identification-of-rna-binding-protein-binding-sites-using-photoactivatable-ribonucleoside-enhanced-crosslinking-immunoprecipitation-par-clip
#9
Henrike Maatz, Marcin Kolinski, Norbert Hubner, Markus Landthaler
RNA-binding proteins (RBPs) mediate important co- and post-transcriptional gene regulation by binding pre-mRNA in a sequence- and/or structure-specific manner. For a comprehensive understanding of RBP function, transcriptome-wide mapping of the RNA-binding sites is essential, and CLIP-seq methods have been developed to elucidate protein/RNA interactions at high resolution. CLIP-seq combines protein/RNA UV-crosslinking with immunoprecipitation (CLIP) followed by high-throughput sequencing of crosslinked RNA fragments...
April 3, 2017: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/28367224/qgqs-granule-in-shr-serum-metabonomics-study-based-on-tools-of-uplc-q-tof-and-renin-angiotensin-aldosterone-system-form-protein-profilin-1
#10
Ke Li, Caicai Li, Jialong Wang, Hanming Cui, Yu Dong, Ruihua Liu, Yuanhui Hu
QGQS granule is effective for the therapeutic of hypertension in clinic. The aim of this research is to observe the antihypertension effect of QGQS granule on SHR and explain the mechanism of its lowering blood pressure. 30 SHR were selected as model group, captopril group, and QGQS group, 10 WKYr were used as control group, and RBP were measured on tail artery consciously. And all the serum sample analysis was carried out on UPLC-TOF-MS system to determine endogenous metabolites and to find the metabonomics pathways...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28360933/extraction-purification-characterization-and-antioxidant-activities-of-polysaccharides-from-ramaria-botrytis-pers-ricken
#11
Hua Li
BACKGROUND: Ramaria botrytis (Pers.) Ricken, a member of the family Clavariaceae, has been widely prescribed for anti-aging and improving immunity. To extract and purify the polysaccharides, the main constituent of the fruiting-body, from R. botrytis and explore antioxidant activities was great significant. RESULTS: Ramaria botrytis polysaccharides (RBP) was extracted with water at 88.47 °C for 1.42 h with a solution to sample ratio of 10.94 mL g(-1) employing response surface methodology...
2017: Chemistry Central Journal
https://www.readbyqxmd.com/read/28344005/mir-342-5p-regulates-neural-stem-cell-proliferation-and-differentiation-downstream-to-notch-signaling-in-mice
#12
Fang Gao, Yu-Fei Zhang, Zheng-Ping Zhang, Luo-An Fu, Xiu-Li Cao, Yi-Zhe Zhang, Chen-Jun Guo, Xian-Chun Yan, Qin-Chuan Yang, Yi-Yang Hu, Xiang-Hui Zhao, Ya-Zhou Wang, Sheng-Xi Wu, Gong Ju, Min-Hua Zheng, Hua Han
Notch signaling is critically involved in neural development, but the downstream effectors remain incompletely understood. In this study, we cultured neurospheres from Nestin-Cre-mediated conditional Rbp-j knockout (Rbp-j cKO) and control embryos and compared their miRNA expression profiles using microarray. Among differentially expressed miRNAs, miR-342-5p showed upregulated expression as Notch signaling was genetically or pharmaceutically interrupted. Consistently, the promoter of the miR-342-5p host gene, the Ena-vasodilator stimulated phosphoprotein-like (Evl), was negatively regulated by Notch signaling, probably through HES5...
April 11, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28343865/regulatory-role-of-rna-chaperone-tdp-43-for-rna-misfolding-and-repeat-associated-translation-in-sca31
#13
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/28340561/ascorbic-acid-ameliorates-renal-injury-in-a-murine-model-of-contrast-induced-nephropathy
#14
K Rollins, A Noorani, L Janeckova, T Jones, M Griffiths, M P Baker, J R Boyle
BACKGROUND: Contrast induced nephropathy (CIN) is the commonest cause of iatrogenic renal injury and its incidence has increased with the advent of complex endovascular procedures. Evidence suggests that ascorbic acid (AA) has a nephroprotective effect in percutaneous coronary interventions when contrast media are used. A variety of biomarkers (NGAL, NGAL:creatinine, mononuclear cell infiltration, apoptosis and RBP-4) in both the urine and kidney were assayed using a mouse model of CIN in order to determine whether AA can reduce the incidence and/or severity of renal injury...
March 24, 2017: BMC Nephrology
https://www.readbyqxmd.com/read/28336542/seten-a-tool-for-systematic-identification-and-comparison-of-processes-phenotypes-and-diseases-associated-with-rna-binding-proteins-from-condition-specific-clip-seq-profiles
#15
Gungor Budak, Rajneesh Srivastava, Sarath Chandra Janga
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single nucleotide resolution in a cell, currently there are very few tools which can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps...
March 23, 2017: RNA
https://www.readbyqxmd.com/read/28334977/sclip-an-integrated-platform-to-study-rna-protein-interactomes-in-biomedical-research-identification-of-cstf2tau-in-alternative-processing-of-small-nuclear-rnas
#16
Yulia Kargapolova, Michal Levin, Karl Lackner, Sven Danckwardt
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334781/auf1-facilitates-microrna-mediated-gene-silencing
#17
Kyung-Won Min, Myung Hyun Jo, Soochul Shin, Sylvia Davila, Richard W Zealy, Soo Im Kang, Lawson T Lloyd, Sungchul Hohng, Je-Hyun Yoon
Eukaryotic mRNA decay is tightly modulated by RNA-binding proteins (RBPs) and microRNAs (miRNAs). RBP AU-binding factor 1 (AUF1) has four isoforms resulting from alternative splicing and is critical for miRNA-mediated gene silencing with a distinct preference of target miRNAs. Previously, we have shown that AUF1 facilitates miRNA loading to Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex. Here, we further demonstrate that depletion of AUF1 abolishes the global interaction of miRNAs and AGO2...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334276/motifmap-rna-a-genome-wide-map-of-rbp-binding-sites
#18
Yu Liu, Sha Sun, Timothy Bredy, Marcelo Wood, Robert C Spitale, Pierre Baldi
Motivation: RNA plays a critical role in gene expression and its regulation. RNA binding proteins (RBPs), in turn, are important regulators of RNA. Thanks to the availability of large scale data for RBP binding motifs and in vivo binding sites results in the form of eCLIP experiments, it is now possible to computationally predict RBP binding sites across the whole genome. Results: We describe MotifMap-RNA, an extension of MotifMap which predicts binding sites for RBP motifs across human and mouse genomes and allows large scale querying of predicted binding sites...
February 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28325876/comprehensive-and-quantitative-mapping-of-rna-protein-interactions-across-a-transcribed-eukaryotic-genome
#19
Richard She, Anupam K Chakravarty, Curtis J Layton, Lauren M Chircus, Johan O L Andreasson, Nandita Damaraju, Peter L McMahon, Jason D Buenrostro, Daniel F Jarosz, William J Greenleaf
RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying these posttranscriptional gene regulators combines transcriptome-wide throughput and biophysical precision. Here, we describe an assay that accomplishes this. Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. We used the platform to quantitatively measure the binding affinity of the prototypical RBP Vts1 for every transcript in the Saccharomyces cerevisiae genome...
April 4, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#20
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of three Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurological processes. Here we synthesize thirty years of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
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