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RNA binding proteins

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https://www.readbyqxmd.com/read/27933075/a-non-specific-setaria-italica-lipid-transfer-protein-gene-plays-a-critical-role-under-abiotic-stress
#1
Yanlin Pan, Jianrui Li, Licong Jiao, Cong Li, Dengyun Zhu, Jingjuan Yu
Lipid transfer proteins (LTPs) are a class of cysteine-rich soluble proteins having small molecular weights. LTPs participate in flower and seed development, cuticular wax deposition, also play important roles in pathogen and abiotic stress responses. A non-specific LTP gene (SiLTP) was isolated from a foxtail millet (Setaria italica) suppression subtractive hybridization library enriched for differentially expressed genes after abiotic stress treatments. A semi-quantitative reverse transcriptase PCR analysis showed that SiLTP was expressed in all foxtail millet tissues...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27932587/a-divalent-cation-dependent-variant-of-the-glms-ribozyme-with-stringent-ca2-selectivity-co-opts-a-pre-existing-non-specific-metal-ion-binding-site
#2
Matthew W L Lau, Robert J Trachman, Adrian R Ferré-D'Amaré
Ribozymes employ divalent cations for structural stabilization, as catalytic cofactors, or both. Because of the prominent role of Ca2+ in intracellular signaling, engineered ribozymes with stringent Ca2+ selectivity would be important in biotechnology. The wild-type glmS ribozyme (glmSWT) requires glucosamine-6-phosphate (GlcN6P) as a catalytic cofactor. Previously, a glmS ribozyme variant with three adenosine mutations (glmSAAA) was identified, which dispenses with GlcN6P and instead uses, with little selectivity, divalent cations as cofactors for site-specific RNA cleavage...
December 8, 2016: RNA
https://www.readbyqxmd.com/read/27932457/structural-basis-for-the-dimerization-of-nab2-generated-by-rna-binding-provides-insight-into-its-contribution-to-both-poly-a-tail-length-determination-and-transcript-compaction-in-saccharomyces-cerevisiae
#3
Shintaro Aibara, James M B Gordon, Anja S Riesterer, Stephen H McLaughlin, Murray Stewart
In Saccharomyces cerevisiae generation of export-competent mRNPs terminates the nuclear phase of the gene expression pathway and facilitates transport to the cytoplasm for translation. Nab2 functions in this process to control both mRNP compaction that facilitates movement through nuclear pore complexes and the length of transcript poly(A) tails. Nab2 has a modular structure that includes seven CCCH Zn fingers that bind to A-rich RNAs and fingers 5-7 are critical for these functions. Here, we demonstrate, using both biophysical and structural methods, that binding A11G RNA induces dimerization of Zn fingers 5-7 mediated by the novel spatial arrangement of the fingers promoting each RNA chain binding two protein chains...
December 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27931282/rnai-mediated-downregulation-of-fkbp14-suppresses-the-growth-of-human-ovarian-cancer-cells
#4
Meng Lu, Yi Miao, Lan Qi, Mingzhu Bai, Jiarong Zhang, Youji Feng
FKBP14 belongs to the family of FK506-binding proteins (FKBPs). Altered expression of FKBPs has been reported in several malignancies. This study aimed to reveal the expression profile of FKBP14 in ovarian cancer and evaluate whether FKBP14 is a molecular target for cancer therapy. We found that the FKBP14 mRNA level was significantly higher in ovarian cancer tissues than in normal tissues. FKBP14 expression was then knocked down in two ovarian cancer cell lines, SKOV3 and HO8910 cells, by a lentiviral short hairpin RNA (shRNA) delivery system...
May 2016: Oncology Research
https://www.readbyqxmd.com/read/27931185/characterization-of-the-cytokinin-responsive-transcriptome-in-rice
#5
Tracy Raines, Ivory C Blakley, Yu-Chang Tsai, Jennifer M Worthen, José Manuel Franco-Zorrilla, Roberto Solano, G Eric Schaller, Ann E Loraine, Joseph J Kieber
BACKGROUND: Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies of the dicotyledonous plant Arabidopsis thaliana. To expand the understanding of the cytokinin-regulated transcriptome, we employed RNA-Seq to analyze gene expression in response to cytokinin in roots and shoots of the monocotyledonous plant rice. RESULTS: We identified over 4,600 and approximately 2,400 genes differentially expressed in response to cytokinin in roots and shoots respectively...
December 8, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27930936/sunlight-exposure-increases-vitamin-d-sufficiency-in-growing-pigs-fed-a-diet-formulated-to-exceed-requirements
#6
B M Alexander, B C Ingold, J L Young, S R Fensterseifer, P J Wechsler, K J Austin, D E Larson-Meyer
Traditional confinement practices limit exposure to sunlight and vitamin D synthesis, and vitamin insufficiency occurs even with dietary supplementation. The aim of this study was to determine the effect of limited sun exposure on serum concentration of vitamin D and the expression of vitamin D synthesizing enzymes in the liver and kidney of pigs on a vitamin D sufficient diet. White-pigmented grower pigs (29.7 ± 2.3 kg) fed 15% CP diet ad libitum providing >1,200 IU vitamin D3/kg of feed were exposed to sunlight for 1 h each day at solar noon for 14 d at the spring equinox (March pigs, n = 10) or summer solstice (June pigs, n = 5) and again before slaughter in June (March pigs) and September (June pigs)...
November 11, 2016: Domestic Animal Endocrinology
https://www.readbyqxmd.com/read/27930710/urb-rip-an-adaptable-and-efficient-approach-for-immunoprecipitation-of-rnas-and-associated-rnas-proteins
#7
Kyle A Cottrell, Sergej Djuranovic
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application...
2016: PloS One
https://www.readbyqxmd.com/read/27930406/stress-response-protein-rbm3-promotes-the-development-of-colitis-associated-cancer
#8
Toshiharu Sakurai, Hiroshi Kashida, Yoriaki Komeda, Tomoyuki Nagai, Satoru Hagiwara, Tomohiro Watanabe, Masayuki Kitano, Naoshi Nishida, Jun Fujita, Masatoshi Kudo
BACKGROUND: Colitis-associated cancer (CAC) is caused by chronic intestinal inflammation and often results from refractory inflammatory bowel disease (IBD). Stress response proteins Cirp and HSPA4 are involved in the refractory clinical course and development of CAC. RNA-binding motif protein 3 (RBM3) is induced in response to various stresses and is upregulated in several cancers. However, the role of RBM3 in CAC is unclear. METHODS: We assessed RBM3 expression and function in 263 human intestinal mucosa samples from patients with IBD and in Rbm3-deficient (Rbm3) mice...
December 7, 2016: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/27929749/critical-role-of-x-box-binding-protein-1-in-nadph-oxidase-4-triggered-cardiac-hypertrophy-is-mediated-by-receptor-interacting-protein-kinase-1
#9
Li Chen, Mingyue Zhao, Junli Li, Yu Wang, Qinxue Bao, Siyuan Wu, Xueqin Deng, Xiaoju Tang, Wenchao Wu, Xiaojing Liu
NADPH oxidase 4 (NOX4) and the NOX4-related redox signaling are implicated in cardiac hypertrophy. NOX4 is interrelated with endoplasmic reticulum stress (ERS). Spliced X-box binding protein 1 (Xbp1s) is a key mediator of ERS while its role in cardiac hypertrophy is still poorly understood. Recently, receptor interacting protein kinase 1(RIPK1) has been increasingly reported to be associated with ERS. Therefore, we aimed to test the hypothesis that Xbp1s mediates NOX4-triggered cardiac hypertrophy via RIPK1 signaling...
December 8, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27929740/role-for-padi6-in-securing-the-mrna-msy2-complex-to-the-oocyte-cytoplasmic-lattices
#10
Xiaoqiu Liu, Eric Morency, Tingting Li, Hao Qin, Xiaoqian Zhang, Xuesen Zhang, Scott Coonrod
The oocyte cytoplasmic lattices (CPLs) have long been predicted to function as a storage form for the maternal contribution of ribosomes to the early embryo. Our previous studies have demonstrated that ribosomal component S6 is stored in the oocyte CPLs and peptidylarginine deiminase 6 (PADI6) is critical for CPLs formation. Additionally, we found that depletion of PADI6 reduced de novo protein synthesis prior to the maternal-to-embryonic transition, therefore causing embryos to arrest at the two-cell stage...
December 8, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27929413/exosome-proteome-of-u-87mg-glioblastoma-cells
#11
Sohyun Chun, Seunghyun Ahn, Chang-Hwan Yeom, Seyeon Park
Exosomes are small membrane vesicles between 30 and 100 nm in diameter secreted by many cell types, and are associated with a wide range of physiological and/or pathological processes. Exosomes containing proteins, lipids, mRNA, and microRNA contribute to cell-to-cell communication and cell-to-environment regulation, however, their biological functions are not yet fully understood. In this report, exosomes in the glioblastoma cell line, U-87MG, were isolated and the proteome was investigated. In addition, exosome proteome changes in U-87MG cells exposed to a low temperature were investigated to elucidate whether the exosome proteome could respond to an external stimulus...
December 6, 2016: Biology
https://www.readbyqxmd.com/read/27929351/expression-of-the-cardiac-maintenance-and-survival-factor-fgf-16-gene-is-regulated-by-csx-nkx2-5-and-is-an-early-target-of-doxorubicin-cardiotoxicity
#12
Jie Wang, Yan Jin, Peter A Cattini
The fibroblast growth factor (FGF) 16 gene (Fgf-16) is preferentially expressed by neonatal cardiomyocytes after birth, with levels increasing into adulthood. Null mice and isolated heart studies suggest a role for FGF-16 in cardiac maintenance and survival, including increased resistance to doxorubicin (DOX)-induced injury. However, the effect of DOX on endogenous FGF-16 synthesis and specifically regulation of cardiac Fgf-16 expression has not been reported. To assess the effect of DOX on FGF-16 RNA levels and stability, as well as promoter activity and use sequence analysis, knockdown, and overexpression to investigate the role of cardiac transcription factor(s) implicated in the response...
December 8, 2016: DNA and Cell Biology
https://www.readbyqxmd.com/read/27929099/stat1-is-essential-for-the-inhibition-of-hepatitis-c-virus-replication-by-interferon-%C3%AE-but-not-by-interferon-%C3%AE
#13
Shota Yamauchi, Kenji Takeuchi, Kazuyasu Chihara, Chisato Honjoh, Yuji Kato, Hatsumi Yoshiki, Hak Hotta, Kiyonao Sada
Interferon-α (IFN-α) and IFN-λ are structurally distinct cytokines that bind to different receptors, but induce expression of similar sets of genes through Janus kinase (JAK)-signal transducers and activators of transcription (STAT) pathways. The difference between IFN-α and IFN-λ signaling remains poorly understood. Here, using the CRISPR/Cas9 system, we examine the role of STAT1 and STAT2 in the inhibition of hepatitis C virus (HCV) replication by IFN-α and IFN-λ. Treatment with IFN-α increases expression of IFN-stimulated genes (ISGs) such as double-stranded RNA-activated protein kinase (PKR) and decreases viral RNA and protein levels in HCV-infected Huh-7...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27928058/identification-of-senescence-associated-circular-rnas-sac-rnas-reveals-senescence-suppressor-circpvt1
#14
Amaresh C Panda, Ioannis Grammatikakis, Kyoung Mi Kim, Supriyo De, Jennifer L Martindale, Rachel Munk, Xiaoling Yang, Kotb Abdelmohsen, Myriam Gorospe
Using RNA sequencing (RNA-Seq), we compared the expression patterns of circular RNAs in proliferating (early-passage) and senescent (late-passage) human diploid WI-38 fibroblasts. Among the differentially expressed senescence-associated circRNAs (which we termed 'SAC-RNAs'), we identified CircPVT1, generated by circularization of an exon of the PVT1 gene, as a circular RNA showing markedly reduced levels in senescent fibroblasts. Reducing CircPVT1 levels in proliferating fibroblasts triggered senescence, as determined by a rise in senescence-associated β-galactosidase activity, higher abundance of CDKN1A/P21 and TP53, and reduced cell proliferation...
December 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27927741/a-strong-neutrophil-elastase-proteolytic-fingerprint-marks-the-carcinoma-tumor-proteome
#15
Michal Kistowski, Janusz Dębski, Jakub Karczmarski, Agnieszka Paziewska, Jacek Olędzki, Michał Mikula, Jerzy Ostrowski, Michał Dadlez
Proteolytic cascades are deeply involved in critical stages of cancer progression. During the course of peptide-wise analysis of shotgun proteomic datasets representative of colon adenocarcinoma (AC) and ulcerative colitis (UC), we detected a cancer-specific proteolytic fingerprint composed of a set of numerous protein fragments cleaved C-terminally to V, I, A, T, or C residues, significantly overrepresented in AC. A peptide set linked by a common VIATC cleavage consensus was the only prominent cancer-specific proteolytic fingerprint detected...
December 7, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27927715/chromatin-environment-transcriptional-regulation-and-splicing-distinguish-lincrnas-and-mrnas
#16
Marta Melé, Kaia Mattioli, William Mallard, David M Shechner, Chiara Gerhardinger, John L Rinn
While long intergenic noncoding RNAs (lincRNAs) and mRNAs share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre- and post-transcriptional regulation is different from that of mRNAs. Here, we perform an in-depth characterization of the features that contribute to lincRNA regulation in multiple human cell lines. We find that lincRNA promoters are depleted of transcription factor (TF) binding sites, yet enriched for some specific factors such as GATA and FOS relative to mRNA promoters...
December 7, 2016: Genome Research
https://www.readbyqxmd.com/read/27926995/frozen-but-no-accident-why-the-20-standard-amino-acids-were-selected
#17
REVIEW
Andrew J Doig
The 20 standard amino acids encoded by the Genetic Code were adopted during the RNA World, around 4 billion years ago. This amino acid set could be regarded as a frozen accident, implying that other possible structures could equally well have been chosen to use in proteins. Amino acids were not primarily selected for their ability to support catalysis, since the RNA World already had highly effective cofactors to perform reactions, such as oxidation, reduction and transfer of small molecules. Rather, they were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets...
December 7, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27926877/ptbp1-and-ptbp2-serve-both-specific-and-redundant-functions-in-neuronal-pre-mrna-splicing
#18
John K Vuong, Chia-Ho Lin, Min Zhang, Liang Chen, Douglas L Black, Sika Zheng
Families of alternative splicing regulators often contain multiple paralogs presumed to fulfill different functions. Polypyrimidine tract binding proteins PTBP1 and PTBP2 reprogram developmental pre-mRNA splicing in neurons, but how their regulatory networks differ is not understood. To compare their targeting, we generated a knockin allele that conditionally expresses PTBP1. Bred to a Ptbp2 knockout, the transgene allowed us to compare the developmental and molecular phenotypes of mice expressing only PTBP1, only PTBP2, or neither protein in the brain...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27924926/identification-of-protein-structural-elements-responsible-for-the-diversity-of-sequence-preferences-among-mini-iii-rnases
#19
Dawid Głów, Małgorzata Kurkowska, Justyna Czarnecka, Krzysztof Szczepaniak, Dariusz Pianka, Verena Kappert, Janusz M Bujnicki, Krzysztof J Skowronek
Many known endoribonucleases select their substrates based on the presence of one or a few specific nucleotides at or near the cleavage site. In some cases, selectivity is also determined by the structural features of the substrate. We recently described the sequence-specific cleavage of double-stranded RNA by Mini-III RNase from Bacillus subtilis in vitro. Here, we characterized the sequence specificity of eight other members of the Mini-III RNase family from different bacterial species. High-throughput analysis of the cleavage products of Φ6 bacteriophage dsRNA indicated subtle differences in sequence preference between these RNases, which were confirmed and characterized by systematic analysis of the cleavage kinetics of a set of short dsRNA substrates...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924491/single-molecule-fluorescence-energy-transfer-assays-for-the-characterization-of-reaction-pathways-of-mirna-argonaute-complex
#20
Myung Hyun Jo, Sungchul Hohng
Argonaute proteins are key components of the microRNA-induced silencing complexes (miRISCs) that mediate the posttranscriptional gene silencing of microRNAs and small interfering RNA (siRNAs). The complex reaction mechanism of miRISC is expected to be characterized by tracing the reaction pathways of miRISC at the single-molecule level in real time. In this chapter, we describe single-molecule fluorescence resonance energy transfer (FRET) assays to observe the target binding and reaction pathways of miRISC composed of a recombinant Argonaute and a small RNA...
2017: Methods in Molecular Biology
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