Ribonomic approaches to study the RNA-binding proteome.

Abstract:

:Gene expression is controlled through a complex interplay among mRNAs, non-coding RNAs and RNA-binding proteins (RBPs), which all assemble along with other RNA-associated factors in dynamic and functional ribonucleoprotein complexes (RNPs). To date, our understanding of RBPs is largely limited to proteins with known or predicted RNA-binding domains. However, various methods have been recently developed to capture an RNA of interest and comprehensively identify its associated RBPs. In this review, we discuss the RNA-affinity purification methods followed by mass spectrometry analysis (AP-MS); RBP screening within protein libraries and computational methods that can be used to study the RNA-binding proteome (RBPome).

journal_name

FEBS Lett

journal_title

FEBS letters

authors

Faoro C,Ataide SF

doi

10.1016/j.febslet.2014.07.039

subject

Has Abstract

pub_date

2014-10-16 00:00:00

pages

3649-64

issue

20

eissn

0014-5793

issn

1873-3468

pii

S0014-5793(14)00616-4

journal_volume

588

pub_type

杂志文章,评审
  • In memory of Professor Leonor Michaelis in Nagoya: great contributions to biochemistry in Japan in the first half of the 20th century.

    abstract::Leonor Michaelis spent the years of 1922-1926 as Professor of Biochemistry of the Aichi Medical College (now Graduate School of Medicine, Nagoya University) in Nagoya, Japan. Michaelis succeeded in gathering many bright young biochemists from all over Japan into his laboratory, and made tremendous contributions to the...

    journal_title:FEBS letters

    pub_type: 传,历史文章,杂志文章

    doi:10.1016/j.febslet.2013.04.020

    authors: Nagatsu TT

    更新日期:2013-09-02 00:00:00

  • A new hemoglobin variant, Hb Mito [beta 144(HC 1) Lys----Glu], with increased oxygen affinity.

    abstract::A new abnormal hemoglobin, Hb Mito [beta 144(HC 1) Lys----Glu], with an amino acid substitution in the 2,3-DPG pocket, was discovered in a Japanese female. This hemoglobin showed increased oxygen affinity, and decreased organic phosphate and Bohr effects, while the Hill constant n was normal. ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(85)80046-6

    authors: Harano K,Harano T,Ueda S,Ohkushi T,Imai K

    更新日期:1985-11-11 00:00:00

  • Inhibition of Na,K-ATPase activity by cGMP is isoform-specific in brain endothelial cells.

    abstract::cGMP has been shown to either activate or inhibit Na,K-ATPase activity. Using mouse brain endothelial cells which express both ouabain-resistant alpha1 and ouabain-sensitive alpha2 and alpha3 isoforms, we show that cGMP reduces total Na,KATPase activity to about 58%. The inhibition is prevented by the protein kinase G...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(98)01183-1

    authors: Pontiggia L,Winterhalter K,Gloor SM

    更新日期:1998-10-09 00:00:00

  • Biochemical characterization and subcellular localization of the sterol C-24(28) reductase, erg4p, from the yeast saccharomyces cerevisiae.

    abstract::The yeast ERG4 gene encodes sterol C-24(28) reductase which catalyzes the final step in the biosynthesis of ergosterol. Deletion of ERG4 resulted in a complete lack of ergosterol and accumulation of the precursor ergosta-5,7,22,24(28)-tetraen-3beta-ol. An erg4 mutant strain exhibited pleiotropic defects such as hypers...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(00)01290-4

    authors: Zweytick D,Hrastnik C,Kohlwein SD,Daum G

    更新日期:2000-03-17 00:00:00

  • Positive and negative regulation of JNK1 by protein kinase C and p42(MAP kinase) in adult rat hepatocytes.

    abstract::The role of protein kinase C (PKC) and p42(MAP kinase) signaling in the regulation of proliferation and apoptosis was investigated in freshly isolated and primary cultured rat hepatocytes. Acute treatment of freshly isolated hepatocytes with phenylephrine and EGF caused rapid phasic activations of p42(MAP kinase) and ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)00705-9

    authors: Jarvis WD,Auer KL,Spector M,Kunos G,Grant S,Hylemon P,Mikkelsen R,Dent P

    更新日期:1997-07-21 00:00:00

  • Coupling of viral membrane proteins to phosphatidylinositide signalling system.

    abstract::C6 rat glioma cells persistently infected with subacute sclerosing panencephalitis virus (C6/SSPE) were treated with measles antiserum and purified anti-measles IgG. This stimulated phosphoinositide breakdown and an increase in inositol phosphates. In uninfected C6 cells, however, only fetal calf serum (FCS), but not ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(89)81330-4

    authors: Weinmann-Dorsch C,Koschel K

    更新日期:1989-04-24 00:00:00

  • The use of carotenoids and oxonol VI as probes for membrane potential in proteoliposomes.

    abstract::Carotenoids present in lipids extracted from the cyanobacterium Synechococcus 6716 indicate trans-membrane potential in proteoliposomes reconstituted from these lipids and the ATPase complex isolated from the same organism. A carotenoid absorbance band shift to a longer wavelength is obtained with valinomycin-induced ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(85)80661-x

    authors: van Walraven HS,Krab K,Hagendoorn MJ,Kraayenhof R

    更新日期:1985-05-06 00:00:00

  • 31P-NMR studies of Mycoplasma gallisepticum cells using a continuous perfusion technique.

    abstract::31P-NMR studies of Mycoplasma gallisepticum cells have been carried out using a continuous perfusion technique; these are the first such studies with this organism. Using this technique, glucose metabolism was monitored in the intact organisms, and cell extracts were prepared to identify the intermediates. Under glyco...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(86)80846-8

    authors: Egan W,Barile M,Rottem S

    更新日期:1986-08-18 00:00:00

  • Cellular RNA is not degraded in interferon-treated HeLa cells after poliovirus infection.

    abstract::A drastic inhibition of protein synthesis occurs in HeLa cells treated with human lymphoblastoid interferon and infected with poliovirus. At the time when this inhibition has been established no degradation of 32P-labelled ribosomal RNA can be detected. Isolation of the mRNAs from poliovirus-infected cells plus or min...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(83)80942-9

    authors: Muñoz A,Harvey R,Carrasco L

    更新日期:1983-08-22 00:00:00

  • Triphenyltin chloride inhibits superoxide production by human neutrophils stimulated with a surface active agent.

    abstract::Treatment of human neutrophils with triphenyltin chloride (TPTCl)-inhibited superoxide (O-2) production stimulated with phorbol myristate acetate (PMA). TPTCl was more potent as inhibitor of O-2 production than other phenyltin compounds. The O-2 production by the xanthine oxidase-acetaldehyde system was not inhibited ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(83)80296-8

    authors: Matsui H,Wada O,Ushijima Y,Akuzawa T

    更新日期:1983-12-12 00:00:00

  • Bile salt activation of human cholesterol esterase does not require protein dimerisation.

    abstract::Human milk cholesterol esterase (bile salt-activated lipase) plays a role in the dietary uptake of triacylglyceride and cholesteryl ester. The activities toward these substrates are mediated through a unique bile salt-activated mechanism. Previously, it has been proposed that a necessary step in this process is prior ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)00215-9

    authors: Loomes KM,Senior HE

    更新日期:1997-04-01 00:00:00

  • Insertion of foreign random sequences of 120 amino acid residues into an active enzyme.

    abstract::Random sequences of 120-130 amino acid residues were inserted into a surface loop region of Escherichia coli RNase HI. This library was screened and about 10% of the clones were found to retain RNase H activity. Subsequent random mutagenesis led to an increase in RNase H activity and solubility of the protein. The ins...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(96)01522-0

    authors: Doi N,Itaya M,Yomo T,Tokura S,Yanagawa H

    更新日期:1997-02-03 00:00:00

  • Identification of a novel prokaryotic HEAT-repeats-containing protein which interacts with a cyanobacterial IscA homolog.

    abstract::IscA homologs are known to be involved in iron-sulfur cluster formation in various organisms. Recombinant proteins of two IscA homologs from the cyanobacterium Synechocystis PCC 6803, designated SLR1417 and SLR1565, were purified. The absorption spectrum of purified SLR1565 was typical for [2Fe-2S] cluster-containing ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(02)02736-9

    authors: Morimoto K,Nishio K,Nakai M

    更新日期:2002-05-22 00:00:00

  • Diverse stress signals activate the C1 subgroup MAP kinases of Arabidopsis.

    abstract::Mitogen-activated protein kinase (MAPK) cascades play an important role in mediating stress responses in plants. In Arabidopsis, 20 MAPKs have been identified and classified into four major groups (A-D). Little is known about the role of group C MAPKs. We have studied the activation of Arabidopsis subgroup C1 MAPKs (A...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2007.03.075

    authors: Ortiz-Masia D,Perez-Amador MA,Carbonell J,Marcote MJ

    更新日期:2007-05-01 00:00:00

  • Cytoplasmic polyadenylation element-like sequences are involved in dendritic targeting of BDNF mRNA in hippocampal neurons.

    abstract::Several mRNAs are known to be targeted to dendrites in hippocampal neurons. In this study, we show that brain-derived neurotrophic factor (BDNF) mRNA has two distinct cis-acting dendritic targeting elements in the short 3' untranslated region (UTR): a constitutive element and an activity-dependent one. Moreover, delet...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2010.06.040

    authors: Oe S,Yoneda Y

    更新日期:2010-08-04 00:00:00

  • Characterization of membrane-associated prothrombin activator in normal and injured murine tissues.

    abstract::Thrombin is a multifunctional enzyme involved in coagulation, cell modulation and inflammation. We recently reported a novel membrane-associated prothrombin activator, abbreviated as MAPA, found in cultured fibroblasts and glial cell lines. In this study, we examined the physiological role of this enzyme. MAPA-like ac...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)00852-1

    authors: Shikamoto Y,Shibusawa S,Okuyama I,Morita T

    更新日期:1997-08-04 00:00:00

  • The PsbP protein, but not the PsbQ protein, is required for normal thylakoid architecture in Arabidopsis thaliana.

    abstract::Interfering RNA was used to suppress the expression of the genes At1g06680 and At2g30790 in Arabidopsis thaliana, which encode the PsbP-1 and PsbP-2 proteins, respectively, of Photosystem II. A phenotypic series of transgenic plants was recovered that expressed intermediate and low amounts of PsbP. Earlier we had docu...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2009.05.048

    authors: Yi X,Hargett SR,Frankel LK,Bricker TM

    更新日期:2009-06-18 00:00:00

  • High levels of rhodopsin phosphorylation in missense mutations of C-terminal region of rhodopsin.

    abstract::Rhodopsin phosphorylation was investigated using synthetic C-terminal peptides from rhodopsin. The peptides were phosphorylated by expressed rhodopsin kinase (RK) in the presence of a photolyzed truncated rhodopsin at the C-terminus. No peptide phosphorylation was detected under dark or in conditions in which RK was i...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)00957-5

    authors: Ohguro H

    更新日期:1997-08-25 00:00:00

  • A new phagemid vector for positive selection of recombinants based on a conditionally lethal barnase gene.

    abstract::A new phagemid cloning vector for positive selection of recombinants, pBa-7, was constructed which contains an active barnase gene encoding the cytotoxic ribonuclease from Bacillus amyloliquefaciens, under control of the lac promoter. PBa-7 is a derivative of the high-copy number pBluescript II KS+ phagemid in which t...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(99)00661-4

    authors: Yazynin S,Lange H,Mokros T,Deyev S,Lemke H

    更新日期:1999-06-11 00:00:00

  • Three-dimensional structure of (Na+ + K+)-ATPase revealed by electron microscopy of two-dimensional crystals.

    abstract::Prolonged incubation of membrane fragments containing homogeneous (Na+ + K+)-ATPase with Mg2+, K+ and VO-3 at 4 degrees C resulted in formation of two-dimensional crystals of this enzyme with unit cell parameters: a = 66 A, b = 118 A, gamma = 108 degrees. The crystals correspond to the two-sided plane group p21. By co...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(85)80430-0

    authors: Ovchinnikov YuA,Demin VV,Barnakov AN,Kuzin AP,Lunev AV,Modyanov NN,Dzhandzhugazyan KN

    更新日期:1985-10-07 00:00:00

  • pH dependence studies provide insight into the structure and mechanism of thimet oligopeptidase (EC 3.4.24.15).

    abstract::Thimet oligopeptidase (EC 3.4.24.15; TOP) is a Zn(II) endopeptidase implicated in physiological regulation of processes involving neuropeptides. The present study clarifies the active site structure and mechanism of catalysis of TOP. The enzyme exhibited a bell-shaped pH dependence of activity having an acidic limb du...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(03)00548-9

    authors: Sigman JA,Edwards SR,Pabon A,Glucksman MJ,Wolfson AJ

    更新日期:2003-06-19 00:00:00

  • Promoted evolution of a shortened variant of heme A synthase in the membrane of Bacillus subtilis.

    abstract::Bacillus subtilis heme A synthase is a membrane protein with 8 transmembrane segments. By using a two-step mutagenesis approach we have generated and selected a fully functional enzyme protein variant with a seven residue internal deletion. The biochemical properties of the shortened variant are similar to those of th...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2008.03.015

    authors: Lewin A,Hederstedt L

    更新日期:2008-04-16 00:00:00

  • Intracellular delivery of acetyl-histone peptides inhibits native bromodomain-chromatin interactions and impairs mitotic progression.

    abstract::Bromodomains present in Brd4 and other chromatin proteins interact with acetylated histones to regulate transcription and cell growth. To study Brd4-chromatin interactions in vivo, histone H4 tail peptides were fused to a synthetic protein transduction domain (PTD) derived from the human immunodeficiency virus Tat and...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2008.03.044

    authors: Nishiyama A,Mochizuki K,Mueller F,Karpova T,McNally JG,Ozato K

    更新日期:2008-04-30 00:00:00

  • Cl- -dependent photovoltage responses of bacteriorhodopsin: comparison of the D85T and D85S mutants and wild-type acid purple form.

    abstract::Laser flash-induced photovoltage responses of the D85S and D85T mutants as well as of the wild-type acid blue form are similar and reflect intraprotein charge redistribution caused by retinal isomerization. The Cl- -induced transition of all of these blue forms into purple ones is accompanied by the appearance of elec...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(97)01390-2

    authors: Kalaidzidis IV,Kaulen AD

    更新日期:1997-12-01 00:00:00

  • Modulation of the alpha 1A Ca2+ channel by beta subunits at physiological Ca2+ concentration.

    abstract::The class A Ca2+ channel alpha 1 subunit (alpha 1A) was expressed in Xenopus oocytes alone or in combination with the beta 1b, beta 2a, beta 3, or beta 4 subunit. Analysis of voltage-dependent activation and inactivation in the presence of 1.8 mM external Ca2+ showed an hyperpolarising shift of both relations when com...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(96)00704-1

    authors: Cens T,Mangoni ME,Nargeot J,Charnet P

    更新日期:1996-08-12 00:00:00

  • IL-2-induced gene expression of protein-tyrosine phosphatase LC-PTP requires acidic and serine-rich regions within IL-2 receptor beta chain.

    abstract::A protein-tyrosine phosphatase LC-PTP is preferentially expressed in hematopoietic cells and is an early response gene in lymphokine stimulated cells. Here, we found the LC-PTP mRNA induction by IL-2 was markedly inhibited by several tyrosine kinase inhibitors. The induction required both the acidic and serine-rich re...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(95)00952-6

    authors: Adachi M,Torigoe T,Sekiya M,Minami Y,Taniguchi T,Hinoda Y,Yachi A,Reed JC,Imai K

    更新日期:1995-09-18 00:00:00

  • Mutational analysis of 6-aminohexanoate-dimer hydrolase: relationship between nylon oligomer hydrolytic and esterolytic activities.

    abstract::Carboxylesterase (EII') from Arthrobacter sp. KI72 has 88% homology to 6-aminohexanoate-dimer hydrolase (EII) and possesses ca. 0.5% of the level of 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity of EII. To study relationship between Ald-hydrolytic and esterolytic activities, random mutations were introduced ...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/j.febslet.2006.08.031

    authors: Ohki T,Wakitani Y,Takeo M,Yasuhira K,Shibata N,Higuchi Y,Negoro S

    更新日期:2006-09-18 00:00:00

  • Raf-1 is activated by the p38 mitogen-activated protein kinase inhibitor, SB203580.

    abstract::SB203580 (4-(4-fluorophenyl)-2-(4-methylsulfinylphenyl)-5-(4-pyridyl)1H-imi dazole) is widely used as a specific inhibitor of p38 mitogen-activated protein kinase (MAPK). Here, we report that SB203580 activates the serine/threonine kinase Raf-1 in quiescent smooth muscle cells in a dose-dependent fashion. The concentr...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/s0014-5793(99)00034-4

    authors: Kalmes A,Deou J,Clowes AW,Daum G

    更新日期:1999-02-05 00:00:00

  • Low resolution solution structure of the Bacillus subtilis glucose permease IIA domain derived from heteronuclear three-dimensional NMR spectroscopy.

    abstract::A low resolution solution structure of the IIA domain of the Bacillus subtilis phosphoenolpyruvate-sugar phosphotransferase system (PTS) glucose permease has been determined using 945 inter-residue and 724 intra-residue distance constraints derived from three-dimensional 15N and 13C edited NOESY spectra. A total of 15...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(92)80367-p

    authors: Fairbrother WJ,Gippert GP,Reizer J,Saier MH Jr,Wright PE

    更新日期:1992-01-20 00:00:00

  • Acidic phospholipids directly inhibit DNA binding of mammalian DNA topoisomerase I.

    abstract::Inhibition of mammalian DNA topoisomerase I by phospholipids was investigated using purified enzyme. Acidic phospholipids inhibited the DNA relaxation activity of topoisomerase I whereas neutral phospholipid, phosphatidylethanolamine, did not. Accumulation of a protein-DNA cleavable complex, an intermediate which is k...

    journal_title:FEBS letters

    pub_type: 杂志文章

    doi:10.1016/0014-5793(90)80658-6

    authors: Tamura H,Ikegami Y,Ono K,Sekimizu K,Andoh T

    更新日期:1990-02-12 00:00:00