Nucleolar proteins Bfr2 and Enp2 interact with DEAD-box RNA helicase Dbp4 in two different complexes.

Abstract:

:Different pre-ribosomal complexes are formed during ribosome biogenesis, and the composition of these complexes is highly dynamic. Dbp4, a conserved DEAD-box RNA helicase implicated in ribosome biogenesis, interacts with nucleolar proteins Bfr2 and Enp2. We show that, like Dbp4, Bfr2 and Enp2 are required for the early processing steps leading to the production of 18S ribosomal RNA. We also found that Bfr2 and Enp2 associate with the U3 small nucleolar RNA (snoRNA), the U3-specific protein Mpp10 and various pre-18S ribosomal RNA species. Thus, we propose that Bfr2, Dbp4 and Enp2 are components of the small subunit (SSU) processome, a large complex of ∼80S. Sucrose gradient sedimentation analyses indicated that Dbp4, Bfr2 and Enp2 sediment in a peak of ∼50S and in a peak of ∼80S. Bfr2, Dbp4 and Enp2 associate together in the 50S complex, which does not include the U3 snoRNA; however, they associate with U3 snoRNA in the 80S complex (SSU processome). Immunoprecipitation experiments revealed that U14 snoRNA associates with Dbp4 in the 50S complex, but not with Bfr2 or Enp2. The assembly factor Tsr1 is not part of the '50S' complex, indicating this complex is not a pre-40S ribosome. A combination of experiments leads us to propose that Bfr2, Enp2 and Dbp4 are recruited at late steps during assembly of the SSU processome.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Soltanieh S,Lapensée M,Dragon F

doi

10.1093/nar/gkt1293

subject

Has Abstract

pub_date

2014-03-01 00:00:00

pages

3194-206

issue

5

eissn

0305-1048

issn

1362-4962

pii

gkt1293

journal_volume

42

pub_type

杂志文章
  • Cloning and sequence analysis of TFE, a helix-loop-helix transcription factor able to recognize the thyroglobulin gene promoter in vitro.

    abstract::A cDNA that encodes a transcription factor able to recognize the thyroglobulin gene promoter in vitro was isolated from a dog thyroid cDNA expression library in lambda gt11. The library was screened with a multimerized 20 bp-oligonucleotide probe corresponding to the -126 to -107 bp region of the bovine thyroglobulin ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.5.1121

    authors: Javaux F,Donda A,Vassart G,Christophe D

    更新日期:1991-03-11 00:00:00

  • chipD: a web tool to design oligonucleotide probes for high-density tiling arrays.

    abstract::chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression profiling. The server implements a probe selection algorithm that takes as an input, in addition to the target sequences...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq517

    authors: Dufour YS,Wesenberg GE,Tritt AJ,Glasner JD,Perna NT,Mitchell JC,Donohue TJ

    更新日期:2010-07-01 00:00:00

  • Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains.

    abstract::Gene expression patterns have been demonstrated to be highly variable between similar cell types, for example lab strains and wild strains of Saccharomyces cerevisiae cultured under identical growth conditions exhibit a wide range of expression differences. We have used a genome-wide approach to characterize transcrip...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkj517

    authors: Llinás M,Bozdech Z,Wong ED,Adai AT,DeRisi JL

    更新日期:2006-02-21 00:00:00

  • Circular dichroism studies of ethidium bromide binding to the isolated nucleolus.

    abstract::Circular dichroism in the 300-360 nm region and fluorescence induced by intercaltating binding of ethidum bromide to both DNA and RNA components were studied in isolated HeLa nucleoli. Both DNA and RNA compoents contribute to the induced dichroic elliticity. Digestion of nucleoli by RNase or DNase shows that most of t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/3.8.1857

    authors: Huang CH,Baserga R

    更新日期:1976-08-01 00:00:00

  • A direct-repeat sequence of the human BiP gene is required for A23187-mediated inducibility and an inducible nuclear factor binding.

    abstract::We have recently isolated a functional promoter encoding the human polypeptide-binding protein (BiP) gene from Burkitt's lymphoma cells by polymerase chain reaction (The EMBL Data Library accession number X59969, 1991). This promoter DNA segment (termed BiP670) was fused to the bacterial chloramphenicol acetyltransfer...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.24.6481

    authors: Chao CC,Lin-Chao S

    更新日期:1992-12-25 00:00:00

  • A conserved heptamer upstream of the IgH promoter region octamer can be the site of a coordinate protein-DNA interaction.

    abstract::Immunoglobulin genes contain a conserved eight base sequence element 5' to the site of transcription initiation. This octamer can serve as a site for the binding of nuclear proteins which are presumably involved in the cell type specific expression of this family of genes. In studying the binding of nuclear proteins t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.12.5503

    authors: Landolfi NF,Yin XM,Capra JD,Tucker PW

    更新日期:1988-06-24 00:00:00

  • The Factor VIII Mutation Database on the World Wide Web: the haemophilia A mutation, search, test and resource site. HAMSTeRS update (version 3.0).

    abstract::The HAMSTeRS WWW site was set up in 1996 in order to facilitate easy access to, and aid understanding of, the causes of haemophilia A at the molecular level; previously, the first and second text editions of the database have been published in Nucleic Acids Research. This report describes the facilities originally ava...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.1.128

    authors: Kemball-Cook G,Tuddenham EG

    更新日期:1997-01-01 00:00:00

  • The signal recognition particle database (SRPDB).

    abstract::The SRPDB (signal recognition particle database) provides annotated SRP RNA sequences from Eucaryotes and Archaea, phylogenetically ordered and aligned with their bacterial equivalents. We also make available representative RNA secondary structure diagrams, where each base pair is proven by comparative sequence analys...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.13.3019

    authors: Larsen N,Zwieb C

    更新日期:1993-07-01 00:00:00

  • Antibody-targeted chromatin enables effective intracellular delivery and functionality of CRISPR/Cas9 expression plasmids.

    abstract::We report a novel system for efficient and specific targeted delivery of large nucleic acids to and into cells. Plasmid DNA and core histones were assembled to chromatin by salt gradient dialysis and subsequently connected to bispecific antibody derivatives (bsAbs) via a nucleic acid binding peptide bridge. The result...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz137

    authors: Killian T,Buntz A,Herlet T,Seul H,Mundigl O,Längst G,Brinkmann U

    更新日期:2019-06-04 00:00:00

  • EMdeCODE: a novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes.

    abstract::Existence of some extra-genetic (epigenetic) codes has been postulated since the discovery of the primary genetic code. Evident effects of histone post-translational modifications or DNA methylation over the efficiency and the regulation of DNA processes are supporting this postulation. EMdeCODE is an original algorit...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1214

    authors: Santoni FA

    更新日期:2013-02-01 00:00:00

  • Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data.

    abstract::Deciphering gene regulatory network architecture amounts to the identification of the regulators, conditions in which they act, genes they regulate, cis-acting motifs they bind, expression profiles they dictate and more complex relationships between alternative regulatory partnerships and alternative regulatory motifs...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki166

    authors: Garten Y,Kaplan S,Pilpel Y

    更新日期:2005-01-31 00:00:00

  • OrysPSSP: a comparative platform for small secreted proteins from rice and other plants.

    abstract::Plants have large diverse families of small secreted proteins (SSPs) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. Oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. However, there had no...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1090

    authors: Pan B,Sheng J,Sun W,Zhao Y,Hao P,Li X

    更新日期:2013-01-01 00:00:00

  • A deafness-associated tRNA mutation caused pleiotropic effects on the m1G37 modification, processing, stability and aminoacylation of tRNAIle and mitochondrial translation.

    abstract::Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa1225

    authors: Meng F,Zhou M,Xiao Y,Mao X,Zheng J,Lin J,Lin T,Ye Z,Cang X,Fu Y,Wang M,Guan MX

    更新日期:2021-01-25 00:00:00

  • End-bridging is required for pol mu to efficiently promote repair of noncomplementary ends by nonhomologous end joining.

    abstract::DNA polymerase mu is a member of the mammalian pol X family and reduces deletion during chromosome break repair by nonhomologous end joining (NHEJ). This biological role is linked to pol mu's ability to promote NHEJ of ends with noncomplementary 3' overhangs, but questions remain regarding how it performs this role. W...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn164

    authors: Davis BJ,Havener JM,Ramsden DA

    更新日期:2008-05-01 00:00:00

  • Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts.

    abstract::The abundance of Alu RNA is transiently increased by heat shock in human cell lines. This effect is specific to Alu repeats among Pol III transcribed genes, since the abundance of 7SL, 7SK, 5S and U6 RNAs is essentially unaffected by heat shock. The rapid induction of Alu expression precedes the heat shock induction o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.10.1758

    authors: Liu WM,Chu WM,Choudary PV,Schmid CW

    更新日期:1995-05-25 00:00:00

  • Structural characterization of a ribonuclease III processing signal.

    abstract::The structure of a ribonuclease III processing signal from bacteriophage T7 was examined by NMR spectroscopy, optical melting, and chemical and enzymatic modification. A 41 nucleotide variant of the T7 R1.1 processing signal has two Watson-Crick base-paired helices separated by an internal loop, consistent with its pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.4.604

    authors: Schweisguth DC,Chelladurai BS,Nicholson AW,Moore PB

    更新日期:1994-02-25 00:00:00

  • The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.

    abstract::This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene e...

    journal_title:Nucleic acids research

    pub_type:

    doi:10.1093/nar/gkw1188

    authors: Galperin MY,Fernández-Suárez XM,Rigden DJ

    更新日期:2017-01-04 00:00:00

  • scIGANs: single-cell RNA-seq imputation using generative adversarial networks.

    abstract::Single-cell RNA-sequencing (scRNA-seq) enables the characterization of transcriptomic profiles at the single-cell resolution with increasingly high throughput. However, it suffers from many sources of technical noises, including insufficient mRNA molecules that lead to excess false zero values, termed dropouts. Comput...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa506

    authors: Xu Y,Zhang Z,You L,Liu J,Fan Z,Zhou X

    更新日期:2020-09-04 00:00:00

  • Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study.

    abstract::Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1003

    authors: Moradi M,Babin V,Roland C,Sagui C

    更新日期:2013-01-07 00:00:00

  • BCNTB bioinformatics: the next evolutionary step in the bioinformatics of breast cancer tissue banking.

    abstract::Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to que...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx913

    authors: Gadaleta E,Pirrò S,Dayem Ullah AZ,Marzec J,Chelala C

    更新日期:2018-01-04 00:00:00

  • Lack of a requirement for strict rotational alignment among transcription factor binding sites in yeast.

    abstract::The MF alpha 1 gene of Saccharomyces cerevisiae is an alpha specific gene whose expression is regulated by two upstream activation sites (UASMF alpha 1S), which are the binding sites for activator proteins, MAT alpha 1 and MCM1. UASMF alpha 1 elements act in a synergistic fashion; lack of either element causes reduced...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.11.3099

    authors: Inokuchi K,Nakayama A

    更新日期:1991-06-11 00:00:00

  • Efficient large-scale purification of restriction fragments by solute-displacement ion-exchange HPLC.

    abstract::Extreme overloading of HPLC columns with sample can create a condition of binding site saturation causing competition and displacement among solutes during column elution. This has been termed solute-displacement chromatography (SD-HPLC). We present an example of this phenomenon for the preparative fractionation and p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.12.2913

    authors: Waterborg JH,Robertson AJ

    更新日期:1993-06-25 00:00:00

  • Interactions between avian myeloblastosis reverse transcriptase and tRNATrp. Mapping of complexed tRNA with chemicals and nucleases.

    abstract::The interactions between beef tRNATrp with avian myeloblastosis reverse transcriptase have been studied by statistical chemical modifications of phosphate (ethylnitrosourea) and cytidine (dimethyl sulfate) residues, as well as by digestion of complexed tRNA by Cobra venom nuclease and Neurospora crassa endonuclease. R...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.5.2259

    authors: Garret M,Romby P,Giegé R,Litvak S

    更新日期:1984-03-12 00:00:00

  • Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases.

    abstract::The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to g...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki317

    authors: Mignon P,Loverix S,Steyaert J,Geerlings P

    更新日期:2005-03-23 00:00:00

  • Intracellular receptor-type transcription factor, LasR, contains a highly conserved amphipathic region which precedes the putative helix-turn-helix DNA binding motif.

    abstract::We have cloned and sequenced the lasR gene, which is involved in the transcriptional activation of several pathogenic factors, from Pseudomonas aeruginosa IFO3455 and PA103. These clones were predicted to be an open reading frame of 239 amino acids as reported for the PAO1 strain. There is only a single base change re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.18.3706

    authors: Fukushima J,Ishiwata T,Kurata M,You Z,Okuda K

    更新日期:1994-09-11 00:00:00

  • A model for the study of ligand binding to the ribosomal RNA helix h44.

    abstract::Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation. Techniques such as selective chemical modification, fluorescence labeling and mutations are cumbersome for the whole ribosome but readily applicabl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq159

    authors: Dibrov SM,Parsons J,Hermann T

    更新日期:2010-07-01 00:00:00

  • Hydration of single-stranded phosphodiester and phosphorothioate oligodeoxyribonucleotides.

    abstract::Infrared spectroscopy was used to identify hydration-sensitive structural differences between single- stranded phosphorothioate (PS) and phosphodiester (PO) oligodeoxyribonucleotides. Spectra were recorded in the mid-infrared region, 500-1800 cm-1, at relative humidities between 0 and 98%; the PS and PO spectra are su...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.16.3261

    authors: White AP,Reeves KK,Snyder E,Farrell J,Powell JW,Mohan V,Griffey RH

    更新日期:1996-08-15 00:00:00

  • Phosphorylated (pT371)TRF1 is recruited to sites of DNA damage to facilitate homologous recombination and checkpoint activation.

    abstract::TRF1, a duplex telomeric DNA-binding protein, plays an important role in telomere metabolism. We have previously reported that a fraction of endogenous TRF1 can stably exist free of telomere chromatin when it is phosphorylated at T371 by Cdk1; however, the role of this telomere-free (pT371)TRF1 has yet to be fully cha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt775

    authors: McKerlie M,Walker JR,Mitchell TR,Wilson FR,Zhu XD

    更新日期:2013-12-01 00:00:00

  • miROrtho: computational survey of microRNA genes.

    abstract::MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally val...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn707

    authors: Gerlach D,Kriventseva EV,Rahman N,Vejnar CE,Zdobnov EM

    更新日期:2009-01-01 00:00:00

  • Rapid synthesis of oligodeoxyribonucleotides. IV. Improved solid phase synthesis of oligodeoxyribonucleotides through phosphotriester intermediates.

    abstract::A phosphotriester solid phase method on a polyamide support has been used to prepare oligodeoxyribonucleotides up to 12 units long. Compared to solid phase phosphodiester synthesis the new methodology is quicker, more flexible and gives 10-60-fold better overall yields. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.5.1081

    authors: Gait MJ,Singh M,Sheppard RC,Edge MD,Greene AR,Heathcliffe GR,Atkinson TC,Newton CR,Markham AF

    更新日期:1980-03-11 00:00:00