Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors.

Abstract:

BACKGROUND:Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence elements, transiently associating with the primary transcript during splicing. Some protein splicing factors, such as the U2 small nuclear RNP auxiliary factor (U2AF), are known to be exported to the cytoplasm, despite being implicated solely in nuclear functions. This observation raises the question of whether U2AF associates with mature mRNA-ribonucleoprotein particles in transit to the cytoplasm, participating in additional cellular functions. RESULTS:Here we report the identification of RNAs immunoprecipitated by a monoclonal antibody specific for the U2AF 65 kDa subunit (U2AF65) and demonstrate its association with spliced mRNAs. For comparison, we analyzed mRNAs associated with the polypyrimidine tract binding protein (PTB), a splicing factor that also binds to intronic pyrimidine-rich sequences but additionally participates in mRNA localization, stability, and translation. Our results show that 10% of cellular mRNAs expressed in HeLa cells associate differentially with U2AF65 and PTB. Among U2AF65-associated mRNAs there is a predominance of transcription factors and cell cycle regulators, whereas PTB-associated transcripts are enriched in mRNA species that encode proteins implicated in intracellular transport, vesicle trafficking, and apoptosis. CONCLUSION:Our results show that U2AF65 associates with specific subsets of spliced mRNAs, strongly suggesting that it is involved in novel cellular functions in addition to splicing.

journal_name

Genome Biol

journal_title

Genome biology

authors

Gama-Carvalho M,Barbosa-Morais NL,Brodsky AS,Silver PA,Carmo-Fonseca M

doi

10.1186/gb-2006-7-11-r113

subject

Has Abstract

pub_date

2006-01-01 00:00:00

pages

R113

issue

11

eissn

1474-7596

issn

1474-760X

pii

gb-2006-7-11-r113

journal_volume

7

pub_type

杂志文章
  • Wrangling for microRNAs provokes much crosstalk.

    abstract::Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-11-132

    authors: Marques AC,Tan J,Ponting CP

    更新日期:2011-11-21 00:00:00

  • Supervised harvesting of expression trees.

    abstract:BACKGROUND:We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models the outcome variable as a sum of the average expression profiles of chosen clusters and their products. It can be applied to many...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2001-2-1-research0003

    authors: Hastie T,Tibshirani R,Botstein D,Brown P

    更新日期:2001-01-01 00:00:00

  • Proteomic view of mitochondrial function.

    abstract::Genomic and proteomic studies have identified hundreds of proteins from mitochondria. A recent study has added a functional twist to these systematic approaches and identified novel mitochondrial modifiers and regulators. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2008-9-2-209

    authors: Dimmer KS,Rapaport D

    更新日期:2008-01-01 00:00:00

  • The amazing world of bacterial structured RNAs.

    abstract::The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2010-11-3-108

    authors: Westhof E

    更新日期:2010-01-01 00:00:00

  • The phytochrome red/far-red photoreceptor superfamily.

    abstract::Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output signaling mechanisms. Over the past few years the first three-dimensional structures of phytochrome light-sensi...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2008-9-8-230

    authors: Sharrock RA

    更新日期:2008-01-01 00:00:00

  • An integrated computational pipeline and database to support whole-genome sequence annotation.

    abstract::We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2002-3-12-research0081

    authors: Mungall CJ,Misra S,Berman BP,Carlson J,Frise E,Harris N,Marshall B,Shu S,Kaminker JS,Prochnik SE,Smith CD,Smith E,Tupy JL,Wiel C,Rubin GM,Lewis SE

    更新日期:2002-01-01 00:00:00

  • Impact of transposable elements on genome structure and evolution in bread wheat.

    abstract:BACKGROUND:Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1479-0

    authors: Wicker T,Gundlach H,Spannagl M,Uauy C,Borrill P,Ramírez-González RH,De Oliveira R,International Wheat Genome Sequencing Consortium.,Mayer KFX,Paux E,Choulet F

    更新日期:2018-08-17 00:00:00

  • Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera.

    abstract:BACKGROUND:Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequenc...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-12-r127

    authors: Mendum TA,Newcombe J,Mannan AA,Kierzek AM,McFadden J

    更新日期:2011-12-30 00:00:00

  • xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features.

    abstract::The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2006-7-11-r111

    authors: Schlueter SD,Wilkerson MD,Dong Q,Brendel V

    更新日期:2006-01-01 00:00:00

  • Decontamination of ambient RNA in single-cell RNA-seq with DecontX.

    abstract::Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a n...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-1950-6

    authors: Yang S,Corbett SE,Koga Y,Wang Z,Johnson WE,Yajima M,Campbell JD

    更新日期:2020-03-05 00:00:00

  • Localizing the proteome.

    abstract::The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae, has been revealed for the first time. Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2003-4-12-240

    authors: Simpson JC,Pepperkok R

    更新日期:2003-01-01 00:00:00

  • The WUS homeobox-containing (WOX) protein family.

    abstract::The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental proc...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2009-10-12-248

    authors: van der Graaff E,Laux T,Rensing SA

    更新日期:2009-01-01 00:00:00

  • Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.

    abstract:BACKGROUND:Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has b...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-12-r125

    authors: Gordân R,Murphy KF,McCord RP,Zhu C,Vedenko A,Bulyk ML

    更新日期:2011-12-21 00:00:00

  • Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum.

    abstract:BACKGROUND:In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and transla...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2013-14-11-r128

    authors: Bunnik EM,Chung DW,Hamilton M,Ponts N,Saraf A,Prudhomme J,Florens L,Le Roch KG

    更新日期:2013-11-22 00:00:00

  • A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems.

    abstract:BACKGROUND:We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. RESULTS:We outline here a conceptual basis for designing such a language and describe Bio...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2001-2-4-research0012

    authors: Cook DL,Farley JF,Tapscott SJ

    更新日期:2001-01-01 00:00:00

  • EMu: probabilistic inference of mutational processes and their localization in the cancer genome.

    abstract::The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific oppo...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2013-14-4-r39

    authors: Fischer A,Illingworth CJ,Campbell PJ,Mustonen V

    更新日期:2013-04-29 00:00:00

  • Quantification of cell identity from single-cell gene expression profiles.

    abstract::The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify ide...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0580-x

    authors: Efroni I,Ip PL,Nawy T,Mello A,Birnbaum KD

    更新日期:2015-01-22 00:00:00

  • Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing.

    abstract:BACKGROUND:Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases an...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-017-1147-9

    authors: Jansen IE,Ye H,Heetveld S,Lechler MC,Michels H,Seinstra RI,Lubbe SJ,Drouet V,Lesage S,Majounie E,Gibbs JR,Nalls MA,Ryten M,Botia JA,Vandrovcova J,Simon-Sanchez J,Castillo-Lizardo M,Rizzu P,Blauwendraat C,Chouhan AK

    更新日期:2017-01-30 00:00:00

  • The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells.

    abstract:BACKGROUND:The time of locus replication during S-phase is tightly regulated and correlates with chromatin state. Embryonic stem (ES) cells have an unusual chromatin profile where many developmental regulator genes that are not yet expressed are marked by both active and repressive histone modifications. This poised or...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-8-r169

    authors: Jørgensen HF,Azuara V,Amoils S,Spivakov M,Terry A,Nesterova T,Cobb BS,Ramsahoye B,Merkenschlager M,Fisher AG

    更新日期:2007-01-01 00:00:00

  • The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication.

    abstract:BACKGROUND:A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02131-y

    authors: Badouin H,Velt A,Gindraud F,Flutre T,Dumas V,Vautrin S,Marande W,Corbi J,Sallet E,Ganofsky J,Santoni S,Guyot D,Ricciardelli E,Jepsen K,Käfer J,Berges H,Duchêne E,Picard F,Hugueney P,Tavares R,Bacilieri R,Rustenh

    更新日期:2020-09-07 00:00:00

  • Mutational signature distribution varies with DNA replication timing and strand asymmetry.

    abstract:BACKGROUND:DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1509-y

    authors: Tomkova M,Tomek J,Kriaucionis S,Schuster-Böckler B

    更新日期:2018-09-10 00:00:00

  • Wheat functional genomics and engineering crop improvement.

    abstract::Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2002-3-5-reviews1013

    authors: Francki M,Appels R

    更新日期:2002-01-01 00:00:00

  • A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.

    abstract:BACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes becau...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-5-r48

    authors: Zuccolo A,Bowers JE,Estill JC,Xiong Z,Luo M,Sebastian A,Goicoechea JL,Collura K,Yu Y,Jiao Y,Duarte J,Tang H,Ayyampalayam S,Rounsley S,Kudrna D,Paterson AH,Pires JC,Chanderbali A,Soltis DE,Chamala S,Barbazuk B,So

    更新日期:2011-01-01 00:00:00

  • Chemical genomics in yeast.

    abstract::Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2004-5-9-240

    authors: Brenner C

    更新日期:2004-01-01 00:00:00

  • The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading.

    abstract:BACKGROUND:The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities,...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-017-1321-0

    authors: Tarallo R,Giurato G,Bruno G,Ravo M,Rizzo F,Salvati A,Ricciardi L,Marchese G,Cordella A,Rocco T,Gigantino V,Pierri B,Cimmino G,Milanesi L,Ambrosino C,Nyman TA,Nassa G,Weisz A

    更新日期:2017-10-06 00:00:00

  • Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients.

    abstract:BACKGROUND:Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 ben...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-014-0568-y

    authors: Lim EL,Trinh DL,Scott DW,Chu A,Krzywinski M,Zhao Y,Robertson AG,Mungall AJ,Schein J,Boyle M,Mottok A,Ennishi D,Johnson NA,Steidl C,Connors JM,Morin RD,Gascoyne RD,Marra MA

    更新日期:2015-01-29 00:00:00

  • Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.

    abstract::Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. Based on this, we introduce a new computational strategy...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-2-r23

    authors: Moses AM,Hériché JK,Durbin R

    更新日期:2007-01-01 00:00:00

  • A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development.

    abstract:BACKGROUND:Some years ago we established an N-ethyl-N-nitrosourea screen for modifiers of transgene variegation in the mouse and a preliminary description of the first six mutant lines, named MommeD1-D6, has been published. We have reported the underlying genes in three cases: MommeD1 is a mutation in SMC hinge domain ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-12-r182

    authors: Ashe A,Morgan DK,Whitelaw NC,Bruxner TJ,Vickaryous NK,Cox LL,Butterfield NC,Wicking C,Blewitt ME,Wilkins SJ,Anderson GJ,Cox TC,Whitelaw E

    更新日期:2008-01-01 00:00:00

  • From biological clock to biological rhythms.

    abstract::The genetic and molecular analysis of circadian timekeeping mechanisms has accelerated as a result of the increasing volume of genomic markers and nucleotide sequence information. Completion of whole genome sequences and the use of differential gene expression technology will hasten the discovery of the clock output p...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2000-1-4-reviews1023

    authors: Hardin PE

    更新日期:2000-01-01 00:00:00

  • Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi.

    abstract::Short hairpin RNAs can provide stable gene silencing via RNA interference. Recent studies have shown toxicity in vivo that appears to be related to saturation of the endogenous microRNA pathway. Will these findings limit the therapeutic use of such hairpins? ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2006-7-8-231

    authors: Snøve O Jr,Rossi JJ

    更新日期:2006-01-01 00:00:00