Systematic discovery of structural elements governing stability of mammalian messenger RNAs.

PubWeight™: 1.80‹?› | Rank: Top 3%

🔗 View Article (PMC 3350620)

Published in Nature on April 08, 2012

Authors

Hani Goodarzi1, Hamed S Najafabadi, Panos Oikonomou, Todd M Greco, Lisa Fish, Reza Salavati, Ileana M Cristea, Saeed Tavazoie

Author Affiliations

1: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA.

Articles citing this

A compendium of RNA-binding motifs for decoding gene regulation. Nature (2013) 4.91

Equitability, mutual information, and the maximal information coefficient. Proc Natl Acad Sci U S A (2014) 2.59

RNA SHAPE analysis in living cells. Nat Chem Biol (2012) 2.02

Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature (2014) 1.73

Massively parallel functional annotation of 3' untranslated regions. Nat Biotechnol (2014) 1.61

HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events. Cell (2015) 1.34

Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome. Plant Cell (2012) 1.29

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res (2013) 1.10

Developing mRNA-vaccine technologies. RNA Biol (2012) 1.04

Frac-seq reveals isoform-specific recruitment to polyribosomes. Genome Res (2013) 1.01

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. Mol Syst Biol (2014) 1.01

Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA (2013) 0.99

High-throughput characterization of protein-RNA interactions. Brief Funct Genomics (2014) 0.95

All's well that ends well: alternative polyadenylation and its implications for stem cell biology. Curr Opin Cell Biol (2013) 0.91

RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay. RNA (2012) 0.90

Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts. Cell Rep (2014) 0.90

The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming. Curr Top Dev Biol (2015) 0.89

Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface. Cell Rep (2013) 0.88

Posttranscriptional regulation of gene expression-adding another layer of complexity to the DNA damage response. Front Genet (2012) 0.87

Systematic analysis of the Hmga2 3' UTR identifies many independent regulatory sequences and a novel interaction between distal sites. RNA (2015) 0.86

Global identification of conserved post-transcriptional regulatory programs in trypanosomatids. Nucleic Acids Res (2013) 0.85

Genome-wide analysis of 3'-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes. PeerJ (2013) 0.85

Arabidopsis mRNA secondary structure correlates with protein function and domains. Plant Signal Behav (2013) 0.84

Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. Plant Sci (2013) 0.84

Proteomic analysis of high NaCl-induced changes in abundance of nuclear proteins. Physiol Genomics (2012) 0.84

Suppression of HPV-16 late L1 5'-splice site SD3632 by binding of hnRNP D proteins and hnRNP A2/B1 to upstream AUAGUA RNA motifs. Nucleic Acids Res (2013) 0.83

LincRNA-Cox2 modulates TNF-α-induced transcription of Il12b gene in intestinal epithelial cells through regulation of Mi-2/NuRD-mediated epigenetic histone modifications. FASEB J (2015) 0.82

Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput. Wiley Interdiscip Rev RNA (2014) 0.81

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress. RNA Biol (2014) 0.81

Maize transformation technology development for commercial event generation. Front Plant Sci (2014) 0.80

An Untranslated cis-Element Regulates the Accumulation of Multiple C4 Enzymes in Gynandropsis gynandra Mesophyll Cells. Plant Cell (2016) 0.79

LincRNA-Cox2 Promotes Late Inflammatory Gene Transcription in Macrophages through Modulating SWI/SNF-Mediated Chromatin Remodeling. J Immunol (2016) 0.79

Dynamic regulation of mRNA decay during neural development. Neural Dev (2015) 0.79

Transcriptome-wide measurement of plant RNA secondary structure. Curr Opin Plant Biol (2015) 0.78

Shutdown of achaete-scute homolog-1 expression by heterogeneous nuclear ribonucleoprotein (hnRNP)-A2/B1 in hypoxia. J Biol Chem (2014) 0.78

Number variation of high stability regions is correlated with gene functions. Genome Biol Evol (2013) 0.78

Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes. Nucleic Acids Res (2012) 0.78

Deciphering RNA Regulatory Elements Involved in the Developmental and Environmental Gene Regulation of Trypanosoma brucei. PLoS One (2015) 0.76

Galectin-3 interacts with components of the nuclear ribonucleoprotein complex. BMC Cancer (2016) 0.76

Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models. Nucleic Acids Res (2014) 0.76

A novel heat shock protein alpha 8 (Hspa8) molecular network mediating responses to stress- and ethanol-related behaviors. Neurogenetics (2016) 0.76

A widespread sequence-specific mRNA decay pathway mediated by hnRNPs A1 and A2/B1. Genes Dev (2016) 0.75

The Conservation and Function of RNA Secondary Structure in Plants. Annu Rev Plant Biol (2016) 0.75

Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence. BMC Genomics (2017) 0.75

TARBP2 binding structured RNA elements drives metastasis. Cell Cycle (2014) 0.75

An RNA matchmaker protein regulates the activity of the long noncoding RNA HOTAIR. RNA (2016) 0.75

A position-specific 3'UTR sequence that accelerates mRNA decay. RNA Biol (2016) 0.75

Regulatory elements in molecular networks. Wiley Interdiscip Rev Syst Biol Med (2017) 0.75

Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts. PLoS One (2013) 0.75

Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome). RNA Biol (2015) 0.75

Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe. BMC Genomics (2016) 0.75

DynaMIT: the dynamic motif integration toolkit. Nucleic Acids Res (2015) 0.75

Impact of RNA structure on ZFP36L2 interaction with Luteinizing Hormone Receptor mRNA. RNA (2017) 0.75

The identification and functional annotation of RNA structures conserved in vertebrates. Genome Res (2017) 0.75

Genetic mutations in RNA-binding proteins and their roles in ALS. Hum Genet (2017) 0.75

Articles cited by this

Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet (2000) 24.22

Global quantification of mammalian gene expression control. Nature (2011) 22.36

Universal sample preparation method for proteome analysis. Nat Methods (2009) 16.88

HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature (2009) 14.07

Secondary structure prediction for aligned RNA sequences. J Mol Biol (2002) 8.80

Predicting gene expression from sequence. Cell (2004) 8.12

The cap-to-tail guide to mRNA turnover. Nat Rev Mol Cell Biol (2001) 6.67

Deciphering the splicing code. Nature (2010) 6.27

Genome-wide measurement of RNA secondary structure in yeast. Nature (2010) 5.74

A universal framework for regulatory element discovery across all genomes and data types. Mol Cell (2007) 4.50

RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc (2006) 4.28

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA (2008) 3.13

Revealing global regulatory perturbations across human cancers. Mol Cell (2009) 2.62

Understanding the transcriptome through RNA structure. Nat Rev Genet (2011) 2.46

Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis. Nat Struct Mol Biol (2010) 2.30

An integrated ChIP-seq analysis platform with customizable workflows. BMC Bioinformatics (2011) 1.92

CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. Methods Mol Biol (2008) 1.79

The language of genes. Nature (2002) 1.59

Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation. Mol Cell Proteomics (2010) 1.52

Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes. Proc Natl Acad Sci U S A (2008) 1.51

RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences. Nucleic Acids Res (2004) 1.38

RNA secondary structure in mutually exclusive splicing. Nat Struct Mol Biol (2011) 1.18

Isolation of specific RNA-binding proteins using the streptomycin-binding RNA aptamer. Nat Protoc (2006) 1.07

Two homologous genes, originated by duplication, encode the human hnRNP proteins A2 and A1. Nucleic Acids Res (1994) 1.07

Silencing or knocking out eukaryotic gene expression by oligodeoxynucleotide decoys. Crit Rev Eukaryot Gene Expr (2006) 0.96

Articles by these authors

Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell (2010) 8.79

Predicting gene expression from sequence. Cell (2004) 8.12

Mapping global histone acetylation patterns to gene expression. Cell (2004) 5.57

A compendium of RNA-binding motifs for decoding gene regulation. Nature (2013) 4.91

A universal framework for regulatory element discovery across all genomes and data types. Mol Cell (2007) 4.50

Predictive behavior within microbial genetic networks. Science (2008) 4.48

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods (2013) 4.34

Hypoglycemia and diabetes: a report of a workgroup of the American Diabetes Association and the Endocrine Society. Diabetes Care (2013) 3.89

Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol (2007) 3.53

Induction of autophagy in axonal dystrophy and degeneration. J Neurosci (2006) 3.28

Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat Genet (2002) 3.18

DJ-1 gene deletion reveals that DJ-1 is an atypical peroxiredoxin-like peroxidase. Proc Natl Acad Sci U S A (2007) 2.87

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol (2005) 2.82

Revealing global regulatory perturbations across human cancers. Mol Cell (2009) 2.62

Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome Res (2003) 2.54

A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics (2011) 2.34

A comprehensive genetic characterization of bacterial motility. PLoS Genet (2007) 2.33

Identification of novel components of Trypanosoma brucei editosomes. RNA (2003) 2.30

Protein occupancy landscape of a bacterial genome. Mol Cell (2009) 2.24

Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol (2005) 2.04

Bacterial adaptation through loss of function. PLoS Genet (2013) 1.99

Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex. Mol Cell (2003) 1.94

A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep (2013) 1.92

Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16. Proc Natl Acad Sci U S A (2012) 1.88

TbMP57 is a 3' terminal uridylyl transferase (TUTase) of the Trypanosoma brucei editosome. Mol Cell (2003) 1.88

Structural profiling of endogenous S-nitrosocysteine residues reveals unique features that accommodate diverse mechanisms for protein S-nitrosylation. Proc Natl Acad Sci U S A (2010) 1.87

Compositionally and functionally distinct editosomes in Trypanosoma brucei. RNA (2006) 1.86

Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex. Cell Host Microbe (2008) 1.85

Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. PLoS Biol (2004) 1.76

High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. J Mol Biol (2004) 1.67

let-7 Overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts. J Biol Chem (2009) 1.65

TbMP81 is required for RNA editing in Trypanosoma brucei. EMBO J (2002) 1.65

Cell-cycle-dependent phosphorylation of the nuclear pore Nup107-160 subcomplex. Proc Natl Acad Sci U S A (2007) 1.64

The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol (2013) 1.63

Genetic architecture of intrinsic antibiotic susceptibility. PLoS One (2009) 1.61

Increased expression of LDL receptor-related protein 1 during human cytomegalovirus infection reduces virion cholesterol and infectivity. Cell Host Microbe (2012) 1.59

Fitness landscape transformation through a single amino acid change in the rho terminator. PLoS Genet (2012) 1.59

Role of uridylate-specific exoribonuclease activity in Trypanosoma brucei RNA editing. Eukaryot Cell (2002) 1.55

Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation. Mol Cell Proteomics (2010) 1.52

Comparative analysis of editosome proteins in trypanosomatids. Nucleic Acids Res (2003) 1.52

Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics (2012) 1.49

Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol (2006) 1.49

A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation. Mol Cell Proteomics (2009) 1.48

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol (2010) 1.47

Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion. Cell Host Microbe (2013) 1.44

Evidence for a genetic and physical interaction between nonstructural proteins NS1 and NS4B that modulates replication of West Nile virus. J Virol (2012) 1.43

Immunoglobulins against tyrosine-nitrated epitopes in coronary artery disease. Circulation (2012) 1.42

TbMP44 is essential for RNA editing and structural integrity of the editosome in Trypanosoma brucei. Eukaryot Cell (2003) 1.39

Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis. Development (2011) 1.36

Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition. Development (2009) 1.34

Identification of staphylococcal nuclease domain-containing 1 (SND1) as a Metadherin-interacting protein with metastasis-promoting functions. J Biol Chem (2011) 1.33

The clinical endocrinology workforce: current status and future projections of supply and demand. J Clin Endocrinol Metab (2014) 1.30

Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene. Nucleic Acids Res (2003) 1.29

DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase. Genes Dev (2012) 1.28

The free and bound forms of Lpp occupy distinct subcellular locations in Escherichia coli. Mol Microbiol (2011) 1.27

A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res (2004) 1.23

Global discovery of adaptive mutations. Nat Methods (2009) 1.23

Resolving the composition of protein complexes using a MALDI LTQ Orbitrap. J Am Soc Mass Spectrom (2009) 1.20

Co-compartmentalization of the astroglial glutamate transporter, GLT-1, with glycolytic enzymes and mitochondria. J Neurosci (2011) 1.18

Mass spectrometric and computational analysis of cytokine-induced alterations in the astrocyte secretome. Proteomics (2009) 1.17

Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA. PLoS Pathog (2010) 1.16

Kinesin-3 mediates axonal sorting and directional transport of alphaherpesvirus particles in neurons. Cell Host Microbe (2012) 1.14

Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. J Bacteriol (2011) 1.13

Mechanism of Mediator recruitment by tandem Gcn4 activation domains and three Gal11 activator-binding domains. Mol Cell Biol (2010) 1.12

Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS One (2010) 1.11

Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse. PLoS Biol (2009) 1.11

Conjugation of magnetic beads for immunopurification of protein complexes. Cold Spring Harb Protoc (2011) 1.10

Hypoglycemia and diabetes: a report of a workgroup of the American Diabetes Association and the Endocrine Society. J Clin Endocrinol Metab (2013) 1.08

Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol (2008) 1.08

Sirtuin 7 plays a role in ribosome biogenesis and protein synthesis. Mol Cell Proteomics (2013) 1.08

Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics (2011) 1.07

Affinity purification of protein complexes. Cold Spring Harb Protoc (2011) 1.06

The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome. Mol Biol Cell (2013) 1.06

Kinetoplastid RNA editing ligases: complex association, characterization, and substrate requirements. Mol Biochem Parasitol (2003) 1.05

Global analysis of Cdc14 phosphatase reveals diverse roles in mitotic processes. J Biol Chem (2010) 1.04

Large mutational target size for rapid emergence of bacterial persistence. Proc Natl Acad Sci U S A (2012) 1.03

Glycoproteins gE and gI are required for efficient KIF1A-dependent anterograde axonal transport of alphaherpesvirus particles in neurons. J Virol (2013) 1.03

Universal function-specificity of codon usage. Nucleic Acids Res (2009) 1.02

Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E. coli. PLoS Pathog (2009) 1.02

The response regulator SprE (RssB) is required for maintaining poly(A) polymerase I-degradosome association during stationary phase. J Bacteriol (2010) 1.01

Mechanistic investigations of the pseudouridine synthase RluA using RNA containing 5-fluorouridine. Biochemistry (2006) 1.01

Dyskinetoplastic Trypanosoma brucei contains functional editing complexes. Eukaryot Cell (2003) 0.99

Tcf21 regulates the specification and maturation of proepicardial cells. Development (2013) 0.98

Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem (2012) 0.98

Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions. PLoS Genet (2009) 0.98

Cytochrome c oxidase subunit 1 and 12S ribosomal RNA characterization of Coenurus cerebralis from sheep in Iran. Vet Parasitol (2013) 0.97

Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway. Mol Cell Biol (2006) 0.97

Proteomic profiling of cardiac tissue by isolation of nuclei tagged in specific cell types (INTACT). Development (2014) 0.92

Guanidination chemistry for qualitative and quantitative proteomics. Rapid Commun Mass Spectrom (2006) 0.91

Noise underlies switching behavior of the bacterial flagellum. Biophys J (2011) 0.91

Aurora B-dependent regulation of class IIa histone deacetylases by mitotic nuclear localization signal phosphorylation. Mol Cell Proteomics (2012) 0.91