Nova regulates brain-specific splicing to shape the synapse.

PubWeight™: 6.58‹?› | Rank: Top 1%

🔗 View Article (PMID 16041372)

Published in Nat Genet on July 24, 2005

Authors

Jernej Ule1, Aljaz Ule, Joanna Spencer, Alan Williams, Jing-Shan Hu, Melissa Cline, Hui Wang, Tyson Clark, Claire Fraser, Matteo Ruggiu, Barry R Zeeberg, David Kane, John N Weinstein, John Blume, Robert B Darnell

Author Affiliations

1: Howard Hughes Medical Institute and Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York, USA.

Articles citing this

(truncated to the top 100)

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

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res (2010) 9.80

Repeatability of published microarray gene expression analyses. Nat Genet (2008) 8.24

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol (2009) 7.11

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol (2010) 5.98

A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev (2007) 5.83

Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics (2006) 5.59

Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol (2007) 5.53

RNA processing and its regulation: global insights into biological networks. Nat Rev Genet (2010) 5.34

ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Mol Cell (2009) 5.03

Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev (2007) 4.75

Epigenetics in alternative pre-mRNA splicing. Cell (2011) 4.74

SMN deficiency causes tissue-specific perturbations in the repertoire of snRNAs and widespread defects in splicing. Cell (2008) 4.54

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol (2008) 4.34

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev (2008) 4.24

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet (2008) 3.78

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res (2008) 3.33

Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet (2011) 3.27

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res (2006) 3.23

Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol Cell (2007) 3.22

Heritability of alternative splicing in the human genome. Genome Res (2007) 2.76

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat Struct Mol Biol (2011) 2.73

Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science (2010) 2.69

Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. PLoS Genet (2007) 2.60

HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA (2010) 2.59

The pathobiology of splicing. J Pathol (2010) 2.52

Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis. RNA (2007) 2.48

Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB. Nat Struct Mol Biol (2010) 2.19

Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet (2014) 2.17

Understanding splicing regulation through RNA splicing maps. Trends Genet (2011) 2.12

Global analysis of alternative splicing during T-cell activation. RNA (2007) 2.11

The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet (2011) 2.10

Nova2 regulates neuronal migration through an RNA switch in disabled-1 signaling. Neuron (2010) 2.08

Stochastic noise in splicing machinery. Nucleic Acids Res (2009) 2.06

Nova2 interacts with a cis-acting polymorphism to influence the proportions of drug-responsive splice variants of SCN1A. Am J Hum Genet (2007) 2.04

Subcellular profiling reveals distinct and developmentally regulated repertoire of growth cone mRNAs. J Neurosci (2010) 2.02

MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res (2010) 1.94

A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res (2007) 1.94

Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Proc Natl Acad Sci U S A (2010) 1.93

Systems biology of innate immunity. Immunol Rev (2009) 1.87

Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet (2012) 1.82

Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biol (2007) 1.80

Multiple and specific mRNA processing targets for the major human hnRNP proteins. Mol Cell Biol (2008) 1.78

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep (2014) 1.78

Global analysis of mRNA splicing. RNA (2007) 1.77

The expanding transcriptome: the genome as the 'Book of Sand'. EMBO J (2006) 1.73

Alternative polyadenylation: new insights from global analyses. RNA (2012) 1.72

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev (2012) 1.70

The Fox-1 family and SUP-12 coordinately regulate tissue-specific alternative splicing in vivo. Mol Cell Biol (2007) 1.67

HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Res (2006) 1.66

Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder. Nat Genet (2011) 1.63

Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci U S A (2011) 1.62

Identification of RNA-protein interaction networks using PAR-CLIP. Wiley Interdiscip Rev RNA (2011) 1.61

SAM68 regulates neuronal activity-dependent alternative splicing of neurexin-1. Cell (2011) 1.60

Tissue effect on genetic control of transcript isoform variation. PLoS Genet (2009) 1.59

The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. RNA Biol (2009) 1.57

Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Sci Rep (2012) 1.54

Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF. PLoS One (2008) 1.51

A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell (2014) 1.50

Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. PLoS Biol (2007) 1.49

The splicing regulator Rbfox2 is required for both cerebellar development and mature motor function. Genes Dev (2012) 1.48

A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res (2008) 1.44

Exon silencing by UAGG motifs in response to neuronal excitation. PLoS Biol (2007) 1.43

The function of introns. Front Genet (2012) 1.42

SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics (2011) 1.42

OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Res (2013) 1.41

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc (2014) 1.41

Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics (2006) 1.39

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res (2011) 1.35

Exon expression profiling reveals stimulus-mediated exon use in neural cells. Genome Biol (2007) 1.35

Identification of RNA-binding proteins that regulate FGFR2 splicing through the use of sensitive and specific dual color fluorescence minigene assays. RNA (2006) 1.35

A nuclear function of Hu proteins as neuron-specific alternative RNA processing regulators. Mol Biol Cell (2006) 1.31

RNA protein interaction in neurons. Annu Rev Neurosci (2013) 1.31

Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability. Neuron (2012) 1.27

Rescuing Z+ agrin splicing in Nova null mice restores synapse formation and unmasks a physiologic defect in motor neuron firing. Proc Natl Acad Sci U S A (2009) 1.27

Regulation of neuron-specific alternative splicing of neurofibromatosis type 1 pre-mRNA. Mol Cell Biol (2007) 1.27

Identification of a set of KSRP target transcripts upregulated by PI3K-AKT signaling. BMC Mol Biol (2007) 1.23

Widespread splicing changes in human brain development and aging. Mol Syst Biol (2013) 1.23

Evolution of Nova-dependent splicing regulation in the brain. PLoS Genet (2007) 1.23

Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PLoS Comput Biol (2014) 1.15

Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts. RNA (2011) 1.14

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Brief Funct Genomics (2010) 1.14

Complex changes in alternative pre-mRNA splicing play a central role in the epithelial-to-mesenchymal transition (EMT). Semin Cancer Biol (2012) 1.13

Rbfox3-regulated alternative splicing of Numb promotes neuronal differentiation during development. J Cell Biol (2013) 1.13

Building robust transcriptomes with master splicing factors. Cell (2014) 1.12

The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet (2014) 1.11

Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer. Elife (2014) 1.06

Splicing programs and cancer. J Nucleic Acids (2011) 1.06

easyExon--a Java-based GUI tool for processing and visualization of Affymetrix exon array data. BMC Bioinformatics (2008) 1.05

The Neuronal Splicing Factor Nova Co-Localizes with Target RNAs in the Dendrite. Front Neural Circuits (2010) 1.05

Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res (2013) 1.05

Alternative splicing: functional diversity among voltage-gated calcium channels and behavioral consequences. Biochim Biophys Acta (2012) 1.04

Identification of recurrent regulated alternative splicing events across human solid tumors. Nucleic Acids Res (2015) 1.03

The impact of alternative splicing in vivo: mouse models show the way. RNA (2007) 1.03

NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. Elife (2013) 1.03

Emerging Roles of Alternative Pre-mRNA Splicing Regulation in Neuronal Development and Function. Front Neurosci (2012) 1.02

The function of spliceosome components in open mitosis. Nucleus (2010) 1.01

Pathway-driven discovery of epilepsy genes. Nat Neurosci (2015) 1.00

Human brain evolution: harnessing the genomics (r)evolution to link genes, cognition, and behavior. Neuron (2010) 0.99

Articles by these authors

GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63

An integrated semiconductor device enabling non-optical genome sequencing. Nature (2011) 20.85

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87

Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet (2008) 19.55

Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21

A call for transparent reporting to optimize the predictive value of preclinical research. Nature (2012) 14.63

NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res (2003) 14.37

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

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics (2005) 14.02

The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29

Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science (2011) 11.12

De novo gene disruptions in children on the autistic spectrum. Neuron (2012) 9.69

The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19

CLIP identifies Nova-regulated RNA networks in the brain. Science (2003) 8.88

MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol (2003) 8.66

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55

FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell (2011) 8.46

The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23

An RNA map predicting Nova-dependent splicing regulation. Nature (2006) 7.63

Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect Dis (2013) 6.60

Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer (2005) 6.46

Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res (2006) 6.45

CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods (2005) 6.26

Hypoxia-inducible factors regulate tumorigenic capacity of glioma stem cells. Cancer Cell (2009) 5.81

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71

Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics (2006) 5.59

Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol (2007) 5.53

RNA processing and its regulation: global insights into biological networks. Nat Rev Genet (2010) 5.34

Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol (2006) 4.63

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res (2013) 4.32

Pten in stromal fibroblasts suppresses mammary epithelial tumours. Nature (2009) 4.21

Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Mol Cancer Ther (2006) 4.09

Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Mol Cancer Ther (2007) 3.84

Identification of a universal Group B streptococcus vaccine by multiple genome screen. Science (2005) 3.83

Musculoskeletal ultrasound including definitions for ultrasonographic pathology. J Rheumatol (2005) 3.80

A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery. Proc Natl Acad Sci U S A (2007) 3.78

The ecology of seamounts: structure, function, and human impacts. Ann Rev Mar Sci (2010) 3.78

Predicting drug sensitivity and resistance: profiling ABC transporter genes in cancer cells. Cancer Cell (2004) 3.72

Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci U S A (2003) 3.66

Mistaken identifiers: gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics (2004) 3.65

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest (2012) 3.64

Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping. Cancer Res (2003) 3.52

Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet (2006) 3.51

An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin Cancer Res (2012) 3.48

Karyotypic complexity of the NCI-60 drug-screening panel. Cancer Res (2003) 3.42

Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nat Neurosci (2010) 3.41

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol (2011) 3.18

Human genomic deletions mediated by recombination between Alu elements. Am J Hum Genet (2006) 3.15

MicroRNAs modulate the chemosensitivity of tumor cells. Mol Cancer Ther (2008) 3.06

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00

Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics (2003) 2.97

Targeting cancer stem cells through L1CAM suppresses glioma growth. Cancer Res (2008) 2.97

AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics (2007) 2.93

Genome-wide RNAi screen reveals a specific sensitivity of IRES-containing RNA viruses to host translation inhibition. Genes Dev (2005) 2.83

Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell (2005) 2.82

A new family of potent AB(5) cytotoxins produced by Shiga toxigenic Escherichia coli. J Exp Med (2004) 2.81

An alternative mode of microRNA target recognition. Nat Struct Mol Biol (2012) 2.77

Heritability of alternative splicing in the human genome. Genome Res (2007) 2.76

Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science (2010) 2.69

Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov (2012) 2.68

Changing trends in antimicrobial resistance and serotypes of Streptococcus pneumoniae isolates in Asian countries: an Asian Network for Surveillance of Resistant Pathogens (ANSORP) study. Antimicrob Agents Chemother (2012) 2.65

A randomized, double-blind, controlled study of ultrasound-guided corticosteroid injection into the joint of patients with inflammatory arthritis. Arthritis Rheum (2010) 2.55

Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther (2006) 2.55

Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Mol Cell (2012) 2.54

Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. Cell (2012) 2.54

DNA fingerprinting of the NCI-60 cell line panel. Mol Cancer Ther (2009) 2.53

MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol Cancer Ther (2007) 2.53

Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biol (2003) 2.52

Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov (2013) 2.49

Splicing regulation in neurologic disease. Neuron (2006) 2.46

A Drosophila resource of transgenic RNAi lines for neurogenetics. Genetics (2009) 2.45

Cell-specific aptamer probes for membrane protein elucidation in cancer cells. J Proteome Res (2008) 2.44

Increased CCR5 affinity and reduced CCR5/CD4 dependence of a neurovirulent primary human immunodeficiency virus type 1 isolate. J Virol (2002) 2.43

c-Myc is required for maintenance of glioma cancer stem cells. PLoS One (2008) 2.41

Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes. Genes Dev (2005) 2.38

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics (2006) 2.37

In vitro anti-cancer activity and structure-activity relationships of natural products isolated from fruits of Panax ginseng. Cancer Chemother Pharmacol (2006) 2.33

Agricultural origins and the isotopic identity of domestication in northern China. Proc Natl Acad Sci U S A (2009) 2.32

Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics (2011) 2.31

Spread of methicillin-resistant Staphylococcus aureus between the community and the hospitals in Asian countries: an ANSORP study. J Antimicrob Chemother (2011) 2.30

QALY maximisation and people's preferences: a methodological review of the literature. Health Econ (2005) 2.29

Aberrant light directly impairs mood and learning through melanopsin-expressing neurons. Nature (2012) 2.26

The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res (2010) 2.25

Novel rank-based statistical methods reveal microRNAs with differential expression in multiple cancer types. PLoS One (2009) 2.21

Fragile X mental retardation protein is associated with translating polyribosomes in neuronal cells. J Neurosci (2004) 2.20

A stromal gene signature associated with inflammatory breast cancer. Int J Cancer (2008) 2.18

The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res (2012) 2.18

The Belfast musculoskeletal ultrasound course. Rheumatology (Oxford) (2009) 2.16

Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance. Cancer Res (2004) 2.10

Nova2 regulates neuronal migration through an RNA switch in disabled-1 signaling. Neuron (2010) 2.08