Published in Mol Cell on June 22, 2007
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol (2009) 7.11
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA (2008) 6.29
Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol (2009) 5.14
Epigenetics in alternative pre-mRNA splicing. Cell (2011) 4.74
The splicing factor SC35 has an active role in transcriptional elongation. Nat Struct Mol Biol (2008) 3.86
Biased chromatin signatures around polyadenylation sites and exons. Mol Cell (2009) 3.74
Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol (2013) 3.33
"Cotranscriptionality": the transcription elongation complex as a nexus for nuclear transactions. Mol Cell (2009) 3.28
RNA polymerase II elongation control. Annu Rev Biochem (2012) 3.09
U1 snRNP determines mRNA length and regulates isoform expression. Cell (2012) 2.92
Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell (2011) 2.86
Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription. Nat Cell Biol (2009) 2.60
The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol (2011) 2.58
Splicing-dependent RNA polymerase pausing in yeast. Mol Cell (2010) 2.49
Functional integration of transcriptional and RNA processing machineries. Curr Opin Cell Biol (2008) 2.38
Coupling mRNA processing with transcription in time and space. Nat Rev Genet (2014) 2.09
Function of alternative splicing. Gene (2012) 2.00
Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev (2011) 1.87
R-loop-mediated genomic instability is caused by impairment of replication fork progression. Genes Dev (2011) 1.82
Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res (2010) 1.80
A splicing-dependent transcriptional checkpoint associated with prespliceosome formation. Mol Cell (2014) 1.73
7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development. Proc Natl Acad Sci U S A (2009) 1.71
The human cap-binding complex is functionally connected to the nuclear RNA exosome. Nat Struct Mol Biol (2013) 1.67
Mechanisms and Regulation of Alternative Pre-mRNA Splicing. Annu Rev Biochem (2015) 1.59
Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. EMBO J (2010) 1.53
Regulation of splicing by SR proteins and SR protein-specific kinases. Chromosoma (2013) 1.53
SON controls cell-cycle progression by coordinated regulation of RNA splicing. Mol Cell (2011) 1.52
FUS-SMN protein interactions link the motor neuron diseases ALS and SMA. Cell Rep (2012) 1.50
Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol Cell (2012) 1.48
The function of introns. Front Genet (2012) 1.42
FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2. Genes Dev (2012) 1.39
Histone deacetylase activity modulates alternative splicing. PLoS One (2011) 1.37
The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex. Genes Dev (2011) 1.37
A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast. Mol Cell (2008) 1.36
RNA seeds higher-order assembly of FUS protein. Cell Rep (2013) 1.36
RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev (2013) 1.35
Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function. Trends Cell Biol (2009) 1.33
Functional coupling of last-intron splicing and 3'-end processing to transcription in vitro: the poly(A) signal couples to splicing before committing to cleavage. Mol Cell Biol (2007) 1.33
Degrade, move, regroup: signaling control of splicing proteins. Trends Biochem Sci (2011) 1.32
Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner. Proc Natl Acad Sci U S A (2011) 1.30
A complex network of factors with overlapping affinities represses splicing through intronic elements. Nat Struct Mol Biol (2012) 1.26
A syn-anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well. EMBO J (2011) 1.18
Protein characterization of Saccharomyces cerevisiae RNA polymerase II after in vivo cross-linking. Proc Natl Acad Sci U S A (2007) 1.17
Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture. RNA (2013) 1.14
Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing. Nat Struct Mol Biol (2009) 1.12
The proteomes of transcription factories containing RNA polymerases I, II or III. Nat Methods (2011) 1.10
Splicing-factor oncoprotein SRSF1 stabilizes p53 via RPL5 and induces cellular senescence. Mol Cell (2013) 1.10
Depletion of T-cell intracellular antigen proteins promotes cell proliferation. Genome Biol (2009) 1.08
Co-transcriptional regulation of alternative pre-mRNA splicing. Biochim Biophys Acta (2012) 1.08
Cap-binding protein complex links pre-mRNA capping to transcription elongation and alternative splicing through positive transcription elongation factor b (P-TEFb). J Biol Chem (2011) 1.06
Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing. RNA (2009) 1.06
CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo. Nucleic Acids Res (2012) 1.05
Identification of ASF/SF2 as a critical, allele-specific effector of the cyclin D1b oncogene. Cancer Res (2010) 1.04
Role of poly (A) tail as an identity element for mRNA nuclear export. Nucleic Acids Res (2007) 1.04
Specific combinations of SR proteins associate with single pre-messenger RNAs in vivo and contribute different functions. J Cell Biol (2009) 1.01
Spatial mapping of splicing factor complexes involved in exon and intron definition. J Cell Biol (2008) 1.01
FUS is sequestered in nuclear aggregates in ALS patient fibroblasts. Mol Biol Cell (2014) 0.99
Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells. Nucleic Acids Res (2011) 0.99
Promoter-proximal polyadenylation sites reduce transcription activity. Genes Dev (2012) 0.98
PARP-1 dependent recruitment of the amyotrophic lateral sclerosis-associated protein FUS/TLS to sites of oxidative DNA damage. Nucleic Acids Res (2013) 0.97
SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles. Mol Biol Cell (2012) 0.97
HIV-1 transcription is regulated by splicing factor SRSF1. Nucleic Acids Res (2014) 0.96
A BBP-Mud2p heterodimer mediates branchpoint recognition and influences splicing substrate abundance in budding yeast. Nucleic Acids Res (2008) 0.96
Combined proteomic-RNAi screen for host factors involved in human hepatitis delta virus replication. RNA (2009) 0.95
Pre-mRNA splicing during transcription in the mammalian system. Wiley Interdiscip Rev RNA (2011) 0.95
A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis. PLoS Genet (2013) 0.94
Cotranscriptional splicing potentiates the mRNA production from a subset of estradiol-stimulated genes. Mol Cell Biol (2008) 0.92
Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing. J Mol Biol (2016) 0.92
Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. EMBO J (2015) 0.91
Heterogeneous ribonucleoprotein C displays a repressor activity mediated by T-cell intracellular antigen-1-related/like protein to modulate Fas exon 6 splicing through a mechanism involving Hu antigen R. Nucleic Acids Res (2010) 0.91
The transcriptional transactivator Tat selectively regulates viral splicing. Nucleic Acids Res (2009) 0.88
Coupling pre-mRNA processing to transcription on the RNA factory assembly line. RNA Biol (2013) 0.87
The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression. Hum Mol Genet (2013) 0.87
The RNA polymerase C-terminal domain: a new role in spliceosome assembly. Transcription (2012) 0.86
Efficient transcription through an intron requires the binding of an Sm-type U1 snRNP with intact stem loop II to the splice donor. Nucleic Acids Res (2010) 0.86
Identification of a set of miRNAs differentially expressed in transiently TIA-depleted HeLa cells by genome-wide profiling. BMC Mol Biol (2013) 0.85
Dynamic nucleocytoplasmic shuttling of an Arabidopsis SR splicing factor: role of the RNA-binding domains. Plant Physiol (2010) 0.85
RNA Polymerase II Elongation at the Crossroads of Transcription and Alternative Splicing. Genet Res Int (2011) 0.84
The role of SON in splicing, development, and disease. Wiley Interdiscip Rev RNA (2014) 0.84
Human Papillomavirus 16 Oncoprotein Expression Is Controlled by the Cellular Splicing Factor SRSF2 (SC35). J Virol (2015) 0.83
Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes. J Virol (2008) 0.83
Mitofilin and CHCHD6 physically interact with Sam50 to sustain cristae structure. Sci Rep (2015) 0.83
Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing in Trypanosoma brucei. RNA Biol (2014) 0.83
Pre-mRNA splicing is a determinant of nucleosome organization. PLoS One (2013) 0.82
T-cell intracellular antigen (TIA)-proteins deficiency in murine embryonic fibroblasts alters cell cycle progression and induces autophagy. PLoS One (2013) 0.82
Ceramide modulates pre-mRNA splicing to restore the expression of wild-type tumor suppressor p53 in deletion-mutant cancer cells. Biochim Biophys Acta (2014) 0.81
The SR protein B52/SRp55 is required for DNA topoisomerase I recruitment to chromatin, mRNA release and transcription shutdown. PLoS Genet (2010) 0.81
RSR-2, the Caenorhabditis elegans ortholog of human spliceosomal component SRm300/SRRM2, regulates development by influencing the transcriptional machinery. PLoS Genet (2013) 0.81
Coupled transcription-splicing regulation of mutually exclusive splicing events at the 5' exons of protein 4.1R gene. Blood (2009) 0.81
Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions. Nucleic Acids Res (2015) 0.80
Spliceosome mutations in myelodysplastic syndromes and chronic myelomonocytic leukemia. Oncotarget (2012) 0.80
Making a Short Story Long: Regulation of P-TEFb and HIV-1 Transcriptional Elongation in CD4+ T Lymphocytes and Macrophages. Biology (Basel) (2012) 0.80
SR and SR-related proteins redistribute to segregated fibrillar components of nucleoli in a response to DNA damage. Nucleus (2010) 0.80
FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP. Proc Natl Acad Sci U S A (2015) 0.80
Construction and evaluation of an adenoviral vector for the liver-specific expression of the serine/arginine-rich splicing factor, SRSF3. Plasmid (2015) 0.79
Mechanisms of FUS mutations in familial amyotrophic lateral sclerosis. Brain Res (2016) 0.79
In vitro systems for coupling RNAP II transcription to splicing and polyadenylation. Methods Mol Biol (2014) 0.79
T-cell intracellular antigens function as tumor suppressor genes. Cell Death Dis (2015) 0.79
T-cell intracellular antigens in health and disease. Cell Cycle (2015) 0.79
The impact of microRNAs on protein output. Nature (2008) 32.39
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods (2007) 25.29
ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science (2007) 20.11
Nutrient control of glucose homeostasis through a complex of PGC-1alpha and SIRT1. Nature (2005) 18.41
Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell (2007) 17.98
Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science (2004) 17.38
Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet (2002) 16.29
A PGC1-α-dependent myokine that drives brown-fat-like development of white fat and thermogenesis. Nature (2012) 14.67
ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res (2003) 12.81
A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol (2006) 12.13
Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res (2003) 11.96
An extensive network of coupling among gene expression machines. Nature (2002) 11.84
Defining the human deubiquitinating enzyme interaction landscape. Cell (2009) 11.39
Network organization of the human autophagy system. Nature (2010) 11.38
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A (2003) 10.82
Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A (2004) 10.78
A proteomics approach to understanding protein ubiquitination. Nat Biotechnol (2003) 10.51
A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A (2008) 10.07
A tissue-specific atlas of mouse protein phosphorylation and expression. Cell (2010) 8.65
Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell (2011) 7.30
Comprehensive proteomic analysis of the human spliceosome. Nature (2002) 6.85
Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response. Science (2007) 6.77
Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat Methods (2005) 6.73
mTOR and S6K1 mediate assembly of the translation preinitiation complex through dynamic protein interchange and ordered phosphorylation events. Cell (2005) 6.71
Identification of the FANCI protein, a monoubiquitinated FANCD2 paralog required for DNA repair. Cell (2007) 6.68
TREX is a conserved complex coupling transcription with messenger RNA export. Nature (2002) 6.53
The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat Struct Mol Biol (2007) 6.16
Large-scale phosphorylation analysis of mouse liver. Proc Natl Acad Sci U S A (2007) 6.08
An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol (2005) 5.93
Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat Genet (2002) 5.80
Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science (2011) 5.73
An AMPK-FOXO pathway mediates longevity induced by a novel method of dietary restriction in C. elegans. Curr Biol (2007) 5.48
Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. Cell (2009) 5.41
Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science (2009) 5.37
Human ESCRT and ALIX proteins interact with proteins of the midbody and function in cytokinesis. EMBO J (2007) 5.31
Tumor-promoting phorbol esters and activated Ras inactivate the tuberous sclerosis tumor suppressor complex via p90 ribosomal S6 kinase. Proc Natl Acad Sci U S A (2004) 5.16
The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat Protoc (2008) 5.10
Enhancement of proteasome activity by a small-molecule inhibitor of USP14. Nature (2010) 5.08
Signaling networks assembled by oncogenic EGFR and c-Met. Proc Natl Acad Sci U S A (2008) 5.08
Initiation of myoblast to brown fat switch by a PRDM16-C/EBP-beta transcriptional complex. Nature (2009) 4.98
BAD and glucokinase reside in a mitochondrial complex that integrates glycolysis and apoptosis. Nature (2003) 4.80
Regulation of monoubiquitinated PCNA by DUB autocleavage. Nat Cell Biol (2006) 4.67
An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet (2006) 4.56
Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell (2004) 4.34
Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat Cell Biol (2006) 4.25
Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Mol Cell Proteomics (2006) 4.25
Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev (2008) 4.24
The energy sensor AMP-activated protein kinase directly regulates the mammalian FOXO3 transcription factor. J Biol Chem (2007) 4.22
Toca-1 mediates Cdc42-dependent actin nucleation by activating the N-WASP-WIP complex. Cell (2004) 4.21
Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Science (2008) 4.15
Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model. Nature (2011) 4.04
Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89
The conserved Bardet-Biedl syndrome proteins assemble a coat that traffics membrane proteins to cilia. Cell (2010) 3.83
Correction of disease-associated exon skipping by synthetic exon-specific activators. Nat Struct Biol (2003) 3.75
Identification of aneuploidy-tolerating mutations. Cell (2010) 3.73
SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma. Science (2009) 3.72
The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods (2005) 3.71
RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat Rev Drug Discov (2012) 3.70
Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem (2002) 3.70
SCF(FBW7) regulates cellular apoptosis by targeting MCL1 for ubiquitylation and destruction. Nature (2011) 3.69
Certain pairs of ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s) synthesize nondegradable forked ubiquitin chains containing all possible isopeptide linkages. J Biol Chem (2007) 3.68
Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. Nature (2013) 3.57
MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods (2011) 3.40
A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans. Science (2012) 3.39
A molecular determinant for the establishment of sister chromatid cohesion. Science (2008) 3.39
Human mRNA export machinery recruited to the 5' end of mRNA. Cell (2006) 3.32
A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage. Proc Natl Acad Sci U S A (2010) 3.31
A protein complex network of Drosophila melanogaster. Cell (2011) 3.31
Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res (2006) 3.30
Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat Biotechnol (2004) 3.30
Activation of multiple proto-oncogenic tyrosine kinases in breast cancer via loss of the PTPN12 phosphatase. Cell (2011) 3.27
A UAF1-containing multisubunit protein complex regulates the Fanconi anemia pathway. Mol Cell (2007) 3.27
Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am J Hum Genet (2008) 3.24
Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell (2011) 3.23
Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell (2006) 3.21
Sus1, a functional component of the SAGA histone acetylase complex and the nuclear pore-associated mRNA export machinery. Cell (2004) 3.16
Recruitment of the human TREX complex to mRNA during splicing. Genes Dev (2005) 3.13
Profiling of UV-induced ATM/ATR signaling pathways. Proc Natl Acad Sci U S A (2007) 3.12
The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism. Proc Natl Acad Sci U S A (2010) 3.08
During muscle atrophy, thick, but not thin, filament components are degraded by MuRF1-dependent ubiquitylation. J Cell Biol (2009) 3.03
Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model. Genes Dev (2010) 3.02
Hem-1 complexes are essential for Rac activation, actin polymerization, and myosin regulation during neutrophil chemotaxis. PLoS Biol (2006) 3.01
Chemical genetic screen for AMPKα2 substrates uncovers a network of proteins involved in mitosis. Mol Cell (2011) 2.99
Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survival. Cell (2011) 2.98
Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol Cell Biol (2002) 2.93
Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities. Cell (2006) 2.87
Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry. J Biol Chem (2004) 2.84
A function for cyclin D1 in DNA repair uncovered by protein interactome analyses in human cancers. Nature (2011) 2.82
RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell (2007) 2.78
Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases. Sci Signal (2010) 2.64
Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat Cell Biol (2005) 2.62
Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell (2010) 2.59
A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol Cell Proteomics (2004) 2.58
Antisense oligonucleotides delivered to the mouse CNS ameliorate symptoms of severe spinal muscular atrophy. Sci Transl Med (2011) 2.56
Distinct phosphorylation sites on the β(2)-adrenergic receptor establish a barcode that encodes differential functions of β-arrestin. Sci Signal (2011) 2.56
Phosphoproteomic analysis of the developing mouse brain. Mol Cell Proteomics (2004) 2.50