Published in RNA on February 22, 2011
Mechanisms and consequences of alternative polyadenylation. Mol Cell (2011) 3.96
Assessment of transcript reconstruction methods for RNA-seq. Nat Methods (2013) 3.11
A quantitative atlas of polyadenylation in five mammals. Genome Res (2012) 2.87
Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet (2013) 2.37
Extensive alternative polyadenylation during zebrafish development. Genome Res (2012) 2.07
Alternative cleavage and polyadenylation: the long and short of it. Trends Biochem Sci (2013) 2.01
Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep (2012) 1.99
The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol (2012) 1.82
Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing. Nat Methods (2012) 1.80
Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev (2013) 1.74
Alternative polyadenylation: new insights from global analyses. RNA (2012) 1.72
Widespread and extensive lengthening of 3' UTRs in the mammalian brain. Genome Res (2013) 1.72
An in-depth map of polyadenylation sites in cancer. Nucleic Acids Res (2012) 1.71
Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc Natl Acad Sci U S A (2012) 1.54
Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol Cell Biol (2012) 1.49
CFIm25 links alternative polyadenylation to glioblastoma tumour suppression. Nature (2014) 1.38
Global analyses of the effect of different cellular contexts on microRNA targeting. Mol Cell (2014) 1.38
A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation. Genes Dev (2015) 1.31
Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA (2011) 1.31
An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res (2013) 1.30
E2F mediates enhanced alternative polyadenylation in proliferation. Genome Biol (2012) 1.24
Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation. Nucleic Acids Res (2012) 1.23
ePAT: a simple method to tag adenylated RNA to measure poly(A)-tail length and other 3' RACE applications. RNA (2012) 1.17
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome Biol (2015) 1.17
Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation. Nucleic Acids Res (2011) 1.13
Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun (2014) 1.10
3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res (2013) 1.10
Dynamic landscape of tandem 3' UTRs during zebrafish development. Genome Res (2012) 1.09
Proteostasis in complex dendrites. Nat Rev Neurosci (2013) 1.09
CSR-1 RNAi pathway positively regulates histone expression in C. elegans. EMBO J (2012) 1.06
Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet (2015) 1.03
RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci (2015) 1.03
Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. Mol Syst Biol (2014) 1.01
Integrated transcriptome analysis of mouse spermatogenesis. BMC Genomics (2014) 0.98
Regulation of pluripotency by RNA binding proteins. Cell Stem Cell (2014) 0.98
Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells. Genome Res (2012) 0.98
Transcriptome study of differential expression in schizophrenia. Hum Mol Genet (2013) 0.97
Evolution and Biological Roles of Alternative 3'UTRs. Trends Cell Biol (2015) 0.96
The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev (2015) 0.96
Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells. PLoS Genet (2012) 0.96
Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation. RNA Biol (2013) 0.96
Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3' processing. RNA (2013) 0.95
Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. EMBO J (2014) 0.95
Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages. RNA (2013) 0.94
Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements. Nucleic Acids Res (2014) 0.93
A subset of histone H2B genes produces polyadenylated mRNAs under a variety of cellular conditions. PLoS One (2013) 0.92
Implications of polyadenylation in health and disease. Nucleus (2014) 0.92
3'UTRs take a long shot in the brain. Bioessays (2013) 0.92
Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy. BMC Genomics (2013) 0.92
All's well that ends well: alternative polyadenylation and its implications for stem cell biology. Curr Opin Cell Biol (2013) 0.91
Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. Wiley Interdiscip Rev RNA (2013) 0.91
Sequencing degraded RNA addressed by 3' tag counting. PLoS One (2014) 0.90
MicroRNA: a prognostic biomarker and a possible druggable target for circumventing multidrug resistance in cancer chemotherapy. J Biomed Sci (2013) 0.90
Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. Gene (2013) 0.90
Impaired pre-mRNA processing and altered architecture of 3' untranslated regions contribute to the development of human disorders. Int J Mol Sci (2013) 0.89
Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells. Mol Cancer (2012) 0.89
3'LIFE: a functional assay to detect miRNA targets in high-throughput. Nucleic Acids Res (2014) 0.89
CstF-64 supports pluripotency and regulates cell cycle progression in embryonic stem cells through histone 3' end processing. Nucleic Acids Res (2014) 0.88
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation. Bioinformatics (2013) 0.88
Reconstitution of CF IA from overexpressed subunits reveals stoichiometry and provides insights into molecular topology. Biochemistry (2011) 0.86
Towards decrypting cryptobiosis--analyzing anhydrobiosis in the tardigrade Milnesium tardigradum using transcriptome sequencing. PLoS One (2014) 0.86
Alternative polyadenylation of mRNA precursors. Nat Rev Mol Cell Biol (2016) 0.84
IGF-I 3' untranslated region: strain-specific polymorphisms and motifs regulating IGF-I in osteoblasts. Endocrinology (2012) 0.84
mRNA 3'end processing: A tale of the tail reaches the clinic. EMBO Mol Med (2014) 0.84
DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast. Genome Res (2013) 0.84
RNA sequencing: from tag-based profiling to resolving complete transcript structure. Cell Mol Life Sci (2014) 0.83
Expression profiles of PIWIL2 short isoforms differ in testicular germ cell tumors of various differentiation subtypes. PLoS One (2014) 0.82
Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines. Bioinformatics (2013) 0.82
Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives. Front Plant Sci (2011) 0.82
The polyadenylation code: a unified model for the regulation of mRNA alternative polyadenylation. J Zhejiang Univ Sci B (2014) 0.82
RNA regulatory elements and polyadenylation in plants. Front Plant Sci (2012) 0.81
Alterations in polyadenylation and its implications for endocrine disease. Front Endocrinol (Lausanne) (2013) 0.81
High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping. BMC Genomics (2015) 0.81
PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA (2015) 0.81
A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. Genome Res (2016) 0.80
Cell type-specific termination of transcription by transposable element sequences. Mob DNA (2012) 0.80
PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage. Cell Rep (2016) 0.80
EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates. RNA (2015) 0.79
CPSF30 at the Interface of Alternative Polyadenylation and Cellular Signaling in Plants. Biomolecules (2015) 0.79
Differential microRNA regulation correlates with alternative polyadenylation pattern between breast cancer and normal cells. PLoS One (2013) 0.79
Sequencing of first-strand cDNA library reveals full-length transcriptomes. Nat Commun (2015) 0.79
Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics (2014) 0.79
High throughput characterizations of poly(A) site choice in plants. Methods (2013) 0.79
Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation. Cell Res (2015) 0.78
RNA-binding proteins in pluripotency, differentiation, and reprogramming. Front Biol (Beijing) (2014) 0.78
Global and quantitative profiling of polyadenylated RNAs using PAS-seq. Methods Mol Biol (2014) 0.78
Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns. RNA Biol (2016) 0.77
Emerging Themes in Regulation of Global mRNA Turnover in cis. Trends Biochem Sci (2016) 0.77
Kleat: cleavage site analysis of transcriptomes. Pac Symp Biocomput (2015) 0.77
FLT1 and transcriptome-wide polyadenylation site (PAS) analysis in preeclampsia. Sci Rep (2017) 0.76
Global insights into alternative polyadenylation regulation. RNA Biol (2015) 0.76
End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res (2016) 0.76
Epitope-tagged yeast strains reveal promoter driven changes to 3'-end formation and convergent antisense-transcription from common 3' UTRs. Nucleic Acids Res (2015) 0.76
mRNA 3'-UTR shortening is a molecular signature of mTORC1 activation. Nat Commun (2015) 0.76
IVT-SAPAS: Low-Input and Rapid Method for Sequencing Alternative Polyadenylation Sites. PLoS One (2015) 0.76
Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier. Bioinformatics (2013) 0.76
Alternative polyadenylation is associated with lower expression of PABPN1 and poor prognosis in non-small cell lung cancer. Cancer Sci (2014) 0.76
Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq). Genetics (2016) 0.76
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science (2008) 11.33
Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev (1999) 11.32
Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell (2009) 10.50
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques (2008) 10.02
GeneMerge--post-genomic analysis, data mining, and hypothesis testing. Bioinformatics (2003) 9.27
tRNA punctuation model of RNA processing in human mitochondria. Nature (1981) 8.48
Mechanism and regulation of mRNA polyadenylation. Genes Dev (1997) 7.48
Pre-mRNA processing reaches back to transcription and ahead to translation. Cell (2009) 7.45
A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res (2005) 7.24
RNA polymerase II and the integration of nuclear events. Genes Dev (2000) 6.16
Patterns of variant polyadenylation signal usage in human genes. Genome Res (2000) 6.09
Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques (2001) 5.92
Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet (2008) 5.42
Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr Opin Cell Biol (2005) 5.14
Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A (2009) 5.13
The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation. Cell (1996) 4.93
Separation of basal histone synthesis from S-phase histone synthesis in dividing cells. Cell (1981) 4.15
Neurite branching on deformable substrates. Neuroreport (2002) 3.73
Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron (2008) 3.65
Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation. Nucleic Acids Res (2009) 3.44
The landscape of C. elegans 3'UTRs. Science (2010) 3.32
The human and mouse replication-dependent histone genes. Genomics (2002) 3.23
Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res (2001) 2.72
Reprogramming of 3' untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One (2009) 2.64
Alternative polyadenylation: a twist on mRNA 3' end formation. ACS Chem Biol (2008) 2.38
The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev Cell (2010) 2.29
Targeted 3' processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science (2009) 2.24
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res (2007) 2.22
Drosophila stem loop binding protein coordinates accumulation of mature histone mRNA with cell cycle progression. Genes Dev (2001) 2.01
Downstream sequence elements with different affinities for the hnRNP H/H' protein influence the processing efficiency of mammalian polyadenylation signals. Nucleic Acids Res (2002) 2.00
Polyadenylation promotes degradation of 3'-structured RNA by the Escherichia coli mRNA degradosome in vitro. J Biol Chem (1999) 1.74
A genome-wide RNA interference screen reveals that variant histones are necessary for replication-dependent histone pre-mRNA processing. Mol Cell (2007) 1.71
Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc Natl Acad Sci U S A (2002) 1.71
Polyadenylation and degradation of human mitochondrial RNA: the prokaryotic past leaves its mark. Mol Cell Biol (2005) 1.67
Unique dielectric properties distinguish stem cells and their differentiated progeny. Stem Cells (2007) 1.62
The UCSC Genome Browser. Curr Protoc Bioinformatics (2009) 1.59
U7 snRNA mutations in Drosophila block histone pre-mRNA processing and disrupt oogenesis. RNA (2006) 1.20
Heterogeneity in mammalian RNA 3' end formation. Exp Cell Res (2010) 1.13
Polyadenylation in mammalian mitochondria: insights from recent studies. Biochim Biophys Acta (2008) 1.02
Effects of substrate stiffness on cell morphology, cytoskeletal structure, and adhesion. Cell Motil Cytoskeleton (2005) 10.20
Lhx2 selector activity specifies cortical identity and suppresses hippocampal organizer fate. Science (2008) 3.53
Human neural stem cell growth and differentiation in a gradient-generating microfluidic device. Lab Chip (2005) 3.33
The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci U S A (2005) 2.78
Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns. PLoS Biol (2006) 2.51
The SR protein family. Genome Biol (2009) 2.09
Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers. Proc Natl Acad Sci U S A (2005) 1.83
Engineering microscale cellular niches for three-dimensional multicellular co-cultures. Lab Chip (2009) 1.77
Conserved RNA secondary structures promote alternative splicing. RNA (2008) 1.63
Unique dielectric properties distinguish stem cells and their differentiated progeny. Stem Cells (2007) 1.62
Commitment to splice site pairing coincides with A complex formation. Mol Cell (2004) 1.61
A re-assessment of a combinatorial treatment involving Schwann cell transplants and elevation of cyclic AMP on recovery of motor function following thoracic spinal cord injury in rats. Exp Neurol (2010) 1.55
Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc Natl Acad Sci U S A (2012) 1.54
Splice-site pairing is an intrinsically high fidelity process. Proc Natl Acad Sci U S A (2009) 1.44
A general role for splicing enhancers in exon definition. RNA (2002) 1.43
Correction of SMN2 Pre-mRNA splicing by antisense U7 small nuclear RNAs. Mol Ther (2005) 1.42
Evolution of SR protein and hnRNP splicing regulatory factors. Wiley Interdiscip Rev RNA (2011) 1.37
Pre-mRNA 3'-end processing complex assembly and function. Wiley Interdiscip Rev RNA (2010) 1.30
Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms. RNA (2012) 1.28
Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. RNA (2006) 1.22
Dielectrophoresis switching with vertical sidewall electrodes for microfluidic flow cytometry. Lab Chip (2007) 1.20
The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell (2013) 1.19
Analyzing mechanisms of alternative pre-mRNA splicing using in vitro splicing assays. Methods (2005) 1.18
Extended base pair complementarity between U1 snRNA and the 5' splice site does not inhibit splicing in higher eukaryotes, but rather increases 5' splice site recognition. Nucleic Acids Res (2005) 1.17
Spliceosome assembly pathways for different types of alternative splicing converge during commitment to splice site pairing in the A complex. Mol Cell Biol (2008) 1.11
Enhancer-dependent 5'-splice site control of fruitless pre-mRNA splicing. J Biol Chem (2003) 1.08
Enhanced neurite growth from mammalian neurons in three-dimensional salmon fibrin gels. Biomaterials (2007) 1.08
SR proteins induce alternative exon skipping through their activities on the flanking constitutive exons. Mol Cell Biol (2010) 1.07
Dual frequency dielectrophoresis with interdigitated sidewall electrodes for microfluidic flow-through separation of beads and cells. Electrophoresis (2009) 1.05
PARP1 represses PAP and inhibits polyadenylation during heat shock. Mol Cell (2012) 1.05
Spliceosomes walk the line: splicing errors and their impact on cellular function. RNA Biol (2009) 1.02
Phasor fluorescence lifetime microscopy of free and protein-bound NADH reveals neural stem cell differentiation potential. PLoS One (2012) 1.02
Restoration of full-length SMN promoted by adenoviral vectors expressing RNA antisense oligonucleotides embedded in U7 snRNAs. PLoS One (2009) 0.98
Biophysical characteristics reveal neural stem cell differentiation potential. PLoS One (2011) 0.98
Competing upstream 5' splice sites enhance the rate of proximal splicing. Mol Cell Biol (2010) 0.97
Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3' processing. RNA (2013) 0.95
Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. EMBO J (2014) 0.95
Soft materials to treat central nervous system injuries: evaluation of the suitability of non-mammalian fibrin gels. Biochim Biophys Acta (2009) 0.92
The splicing regulators Tra and Tra2 are unusually potent activators of pre-mRNA splicing. Nucleic Acids Res (2006) 0.92
Frequency discretization in dielectrophoretic assisted cell sorting arrays to isolate neural cells. Lab Chip (2012) 0.91
G Run-mediated recognition of proteolipid protein and DM20 5' splice sites by U1 small nuclear RNA is regulated by context and proximity to the splice site. J Biol Chem (2010) 0.91
Co-factors of LIM domains (Clims/Ldb/Nli) regulate corneal homeostasis and maintenance of hair follicle stem cells. Dev Biol (2007) 0.90
Salmon fibrin treatment of spinal cord injury promotes functional recovery and density of serotonergic innervation. Exp Neurol (2012) 0.90
Identification of a novel nuclear localization signal and speckle-targeting sequence of tuftelin-interacting protein 11, a splicing factor involved in spliceosome disassembly. Biochem Biophys Res Commun (2009) 0.89
Efficient internal exon recognition depends on near equal contributions from the 3' and 5' splice sites. Nucleic Acids Res (2011) 0.88
Effect of AKT inhibition on epithelial-mesenchymal transition and ZEB1-potentiated radiotherapy in nasopharyngeal carcinoma. Oncol Lett (2013) 0.85
HEXEvent: a database of Human EXon splicing Events. Nucleic Acids Res (2012) 0.85
Advancing practical usage of microtechnology: a study of the functional consequences of dielectrophoresis on neural stem cells. Integr Biol (Camb) (2012) 0.84
Retention of spliceosomal components along ligated exons ensures efficient removal of multiple introns. RNA (2010) 0.84
Death by splicing: tumor suppressor RBM5 freezes splice-site pairing. Mol Cell (2008) 0.83
The polyadenylation code: a unified model for the regulation of mRNA alternative polyadenylation. J Zhejiang Univ Sci B (2014) 0.82
Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome? Genome Biol (2012) 0.79
Global and quantitative profiling of polyadenylated RNAs using PAS-seq. Methods Mol Biol (2014) 0.78
Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq. Methods Mol Biol (2014) 0.77
In vitro assay of pre-mRNA splicing in mammalian nuclear extract. Methods Mol Biol (2014) 0.77
Embracing the complexity of pre-mRNA splicing. Cell Res (2010) 0.77
Development of a MEMS microsystem to study the effect of mechanical tension on cerebral cortex neurogenesis. Conf Proc IEEE Eng Med Biol Soc (2004) 0.76
Laurdan monitors different lipids content in eukaryotic membrane during embryonic neural development. Cell Biochem Biophys (2014) 0.76
Increasing label-free stem cell sorting capacity to reach transplantation-scale throughput. Biomicrofluidics (2014) 0.75
Kinetic analysis of in vitro pre-mRNA splicing in HeLa nuclear extract. Methods Mol Biol (2014) 0.75
Preparation of splicing competent nuclear extracts. Methods Mol Biol (2014) 0.75
Dangerous play--splitting the message may leave you empty handed. Nat Struct Mol Biol (2009) 0.75
Bioinspired uniform illumination by vibrated sessile droplet pinned by a hydrophilic/superhydrophobic heterogeneous surface. Opt Lett (2013) 0.75