Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.

PubWeight™: 1.34‹?› | Rank: Top 10%

🔗 View Article (PMC 3533403)

Published in Nat Struct Mol Biol on July 22, 2012

Authors

Alexander Sherstnev1, Céline Duc, Christian Cole, Vasiliki Zacharaki, Csaba Hornyik, Fatih Ozsolak, Patrice M Milos, Geoffrey J Barton, Gordon G Simpson

Author Affiliations

1: College of Life Sciences, University of Dundee, Dundee, UK.

Articles citing this

Alternative cleavage and polyadenylation: the long and short of it. Trends Biochem Sci (2013) 2.01

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

A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun (2016) 1.24

Uridylation prevents 3' trimming of oligoadenylated mRNAs. Nucleic Acids Res (2013) 1.02

Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell (2012) 1.02

Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus. Mol Cell (2014) 1.00

Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts. Proc Natl Acad Sci U S A (2013) 0.99

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res (2013) 0.99

Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation. RNA Biol (2013) 0.96

3'UTRs take a long shot in the brain. Bioessays (2013) 0.92

The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana. PLoS Genet (2014) 0.91

Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA. PLoS Genet (2013) 0.91

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. RNA (2013) 0.89

The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis. Plant Physiol (2014) 0.88

A change-point model for identifying 3'UTR switching by next-generation RNA sequencing. Bioinformatics (2014) 0.86

Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. Mol Plant (2013) 0.86

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs. PLoS One (2014) 0.85

Oral biofilms: molecular analysis, challenges, and future prospects in dental diagnostics. Clin Cosmet Investig Dent (2013) 0.85

The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation. Sci Rep (2013) 0.83

RNA sequencing: from tag-based profiling to resolving complete transcript structure. Cell Mol Life Sci (2014) 0.83

Target specificity among canonical nuclear poly(A) polymerases in plants modulates organ growth and pathogen response. Proc Natl Acad Sci U S A (2013) 0.81

Seed Dormancy in Arabidopsis Is Controlled by Alternative Polyadenylation of DOG1. Plant Physiol (2015) 0.81

RNA around the clock - regulation at the RNA level in biological timing. Front Plant Sci (2015) 0.80

Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana. BMC Genomics (2015) 0.79

High throughput characterizations of poly(A) site choice in plants. Methods (2013) 0.79

CPSF30 at the Interface of Alternative Polyadenylation and Cellular Signaling in Plants. Biomolecules (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

Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms. G3 (Bethesda) (2014) 0.78

Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation. Cell Res (2015) 0.78

Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data. BMC Genomics (2014) 0.77

PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants. Front Plant Sci (2016) 0.76

In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings. Plant Cell (2016) 0.76

Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii. PLoS One (2016) 0.76

Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript. Proc Natl Acad Sci U S A (2016) 0.76

Accurate identification of polyadenylation sites from 3' end deep sequencing using a naive Bayes classifier. Bioinformatics (2013) 0.76

Genome-wide dynamics of alternative polyadenylation in rice. Genome Res (2016) 0.75

On the Origin of De Novo Genes in Arabidopsis thaliana Populations. Genome Biol Evol (2016) 0.75

A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana. Sci Rep (2016) 0.75

Active 5' splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes. Nucleic Acids Res (2016) 0.75

Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana. PLoS Genet (2015) 0.75

Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors. Front Endocrinol (Lausanne) (2014) 0.75

Dehydration stress extends mRNA 3' untranslated regions with noncoding RNA functions in Arabidopsis. Genome Res (2017) 0.75

Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia. Plant Cell (2017) 0.75

Articles cited by this

MicroRNAs: target recognition and regulatory functions. Cell (2009) 92.17

Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62

Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell (2009) 10.50

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics (2009) 10.30

Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet (2011) 9.79

Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09

A detailed model of reverse transcription and tests of crucial aspects. Cell (1979) 8.93

Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell (2005) 7.58

Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res (2007) 5.54

The many pathways of RNA degradation. Cell (2009) 5.31

DNA-directed DNA polymerase activity in oncogenic RNA viruses. Nature (1970) 4.81

Direct RNA sequencing. Nature (2009) 4.37

Mechanisms and consequences of alternative polyadenylation. Mol Cell (2011) 3.96

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature (2010) 3.87

Synthetic spike-in standards for RNA-seq experiments. Genome Res (2011) 3.58

A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A (2006) 3.48

Ending the message: poly(A) signals then and now. Genes Dev (2011) 3.47

Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell (2010) 3.42

Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat Struct Mol Biol (2008) 3.40

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34

The landscape of C. elegans 3'UTRs. Science (2010) 3.32

Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A (2005) 3.21

Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotechnol (2004) 3.12

Transcriptional collision between convergent genes in budding yeast. Proc Natl Acad Sci U S A (2002) 2.84

Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell (2007) 2.58

The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev Cell (2010) 2.29

Unravelling the means to an end: RNA polymerase II transcription termination. Nat Rev Mol Cell Biol (2011) 2.21

Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol (2005) 1.98

Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase. EMBO J (2004) 1.92

Crosstalk between mRNA 3' end processing and transcription initiation. Mol Cell (2010) 1.89

Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol (2005) 1.86

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A (2011) 1.85

Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. RNA (2011) 1.76

snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res (2006) 1.73

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

A dissection of the cauliflower mosaic virus polyadenylation signal. Genes Dev (1991) 1.67

Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol (2007) 1.52

Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae. EMBO J (1998) 1.50

Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS One (2010) 1.47

Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci (2003) 1.43

The contribution of AAUAAA and the upstream element UUUGUA to the efficiency of mRNA 3'-end formation in plants. EMBO J (1994) 1.36

Autoregulation of convergent RNAi genes in fission yeast. Genes Dev (2011) 0.99

Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences. RNA (2004) 0.95

Processing of a dicistronic tRNA-snoRNA precursor: combined analysis in vitro and in vivo reveals alternate pathways and coupling to assembly of snoRNP. Plant Physiol (2009) 0.94

Mining small RNA sequencing data: a new approach to identify small nucleolar RNAs in Arabidopsis. Nucleic Acids Res (2009) 0.88

Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli. Nucleic Acids Res (2010) 0.86

Articles by these authors

Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84

The Jalview Java alignment editor. Bioinformatics (2004) 21.74

New models of collaboration in genome-wide association studies: the Genetic Association Information Network. Nat Genet (2007) 13.76

The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32

RNA sequencing: advances, challenges and opportunities. Nat Rev Genet (2010) 8.96

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature (2011) 7.43

Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. Nat Genet (2008) 6.06

Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science (2007) 4.89

GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76

Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res (2006) 4.64

Emerging roles of pseudokinases. Trends Cell Biol (2006) 4.48

Direct RNA sequencing. Nature (2009) 4.37

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics (2003) 4.01

Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res (2004) 3.97

A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs. EMBO J (2002) 3.95

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA (2009) 3.87

The Lkb1 metabolic sensor maintains haematopoietic stem cell survival. Nature (2010) 3.55

System-wide changes to SUMO modifications in response to heat shock. Sci Signal (2009) 3.50

Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell (2010) 3.42

RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis. Nature (2012) 3.40

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol (2010) 2.59

A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science (2011) 2.50

Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time. EMBO J (2003) 2.40

The spen family protein FPA controls alternative cleavage and polyadenylation of RNA. Dev Cell (2010) 2.29

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods (2009) 2.26

MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics (2006) 2.23

Short defective interfering RNAs of tombusviruses are not targeted but trigger post-transcriptional gene silencing against their helper virus. Plant Cell (2002) 2.12

Amplification-free digital gene expression profiling from minute cell quantities. Nat Methods (2010) 2.07

Human miRNA precursors with box H/ACA snoRNA features. PLoS Comput Biol (2009) 2.06

Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biol (2006) 1.98

Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins. Biochem J (2010) 1.94

PIPs: human protein-protein interaction prediction database. Nucleic Acids Res (2008) 1.91

TarO: a target optimisation system for structural biology. Nucleic Acids Res (2008) 1.89

Digital transcriptome profiling from attomole-level RNA samples. Genome Res (2010) 1.83

New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature (2010) 1.78

Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels. Hum Genomics (2004) 1.71

An in-depth map of polyadenylation sites in cancer. Nucleic Acids Res (2012) 1.71

The Scottish Structural Proteomics Facility: targets, methods and outputs. J Struct Funct Genomics (2010) 1.66

Classification and functional annotation of eukaryotic protein kinases. Proteins (2007) 1.62

Nitric oxide contributes to cadmium toxicity in Arabidopsis by promoting cadmium accumulation in roots and by up-regulating genes related to iron uptake. Plant Physiol (2009) 1.49

A comparison of single molecule and amplification based sequencing of cancer transcriptomes. PLoS One (2011) 1.44

Oncogenic MITF dysregulation in clear cell sarcoma: defining the MiT family of human cancers. Cancer Cell (2006) 1.41

Characterization and prediction of protein nucleolar localization sequences. Nucleic Acids Res (2010) 1.40

Caffeoyl shikimate esterase (CSE) is an enzyme in the lignin biosynthetic pathway in Arabidopsis. Science (2013) 1.39

The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. J Mol Biol (2007) 1.38

Identification of human miRNA precursors that resemble box C/D snoRNAs. Nucleic Acids Res (2011) 1.35

New insights into ferritin synthesis and function highlight a link between iron homeostasis and oxidative stress in plants. Ann Bot (2009) 1.35

Visualization of multiple alignments, phylogenies and gene family evolution. Nat Methods (2010) 1.34

Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases. EMBO J (2009) 1.32

Probabilistic prediction and ranking of human protein-protein interactions. BMC Bioinformatics (2007) 1.31

Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects. J Allergy Clin Immunol (2013) 1.30

Ferritins and iron storage in plants. Biochim Biophys Acta (2009) 1.30

Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci U S A (2012) 1.29

In situ characterization of Cymbidium Ringspot Tombusvirus infection-induced posttranscriptional gene silencing in Nicotiana benthamiana. J Virol (2003) 1.25

Regulated RNA processing in the control of Arabidopsis flowering. Int J Dev Biol (2005) 1.19

Protocol dependence of sequencing-based gene expression measurements. PLoS One (2011) 1.19

Defective interfering RNA hinders the activity of a tombusvirus-encoded posttranscriptional gene silencing suppressor. J Virol (2005) 1.16

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. Nucleic Acids Res (2007) 1.15

PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity. Sci Signal (2012) 1.15

A normalised scale for structural genomics target ranking: the OB-Score. FEBS Lett (2006) 1.15

Association of torsades de pointes with novel and known single nucleotide polymorphisms in long QT syndrome genes. Am Heart J (2006) 1.12

Association between single-nucleotide polymorphisms in the endothelial lipase (LIPG) gene and high-density lipoprotein cholesterol levels. Biochim Biophys Acta (2004) 1.12

Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res (2008) 1.12

The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4. EMBO J (2011) 1.11

ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics (2008) 1.10

The serotonin transporter polymorphism, 5HTTLPR, is associated with a faster response time to sertraline in an elderly population with major depressive disorder. Psychopharmacology (Berl) (2003) 1.09

Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma. Nat Genet (2012) 1.08

NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. BMC Bioinformatics (2011) 1.06

An allelic series reveals essential roles for FY in plant development in addition to flowering-time control. Development (2005) 1.06

Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing. Hum Gene Ther (2011) 1.05

Role of a KCNH2 polymorphism (R1047 L) in dofetilide-induced Torsades de Pointes. J Mol Cell Cardiol (2004) 1.05

The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe. BMC Genomics (2007) 1.04

Human box C/D snoRNA processing conservation across multiple cell types. Nucleic Acids Res (2011) 1.04

CETP polymorphisms associated with HDL cholesterol may differ from those associated with cardiovascular disease. Atherosclerosis (2005) 1.04

Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing. PLoS One (2013) 1.03

Single-molecule sequencing: sequence methods to enable accurate quantitation. Methods Enzymol (2010) 1.01

The properties and applications of single-molecule DNA sequencing. Genome Biol (2011) 1.00

Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA. Bioinformatics (2011) 1.00

Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations. Genome Res (2011) 0.99

Drug-metabolizing enzymes: evidence for clinical utility of pharmacogenomic tests. Clin Pharmacol Ther (2005) 0.98

A new family of transcription factors. Development (2008) 0.98

The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics (2008) 0.97

Polymorphisms in the CETP gene and association with CETP mass and HDL levels. Atherosclerosis (2003) 0.96

Identification of a glycosylphosphatidylinositol anchor-modifying beta1-3 N-acetylglucosaminyl transferase in Trypanosoma brucei. Mol Microbiol (2008) 0.96

The kinomes of apicomplexan parasites. Microbes Infect (2012) 0.96

Single-molecule direct RNA sequencing without cDNA synthesis. Wiley Interdiscip Rev RNA (2011) 0.95

Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors. Mol Biol Cell (2010) 0.94

Quantification of the variation in percentage identity for protein sequence alignments. BMC Bioinformatics (2006) 0.94

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities. BMC Res Notes (2011) 0.92

Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA. PLoS Genet (2013) 0.91