LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival

Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma

(2020) Swati Venkat et al.   GENOME RESEARCH

APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms

(2020) Ruijia Wang et al.   BIOINFORMATICS

Modeling Hypoxia-Induced Neuropathies Using a Fast and Scalable Human Motor Neuron Differentiation System

(2020) Laura I. Hudish et al.   Stem Cell Reports

Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors

(2019) Elena Grassi et al.   Frontiers in Cellular Neuroscience

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2

(2019) Shannon Farris et al.   Cell Reports

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism

(2019) Michael A. Cortazar et al.   MOLECULAR CELL

Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation

(2018) Yong Zhu et al.   MOLECULAR CELL

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

(2018) Daniel Dominguez et al.   MOLECULAR CELL

Alternative 3′ UTRs Modify the Localization, Regulatory Potential, Stability, and Plasticity of mRNAs in Neuronal Compartments

(2018) Georgi Tushev et al.   NEURON

QuantSeq 3′ mRNA sequencing for RNA quantification

(2018) Pamela Moll et al.   NATURE METHODS

Alternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartments

(2018) Camilla Ciolli Mattioli et al.   NUCLEIC ACIDS RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Molecular basis for the recognition of the human AAUAAA polyadenylation signal

(2017) Yadong Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster

(2017) Xiaochuan Liu et al.   RNA

CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells

(2017) Louis Philip Benoit Bouvrette et al.   RNA

Extracellular matrix stiffness and cell contractility control RNA localization to promote cell migration

(2017) Tianhong Wang et al.   Nature Communications

RNA localization is a key determinant of neurite-enriched proteome

(2017) Alessandra Zappulo et al.   Nature Communications

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq

(2017) Bin Li et al.   Scientific Reports

Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries

(2016) Elena Grassi et al.   BMC BIOINFORMATICS

Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control

(2016) Wencheng Li et al.   BMC BIOLOGY

Distal Alternative Last Exons Localize mRNAs to Neural Projections

(2016) J. Matthew Taliaferro et al.   MOLECULAR CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

3′READS+, a sensitive and accurate method for 3′ end sequencing of polyadenylated RNA

(2016) Dinghai Zheng et al.   RNA

Polyester: simulating RNA-seq datasets with differential transcript expression

(2015) Alyssa C. Frazee et al.   BIOINFORMATICS

Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions

(2015) Faraz K. Mardakheh et al.   DEVELOPMENTAL CELL

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

(2015) Yongsheng Shi et al.   GENES & DEVELOPMENT

Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization

(2015) Binyamin D. Berkovits et al.   NATURE

Leveraging transcript quantification for fast computation of alternative splicing profiles

(2015) Gael P. Alamancos et al.   RNA

Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

(2015) Wencheng Li et al.   PLoS Genetics

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33

(2014) Lars Schönemann et al.   GENES & DEVELOPMENT

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

(2014) Chioniso P. Masamha et al.   NATURE

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

Subcellular transcriptomics-Dissection of the mRNA composition in the axonal compartment of sensory neurons

(2013) Adi Minis et al.   Developmental Neurobiology

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

(2013) S. Lianoglou et al.   GENES & DEVELOPMENT

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

(2013) J. A. Hurt et al.   GENOME RESEARCH

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Alexander Sherstnev et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cleavage factor Imis a key regulator of 3′ UTR length

(2012) Andreas R. Gruber et al.   RNA Biology

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm

(2012) Milan Spasic et al.   PLoS Genetics

Streamlined platform for short hairpin RNA interference and transgenesis in cultured mammalian cells

(2011) P. Khandelia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

(2011) X. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autoregulation of the nonsense-mediated mRNA decay pathway in human cells

(2011) H. Yepiskoposyan et al.   RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Molecular Architecture of the Human Pre-mRNA 3′ Processing Complex

(2009) Yongsheng Shi et al.   MOLECULAR CELL

Reprogramming of 3′ Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types

(2009) Zhe Ji et al.   PLoS One

Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development

(2009) Z. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct Role of Long 3′ UTR BDNF mRNA in Spine Morphology and Synaptic Plasticity in Hippocampal Neurons

(2008) Juan Ji An et al.   CELL

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE