Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation

Alternative polyadenylation of mRNA precursors

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

Global transcript structure resolution of high gene density genomes through multi-platform data integration

(2016) Tina O'Grady et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Dinghai Zheng et al.   RNA

The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion

(2016) Ina Hollerer et al.   RNA

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

(2016) Nicholas J. Schurch et al.   RNA

KDM5 lysine demethylases are involved in maintenance of 3'UTR length

(2016) L. P. Blair et al.   Science Advances

ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3′-Azido cDNAs

(2015) Andrew Routh et al.   JOURNAL OF MOLECULAR BIOLOGY

ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System

(2015) Katarzyna Oktaba et al.   MOLECULAR CELL

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Picornavirus RNA polyadenylation by 3Dpol, the viral RNA-dependent RNA polymerase

(2015) Brian J. Kempf et al.   VIRUS RESEARCH

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

(2014) B. Lackford et al.   EMBO JOURNAL

Delineating the Structural Blueprint of the Pre-mRNA 3'-End Processing Machinery

(2014) K. Xiang et al.   MOLECULAR AND CELLULAR BIOLOGY

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types

(2014) Zheng Xia et al.   Nature Communications

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

Functional Analysis of the Integrator Subunit 12 Identifies a Microdomain That Mediates Activation of theDrosophilaIntegrator Complex

(2013) Jiandong Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

High throughput characterizations of poly(A) site choice in plants

(2013) Liuyin Ma et al.   METHODS

Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation

(2013) Juan Mata   RNA Biology

Putting an ‘End’ to HIV mRNAs: capping and polyadenylation as potential therapeutic targets

(2013) Jeffrey Wilusz   AIDS Research and Therapy

The Poly(A)-Binding Protein Nuclear 1 Suppresses Alternative Cleavage and Polyadenylation Sites

(2012) Mathias Jenal et al.   CELL

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Control of Polyadenylation Site Choice by CPSF30 in Arabidopsis

(2012) P. E. Thomas et al.   PLANT CELL

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation

(2012) C. Yao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cleavage factor Imis a key regulator of 3′ UTR length

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

An RNAi screen identifies additional members of the Drosophila Integrator complex and a requirement for cyclin C/Cdk8 in snRNA 3'-end formation

(2012) J. Chen et al.   RNA

Alternative polyadenylation: New insights from global analyses

(2012) Y. Shi   RNA

Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

(2012) Peter Smibert et al.   Cell Reports

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

E2F mediates enhanced alternative polyadenylation in proliferation

(2012) Ran Elkon et al.   GENOME BIOLOGY

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Mechanisms and Consequences of Alternative Polyadenylation

(2011) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

Crystal Structure of a Human Cleavage Factor CFIm25/CFIm68/RNA Complex Provides an Insight into Poly(A) Site Recognition and RNA Looping

(2011) Qin Yang et al.   STRUCTURE

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

(2010) Fatih Ozsolak et al.   CELL

A Subset of Drosophila Integrator Proteins Is Essential for Efficient U7 snRNA and Spliceosomal snRNA 3'-End Formation

(2010) N. Ezzeddine et al.   MOLECULAR AND CELLULAR BIOLOGY

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

The Landscape of C. elegans 3'UTRs

(2010) M. Mangone et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Christine Mayr et al.   CELL

Involvement of Pta1, Pcf11 and aKlCYC1AU-rich element in alternative RNA 3′-end processing selection in yeast

(2009) Silvia Seoane et al.   FEBS LETTERS

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

Knockdown of SLBP results in nuclear retention of histone mRNA

(2009) K. D. Sullivan et al.   RNA

Regulation of alternative polyadenylation by genomic imprinting

(2008) A. J. Wood et al.   GENES & DEVELOPMENT

Triazole-Linked Analogue of Deoxyribonucleic Acid (TLDNA): Design, Synthesis, and Double-Strand Formation with Natural DNA

(2008) Hiroyuki Isobe et al.   ORGANIC LETTERS

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

(2008) R. Sandberg et al.   SCIENCE