Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

(2015) Paul L. Boutz et al.   GENES & DEVELOPMENT

Regulated Intron Retention and Nuclear Pre-mRNA Decay Contribute toPABPN1Autoregulation

(2015) Danny Bergeron et al.   MOLECULAR AND CELLULAR BIOLOGY

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3′ processing

(2014) Serena L. Chan et al.   GENES & DEVELOPMENT

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

(2014) Lars Schönemann et al.   GENES & DEVELOPMENT

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Depletion of REF/Aly alters gene expression and reduces RNA polymerase II occupancy

(2014) Sarah H. Stubbs et al.   NUCLEIC ACIDS RESEARCH

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

(2014) Robin Andersson et al.   Nature Communications

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

(2013) Daniel Schulz et al.   CELL

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

CBC–ARS2 stimulates 3′-end maturation of multiple RNA families and favors cap-proximal processing

(2013) Marie Hallais et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The human cap-binding complex is functionally connected to the nuclear RNA exosome

(2013) Peter Refsing Andersen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Introns Regulate Gene Expression in Cryptococcus neoformans in a Pab2p Dependent Pathway

(2013) Carolin Goebels et al.   PLoS Genetics

The emerging role of triple helices in RNA biology

(2013) Nicholas K. Conrad   Wiley Interdisciplinary Reviews-RNA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Chemical Reporters for Monitoring RNA Synthesis and Poly(A) Tail Dynamics

(2012) Markus Grammel et al.   CHEMBIOCHEM

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

(2012) K. Yap et al.   GENES & DEVELOPMENT

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

Rrp6p Controls mRNA Poly(A) Tail Length and Its Decoration with Poly(A) Binding Proteins

(2012) Manfred Schmid et al.   MOLECULAR CELL

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

NMD: a multifaceted response to premature translational termination

(2012) Stephanie Kervestin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Polyadenylation-Dependent Control of Long Noncoding RNA Expression by the Poly(A)-Binding Protein Nuclear 1

(2012) Yves B. Beaulieu et al.   PLoS Genetics

Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor

(2011) Kensuke Ninomiya et al.   JOURNAL OF CELL BIOLOGY

A Pre-mRNA Degradation Pathway that Selectively Targets Intron-Containing Genes Requires the Nuclear Poly(A)-Binding Protein

(2011) Caroline Lemieux et al.   MOLECULAR CELL

Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex

(2011) Michal Lubas et al.   MOLECULAR CELL

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

(2011) Pascal Preker et al.   NUCLEIC ACIDS RESEARCH

The Fission Yeast RNA Binding Protein Mmi1 Regulates Meiotic Genes by Controlling Intron Specific Splicing and Polyadenylation Coupled RNA Turnover

(2011) Huei-Mei Chen et al.   PLoS One

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

(2011) R. A. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1

(2011) Tyler J. Creamer et al.   PLoS Genetics

Importance of polyadenylation in the selective elimination of meiotic mRNAs in growing S. pombe cells

(2010) Soichiro Yamanaka et al.   EMBO JOURNAL

The Nuclear Poly(A)-Binding Protein Interacts with the Exosome to Promote Synthesis of Noncoding Small Nucleolar RNAs

(2010) Jean-François Lemay et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Mechanisms of nuclear mRNA quality control

(2010) Milo B. Fasken et al.   RNA Biology

Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix

(2010) R. M. Mitton-Fry et al.   SCIENCE

Control of poly(A) tail length

(2010) Christian R. Eckmann et al.   Wiley Interdisciplinary Reviews-RNA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Proteome analysis of human nuclear insoluble fractions

(2009) Hideaki Takata et al.   GENES TO CELLS

Poly(A) Tail Length Is Controlled by the Nuclear Poly(A)-binding Protein Regulating the Interaction between Poly(A) Polymerase and the Cleavage and Polyadenylation Specificity Factor

(2009) Uwe Kühn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Aberrant Herpesvirus-Induced Polyadenylation Correlates With Cellular Messenger RNA Destruction

(2009) Yeon J. Lee et al.   PLOS BIOLOGY

Distinct Roles of Non-Canonical Poly(A) Polymerases in RNA Metabolism

(2009) Salvatore San Paolo et al.   PLoS Genetics

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE