The Exosome Component Rrp6 Is Required for RNA Polymerase II Termination at Specific Targets of the Nrd1-Nab3 Pathway

Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

(2014) Agnieszka Tudek et al.   MOLECULAR CELL

Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements

(2014) Daechan Park et al.   NUCLEIC ACIDS RESEARCH

Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast

(2014) Manuele Castelnuovo et al.   NUCLEIC ACIDS RESEARCH

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

(2013) Daniel Schulz et al.   CELL

The RNA Polymerase II C-terminal Domain-interacting Domain of Yeast Nrd1 Contributes to the Choice of Termination Pathway and Couples to RNA Processing by the Nuclear Exosome

(2013) Dong-hyuk Heo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cotranscriptional Recruitment of RNA Exosome Cofactors Rrp47p and Mpp6p and Two Distinct Trf-Air-Mtr4 Polyadenylation (TRAMP) Complexes Assists the Exonuclease Rrp6p in the Targeting and Degradation of an Aberrant Messenger Ribonucleoprotein Particle (mRNP) in Yeast

(2013) Igor Stuparevic et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Network of Interdependent Molecular Interactions Describes a Higher Order Nrd1-Nab3 Complex Involved in Yeast Transcription Termination

(2013) Travis J. Loya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Poly(A) Tail-Mediated Gene Regulation by Opposing Roles of Nab2 and Pab2 Nuclear Poly(A)-Binding Proteins in Pre-mRNA Decay

(2013) V. Grenier St-Sauveur et al.   MOLECULAR AND CELLULAR BIOLOGY

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex

(2013) Debora Lika Makino et al.   NATURE

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

The RNA exosome and proteasome: common principles of degradation control

(2013) Debora L. Makino et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Bimodal expression of PHO84 is modulated by early termination of antisense transcription

(2013) Manuele Castelnuovo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Role of Ctk1 Kinase in Termination of Small Non-Coding RNAs

(2013) Tineke L. Lenstra et al.   PLoS One

Threading the barrel of the RNA exosome

(2013) Claudia Schneider et al.   TRENDS IN BIOCHEMICAL SCIENCES

Long Noncoding RNAs Promote Transcriptional Poising of Inducible Genes

(2013) Sara C. Cloutier et al.   PLOS BIOLOGY

Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA)

(2012) B. Schwalb et al.   BIOINFORMATICS

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

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

In vivoSELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination

(2012) Odil Porrua et al.   EMBO JOURNAL

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

Yeast Nab3 Protein Contains a Self-assembly Domain Found in Human Heterogeneous Nuclear Ribonucleoprotein-C (hnRNP-C) That Is Necessary for Transcription Termination

(2012) Travis J. Loya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptome-wide Analysis of Exosome Targets

(2012) Claudia Schneider 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

Extensive Degradation of RNA Precursors by the Exosome in Wild-Type Cells

(2012) Rajani Kanth Gudipati et al.   MOLECULAR CELL

Kinetic Competition between RNA Polymerase II and Sen1-Dependent Transcription Termination

(2012) Dane Z. Hazelbaker et al.   MOLECULAR CELL

A genetic screen for terminator function in yeast identifies a role for a new functional domain in termination factor Nab3

(2012) T. J. Loya et al.   NUCLEIC ACIDS RESEARCH

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

(2011) Wiebke Wlotzka et al.   EMBO JOURNAL

H3K4 Trimethylation by Set1 Promotes Efficient Termination by the Nrd1-Nab3-Sen1 Pathway

(2011) N. Terzi et al.   MOLECULAR AND CELLULAR BIOLOGY

Sen-sing RNA Terminators

(2011) David A. Brow   MOLECULAR CELL

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

(2011) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing

(2011) N. Jamonnak et al.   RNA

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

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes

(2010) Amber L. Mosley et al.   MOLECULAR & CELLULAR PROTEOMICS

Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain

(2010) Bradley M Lunde et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Uniform transitions of the general RNA polymerase II transcription complex

(2010) Andreas Mayer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nuclear mRNA quality control in yeast is mediated by Nrd1 co-transcriptional recruitment, as revealed by the targeting of Rho-induced aberrant transcripts

(2010) Romy Honorine et al.   NUCLEIC ACIDS RESEARCH

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

(2010) Moran Yassour et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation

(2009) Fabien Bonneau et al.   CELL

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

(2009) J. Camblong et al.   GENES & DEVELOPMENT

Yeast RNase III Triggers Polyadenylation-Independent Transcription Termination

(2009) Ghada Ghazal et al.   MOLECULAR CELL

Fail-Safe Transcriptional Termination for Protein-Coding Genes in S. cerevisiae

(2009) Ana G. Rondón et al.   MOLECULAR CELL

TFIIH Kinase Places Bivalent Marks on the Carboxy-Terminal Domain of RNA Polymerase II

(2009) Md. Sohail Akhtar et al.   MOLECULAR CELL

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Polyadenylation Linked to Transcription Termination Directs the Processing of snoRNA Precursors in Yeast

(2008) Pawel Grzechnik et al.   MOLECULAR CELL

Transcription Termination and RNA Degradation Contribute to Silencing of RNA Polymerase II Transcription within Heterochromatin

(2008) Lidia Vasiljeva et al.   MOLECULAR CELL

A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster

(2008) Jonathan Houseley et al.   MOLECULAR CELL

Structure of the Active Subunit of the Yeast Exosome Core, Rrp44: Diverse Modes of Substrate Recruitment in the RNase II Nuclease Family

(2008) Esben Lorentzen et al.   MOLECULAR CELL

Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice

(2008) Rajani Kanth Gudipati et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain

(2008) Lidia Vasiljeva et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE