Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation

Integrator is a genome-wide attenuator of non-productive transcription

(2021) Søren Lykke-Andersen et al.   MOLECULAR CELL

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

(2020) Dorte B. Bekker-Jensen et al.   MOLECULAR & CELLULAR PROTEOMICS

A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome

(2020) Guifen Wu et al.   Cell Reports

TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples

(2020) Jiaming Li et al.   NATURE METHODS

The RNA exosome shapes the expression of key protein-coding genes

(2020) Mengjun Wu et al.   NUCLEIC ACIDS RESEARCH

EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells

(2020) Seiko Yoshino et al.   Scientific Reports

RNA helicases are hubs that orchestrate exosome-dependent 3′–5′ decay

(2020) Eva-Maria Weick et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control

(2019) Lee Davidson et al.   Cell Reports

Streamlined protocol for deep proteomic profiling of FAC-sorted cells and its application to freshly isolated murine immune cells

(2019) Samuel A Myers et al.   MOLECULAR & CELLULAR PROTEOMICS

Protein aggregation capture on microparticles enables multi-purpose proteomics sample preparation.

(2019) Tanveer Singh Batth et al.   MOLECULAR & CELLULAR PROTEOMICS

Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole

(2019) Aisha Yesbolatova et al.   METHODS

Advances in targeted degradation of endogenous proteins

(2019) Sascha Röth et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A systems view of spliceosomal assembly and branchpoints with iCLIP

(2019) Michael Briese et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set

(2019) Andrew Thompson et al.   ANALYTICAL CHEMISTRY

The human ZC3H3 and RBM26/27 proteins are critical for PAXT-mediated nuclear RNA decay

(2019) Toomas Silla et al.   NUCLEIC ACIDS RESEARCH

Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex

(2018) Eva-Maria Weick et al.   CELL

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

(2018) Joshua D. Eaton et al.   GENES & DEVELOPMENT

Proteome-wide identification of ubiquitin interactions using UbIA-MS

(2018) Xiaofei Zhang et al.   Nature Protocols

Controlling nuclear RNA levels

(2018) Manfred Schmid et al.   NATURE REVIEWS GENETICS

The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts

(2018) Toomas Silla et al.   Cell Reports

The splicing factor SRSF3 is functionally connected to the nuclear RNA exosome for intronless mRNA decay

(2018) Fabrice Mure et al.   Scientific Reports

The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN

(2018) Chi-Kang Tseng et al.   Nature Communications

Small Nucleolar RNAs Tell a Different Tale

(2018) Joanna Kufel et al.   TRENDS IN GENETICS

Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors

(2017) John C. Zinder et al.   GENES & DEVELOPMENT

An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression

(2017) Koichi Ogami et al.   GENES & DEVELOPMENT

Cleavage and polyadenylation: Ending the message expands gene regulation

(2017) Jonathan Neve et al.   RNA Biology

The RNA exosome and RNA exosome-linked disease

(2017) Derrick J. Morton et al.   RNA

Collaborative Control of Cell Cycle Progression by the RNA Exonuclease Dis3 and Ras Is Conserved Across Species

(2016) Mark J. Snee et al.   GENETICS

Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex

(2016) Eva Kowalinski et al.   MOLECULAR CELL

Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts

(2016) Nicola Meola et al.   MOLECULAR CELL

The regulation and functions of the nuclear RNA exosome complex

(2016) Cornelia Kilchert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Structure of the RBM7–ZCCHC8 core of the NEXT complex reveals connections to splicing factors

(2016) Sebastian Falk et al.   Nature Communications

Collaborative Control of Cell Cycle Progression by the RNA Exonuclease Dis3 and Ras Is Conserved Across Species

(2016) Mark J. Snee et al.   GENETICS

DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts

(2015) Teresa Szczepińska et al.   GENOME RESEARCH

RNA degradation paths in a 12-subunit nuclear exosome complex

(2015) Debora Lika Makino et al.   NATURE

RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3′-end extended forms of snRNAs

(2015) Dominika Hrossova et al.   NUCLEIC ACIDS RESEARCH

The Human Nuclear Exosome Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis

(2015) Michal Lubas et al.   Cell Reports

Human Telomerase RNA Processing and Quality Control

(2015) Chi-Kang Tseng et al.   Cell Reports

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

(2015) Stefan M. Bresson et al.   PLoS Genetics

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

The eukaryotic RNA exosome

(2014) Kurt Januszyk et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure of an Rrp6–RNA exosome complex bound to poly(A) RNA

(2014) Elizabeth V. Wasmuth et al.   NATURE

Certain Adenylated Non-Coding RNAs, Including 5′ Leader Sequences of Primary MicroRNA Transcripts, Accumulate in Mouse Cells following Depletion of the RNA Helicase MTR4

(2014) Jane E. Dorweiler et al.   PLoS One

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

The Elg1 Replication Factor C-like Complex Functions in PCNA Unloading during DNA Replication

(2013) Takashi Kubota et al.   MOLECULAR CELL

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

(2013) Debora Lika Makino et al.   NATURE

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

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

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

Multiple myeloma-associated hDIS3 mutations cause perturbations in cellular RNA metabolism and suggest hDIS3 PIN domain as a potential drug target

(2013) R. Tomecki et al.   NUCLEIC ACIDS RESEARCH

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Transcriptome-wide Analysis of Exosome Targets

(2012) Claudia Schneider et al.   MOLECULAR CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming

(2012) H. Berndt et al.   RNA

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

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

Degradation of mRNAs that lack a stop codon: a decade of nonstop progress

(2012) A. Alejandra Klauer et al.   Wiley Interdisciplinary Reviews-RNA

Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex

(2011) Michal Lubas et al.   MOLECULAR CELL

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

(2011) Eivind Valen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Activities of human RRP6 and structure of the human RRP6 catalytic domain

(2011) K. Januszyk et al.   RNA

The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L

(2010) Rafal Tomecki et al.   EMBO JOURNAL

RNA decay modulates gene expression and controls its fidelity

(2010) Shubhendu Ghosh et al.   Wiley Interdisciplinary Reviews-RNA

The Many Pathways of RNA Degradation

(2009) Jonathan Houseley et al.   CELL

An auxin-based degron system for the rapid depletion of proteins in nonplant cells

(2009) Kohei Nishimura et al.   NATURE METHODS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

The RNA Exosome Component hRrp6 Is a Target for 5-Fluorouracil in Human Cells

(2008) S. Kammler et al.   MOLECULAR CANCER RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p

(2008) Kevin P. Callahan et al.   NUCLEIC ACIDS RESEARCH