Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes

Two distinct transcription termination modes dictated by promoters

(2017) Takashi S. Miki et al.   GENES & DEVELOPMENT

Dehydration stress extends mRNA 3′ untranslated regions with noncoding RNA functions in Arabidopsis

(2017) Hai-Xi Sun et al.   GENOME RESEARCH

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

(2017) Carlo Baejen et al.   MOLECULAR CELL

Alternative Polyadenylation of the Sense Transcript Controls Antisense Transcription of DELAY OF GERMINATION 1 in Arabidopsis

(2017) Justyna Kowalczyk et al.   Molecular Plant

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes

(2017) Nicole Uwimana et al.   NUCLEIC ACIDS RESEARCH

Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

(2017) Anna Vilborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription of a 5' extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter

(2017) Minghao Chia et al.   eLife

A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

(2017) Wannarat Pornsiriwong et al.   eLife

Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins

(2016) Huang Wu et al.   MOLECULAR CELL

The regulation and functions of the nuclear RNA exosome complex

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

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans

(2016) Takashi S. Miki et al.   PLoS Genetics

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

(2016) Julio C. Morales et al.   PLoS Genetics

A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5’-3’ Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe

(2016) James Franklin Tucker et al.   PLoS Genetics

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

(2015) C. Yuan et al.   DNA RESEARCH

Endless Quarrels at the End of Genes

(2015) Domenico Libri   MOLECULAR CELL

Poly(A) Signal-Dependent Transcription Termination Occurs through a Conformational Change Mechanism that Does Not Require Cleavage at the Poly(A) Site

(2015) Huimin Zhang et al.   MOLECULAR CELL

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

(2015) Nova Fong et al.   MOLECULAR CELL

Widespread Inducible Transcription Downstream of Human Genes

(2015) Anna Vilborg et al.   MOLECULAR CELL

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

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

The expanding world of small RNAs in plants

(2015) Filipe Borges et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes

(2015) Jean-Sébastien Parent et al.   NUCLEIC ACIDS RESEARCH

Unraveling the mechanistic features of RNA polymerase II termination by the 5′-3′ exoribonuclease Rat1

(2015) Jieun Park et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

(2015) Ana R Grosso et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Recurrent read-through fusion transcripts in breast cancer

(2014) Katherine E. Varley et al.   BREAST CANCER RESEARCH AND TREATMENT

XRN 5′→3′ exoribonucleases: Structure, mechanisms and functions

(2013) Vinay K. Nagarajan et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Dismantling Promoter-driven RNA Polymerase II Transcription Complexesin Vitroby the Termination Factor Rat1

(2013) Erika L. Pearson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Mammalian Pre-mRNA 5′ End Capping Quality Control Mechanism and an Unexpected Link of Capping to Pre-mRNA Processing

(2013) Xinfu Jiao et al.   MOLECULAR CELL

Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation

(2013) Anna Golisz et al.   NUCLEIC ACIDS RESEARCH

Co-transcriptional degradation of aberrant pre-mRNA by Xrn2

(2012) Lee Davidson et al.   EMBO JOURNAL

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

(2012) Kris Brannan 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

Surveillance of 3′ Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis

(2012) Yukio Kurihara et al.   G3-Genes Genomes Genetics

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

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

Evidence for a SAL1-PAP Chloroplast Retrograde Pathway That Functions in Drought and High Light Signaling inArabidopsis

(2011) Gonzalo M. Estavillo et al.   PLANT CELL

RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Yeast 5′-3′ Exonuclease Rat1p Functions during Transcription Elongation by RNA Polymerase II

(2010) Silvia Jimeno-González et al.   MOLECULAR CELL

Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA

(2010) Monika Zakrzewska-Placzek et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Novel Tandem Reporter Quantifies RNA Polymerase II Termination in Mammalian Cells

(2009) Ayan Banerjee et al.   PLoS One

Degradation of a Polyadenylated rRNA Maturation By-Product Involves One of the Three RRP6-Like Proteins in Arabidopsis thaliana

(2008) H. Lange et al.   MOLECULAR AND CELLULAR BIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS