POINT technology illuminates the processing of polymerase-associated intact nascent transcripts

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

(2021) Kirsten A. Reimer et al.   MOLECULAR CELL

Transcriptome maps of general eukaryotic RNA degradation factors

(2019) Salma Sohrabi-Jahromi et al.   eLife

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

The Integrator complex cleaves nascent mRNAs to attenuate transcription

(2019) Deirdre C. Tatomer et al.   GENES & DEVELOPMENT

A Complex of U1 snRNP with Cleavage and Polyadenylation Factors Controls Telescripting, Regulating mRNA Transcription in Human Cells

(2019) Byung Ran So et al.   MOLECULAR CELL

NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements

(2019) Shigeki Hirabayashi et al.   NATURE GENETICS

Transcriptional Control by Premature Termination: A Forgotten Mechanism

(2019) Kinga Kamieniarz-Gdula et al.   TRENDS IN GENETICS

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

(2019) Jernej Ule et al.   MOLECULAR CELL

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes

(2019) Joshua D. Eaton et al.   GENES & DEVELOPMENT

The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes

(2019) Nathan D. Elrod et al.   MOLECULAR CELL

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler et al.   MOLECULAR CELL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

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

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

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

(2018) Lydia Herzel et al.   GENOME RESEARCH

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima et al.   MOLECULAR CELL

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing

(2018) Takayuki Nojima et al.   MOLECULAR CELL

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability

(2017) Amandine Bonnet et al.   MOLECULAR CELL

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

(2017) Margarita Schlackow et al.   MOLECULAR CELL

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Birth and Death of Histone mRNAs

(2017) William F. Marzluff et al.   TRENDS IN GENETICS

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

(2016) Yun Chen et al.   NATURE GENETICS

Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide

(2016) Takayuki Nojima et al.   Nature Protocols

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

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

(2015) Takayuki Nojima et al.   CELL

Molecular Basis of Transcription-Coupled Pre-mRNA Capping

(2015) Fuensanta W. Martinez-Rucobo et al.   MOLECULAR CELL

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs

(2015) Ashish Dhir et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Widespread disruption of host transcription termination in HSV-1 infection

(2015) Andrzej J. Rutkowski et al.   Nature Communications

Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs

(2015) Ashish Dhir et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2015) Ana R Grosso et al.   eLife

A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation

(2014) Keerthi T. Chathoth et al.   MOLECULAR CELL

Regulation of microRNA biogenesis

(2014) Minju Ha et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

(2012) L. Windhager et al.   GENOME RESEARCH

Mechanisms and Consequences of Alternative Polyadenylation

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

snRNA 3′ end formation: the dawn of the Integrator complex

(2010) Jiandong Chen et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production

(2008) Jan M. Pawlicki et al.   JOURNAL OF CELL BIOLOGY

Primary microRNA transcripts are processed co-transcriptionally

(2008) Mariangela Morlando et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE