Using TTchem-seq for profiling nascent transcription and measuring transcript elongation

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins

(2019) Lea H. Gregersen et al.   CELL

Global donor and acceptor splicing site kinetics in human cells

(2019) Leonhard Wachutka et al.   eLife

TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding

(2018) Jeremy A Schofield et al.   NATURE METHODS

Solid phase chemistry to covalently and reversibly capture thiolated RNA

(2018) Erin E Duffy et al.   NUCLEIC ACIDS RESEARCH

The Implication of Early Chromatin Changes in X Chromosome Inactivation

(2018) Jan Jakub Żylicz et al.   CELL

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation

(2017) Margaux Michel et al.   Molecular Systems Biology

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Comprehensive analysis of nucleocytoplasmic dynamics of mRNA in Drosophila cells

(2017) Tao Chen et al.   PLoS Genetics

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture

(2017) Athma A Pai et al.   eLife

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Degradation dynamics of microRNAs revealed by a novel pulse-chase approach

(2016) Matteo J. Marzi et al.   GENOME RESEARCH

Strand‐specific, high‐resolution mapping of modified RNA polymerase II

(2016) Laura Milligan et al.   Molecular Systems Biology

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

(2016) Neelanjan Mukherjee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Integrative classification of human coding and noncoding genes through RNA metabolism profiles

(2016) Neelanjan Mukherjee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Simultaneous measurement of genome-wide transcription elongation speeds and rates of RNA polymerase II transition into active elongation with 4sUDRB-seq

(2015) Gilad Fuchs et al.   Nature Protocols

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

(2014) S. Anders et al.   BIOINFORMATICS

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

(2014) Marco Saponaro et al.   CELL

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani et al.   CELL

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

MOV10 Is a 5′ to 3′ RNA Helicase Contributing to UPF1 mRNA Target Degradation by Translocation along 3′ UTRs

(2014) Lea H. Gregersen et al.   MOLECULAR CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Mapping of Yeast RNA Polymerase II Termination

(2014) Paul Schaughency et al.   PLoS Genetics

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

(2014) Gilad Fuchs et al.   GENOME BIOLOGY

Mouse TU tagging: a chemical/genetic intersectional method for purifying cell type-specific nascent RNA

(2013) L. Gay et al.   GENES & DEVELOPMENT

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response

(2013) Kaspar Burger et al.   RNA Biology

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

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

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

(2012) M. Sun et al.   GENOME RESEARCH

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

(2011) Sarah E. Munchel et al.   MOLECULAR BIOLOGY OF THE CELL

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

TU-tagging: cell type–specific RNA isolation from intact complex tissues

(2009) Michael R Miller et al.   NATURE METHODS

Rates of in situ transcription and splicing in large human genes

(2009) Jarnail Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA

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

(2008) Leighton J. Core et al.   SCIENCE