Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries

The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation

(2021) Cecilia B. Levandowski et al.   PLOS BIOLOGY

Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment

(2021) Jonathan D. Rubin et al.   Communications Biology

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

(2020) Yuki Aoi et al.   MOLECULAR CELL

Batch correction evaluation framework using a-priori gene-gene associations: applied to the GTEx dataset

(2019) Judith Somekh et al.   BMC BIOINFORMATICS

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

(2019) Sarah K. Sasse et al.   GENOME RESEARCH

Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions

(2019) Iris Steinparzer et al.   MOLECULAR CELL

Targeting Spt5-Pol II by Small-Molecule Inhibitors Uncouples Distinct Activities and Reveals Additional Regulatory Roles

(2019) Anat Bahat et al.   MOLECULAR CELL

Nascent RNA analyses: tracking transcription and its regulation

(2019) Erin M. Wissink et al.   NATURE REVIEWS GENETICS

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species

(2019) Tianshun Gao et al.   NUCLEIC ACIDS RESEARCH

Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input

(2019) Dimitra Sarantopoulou et al.   Scientific Reports

Enhancer RNA profiling predicts transcription factor activity

(2018) Joseph G. Azofeifa et al.   GENOME RESEARCH

Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies

(2018) Haridha Shivram et al.   RNA

Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast

(2018) Gregory T. Booth et al.   Nature Communications

Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

(2018) Jing Wang et al.   BMC GENOMICS

Exploring the effect of library preparation on RNA sequencing experiments

(2018) Lei Wang et al.   GENOMICS

Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity

(2017) Zdenek Andrysik et al.   GENOME RESEARCH

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

(2017) Noah Dukler et al.   GENOME RESEARCH

Why Batch Effects Matter in Omics Data, and How to Avoid Them

(2017) Wilson Wen Bin Goh et al.   TRENDS IN BIOTECHNOLOGY

Lingering Questions about Enhancer RNA and Enhancer Transcription-Coupled Genomic Instability

(2017) Gerson Rothschild et al.   TRENDS IN GENETICS

A generative model for the behavior of RNA polymerase

(2016) Joseph G. Azofeifa et al.   BIOINFORMATICS

Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest

(2016) Andrea Orioli et al.   GENOME RESEARCH

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation

(2016) Dig B. Mahat et al.   MOLECULAR CELL

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR

(2015) Thomas C Roberts et al.   Nature Protocols

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

(2014) Robin Andersson et al.   Nature Communications

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms

(2014) Mary Ann Allen et al.   eLife

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

(2014) Iris Jonkers et al.   eLife

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

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

(2013) H. Kwak et al.   SCIENCE

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

Pharmacologic Activation of p53 by Small-Molecule MDM2 Antagonists

(2011) Hong Shen et al.   CURRENT PHARMACEUTICAL DESIGN

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE