GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters

Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing

(2014) Jun Liang et al.   MOLECULAR CELL

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

(2014) Iris Jonkers et al.   eLife

Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

(2013) Jian Li et al.   EMBO JOURNAL

Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing

(2013) Jian Li et al.   MOLECULAR CELL

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

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

Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals

(2013) Telmo Henriques et al.   MOLECULAR CELL

High-resolution mapping of transcription factor binding sites on native chromatin

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

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

(2013) H. Kwak et al.   SCIENCE

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Fcp1 Dephosphorylation of the RNA Polymerase II C-Terminal Domain Is Required for Efficient Transcription of Heat Shock Genes

(2012) N. J. Fuda et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Defining the Status of RNA Polymerase at Promoters

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

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Analysis and recognition of the GAGA transcription factor binding sites in Drosophila genes

(2011) E.S. Omelina et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

The Polycomb Group Mutant esc Leads to Augmented Levels of Paused Pol II in the Drosophila Embryo

(2011) Vivek S. Chopra et al.   MOLECULAR CELL

X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila

(2011) Erica Larschan et al.   NATURE

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

(2010) Michael J. Guertin et al.   PLoS Genetics

A Comprehensive Map of Insulator Elements for the Drosophila Genome

(2010) Nicolas Nègre et al.   PLoS Genetics

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Activation properties of GAGA transcription factor

(2008) A VAQUERO et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3

(2008) Vivek Sarojkumar Chopra et al.   DEVELOPMENTAL BIOLOGY

NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila

(2008) C. Lee et al.   MOLECULAR AND CELLULAR BIOLOGY

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

(2008) D. A. Hendrix et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE

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

(2008) Leighton J. Core et al.   SCIENCE