GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes

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

(2015) Nicholas J. Fuda et al.   PLoS Genetics

New insights for Drosophila GAGA factor in larvae

(2015) M. Blanch et al.   Royal Society Open Science

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Control of Transcriptional Elongation

(2013) Hojoong Kwak et al.   Annual Review of Genetics

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

Genome-wide Association of Yorkie with Chromatin and Chromatin-Remodeling Complexes

(2013) Hyangyee Oh et al.   Cell Reports

RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

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

Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression

(2012) Bjoern Gaertner et al.   Cell Reports

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Paused RNA Polymerase II as a Developmental Checkpoint

(2011) Michael Levine   CELL

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

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

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

(2011) Elizabeth A. Rach et al.   PLoS Genetics

PICS: Probabilistic Inference for ChIP-seq

(2010) Xuekui Zhang et al.   BIOMETRICS

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

(2010) Daniel A. Gilchrist et al.   CELL

Modifications of RNA polymerase II are pivotal in regulating gene expression states

(2009) Emily Brookes et al.   EMBO REPORTS

Polytene chromosome squash methods for studying transcription and epigenetic chromatin modification in Drosophila using antibodies

(2009) Kristen M. Johansen et al.   METHODS

Using ChIP-chip and ChIP-seq to study the regulation of gene expression: Genome-wide localization studies reveal widespread regulation of transcription elongation

(2009) Daniel A. Gilchrist et al.   METHODS

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

(2009) Cizhong Jiang et al.   GENOME BIOLOGY

Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci

(2008) Steven J. Petesch et al.   CELL

The nucleosome remodeling factor (NURF) regulates genes involved in Drosophila innate immunity

(2008) So Yeon Kwon et al.   DEVELOPMENTAL BIOLOGY

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

(2008) Vivek Sarojkumar Chopra et al.   DEVELOPMENTAL BIOLOGY

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

(2008) D. A. Gilchrist et al.   GENES & DEVELOPMENT

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

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

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

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

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

SU(VAR)3-7 Links Heterochromatin and Dosage Compensation in Drosophila

(2008) Anne Spierer et al.   PLoS Genetics