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Seven myths of how transcription factors read the cis-regulatory code

Current opinion in systems biology, 2020-10, Vol.23, p.22-31

Zeitlinger, Julia

2020

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A global change in RNA polymerase II pausing during the Drosophila midblastula transition

eLife, 2013-08, Vol.2, p.e00861-e00861

2013

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TATA and paused promoters active in differentiated tissues have distinct expression characteristics

Molecular systems biology, 2021-02, Vol.17 (2), p.e9866-n/a

2021

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Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation

Genome research, 2015-11, Vol.25 (11), p.1703

2015

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Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

Genome Biology, 2016-09, Vol.17 (1), p.196-196, Article 196

2016

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Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing

eLife, 2019-04, Vol.8

2019

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Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing

G3 : genes - genomes - genetics, 2018-10, Vol.8 (10), p.3131-3141

2018

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Paused RNA polymerase II inhibits new transcriptional initiation

Nature genetics, 2017-07, Vol.49 (7), p.1045-1051

2017

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RNA polymerase is poised for activation across the genome

Nature genetics, 2007-12, Vol.39 (12), p.1507-1511

2007

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Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development

Nature communications, 2023-09, Vol.14 (1), p.5862-5862, Article 5862

2023

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Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

Genes & development, 2007-02, Vol.21 (4), p.385-390

2007

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Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

Cell, 2005-08, Vol.122 (4), p.517-527

2005

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Capicua controls Toll/IL-1 signaling targets independently of RTK regulation

Proceedings of the National Academy of Sciences - PNAS, 2018-02, Vol.115 (8), p.1807-1812

2018

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Activated Signal Transduction Kinases Frequently Occupy Target Genes

Science (American Association for the Advancement of Science), 2006-07, Vol.313 (5786), p.533-536

2006

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High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

Nature genetics, 2011-05, Vol.43 (5), p.414-420

2011

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Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures

PLoS genetics, 2013-01, Vol.9 (1), p.e1003195-e1003195

2013

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Identification of transcription factor binding sites from ChIP-seq data at high resolution

Bioinformatics, 2013-11, Vol.29 (21), p.2705-2713

2013

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

Proceedings of the National Academy of Sciences - PNAS, 2008-06, Vol.105 (22), p.7762-7767

2008

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Molecular evolution of the Yap/Yorkie proto-oncogene and elucidation of its core transcriptional program

Molecular biology and evolution, 2014-06, Vol.31 (6), p.1375-1390

2014

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A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing

Cell reports (Cambridge), 2019-06, Vol.27 (13), p.3770-3779.e7

2019

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RNA polymerase II pausing during development

Development (Cambridge), 2014-03, Vol.141 (6), p.1179-1183

2014

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Genome-Wide Location and Function of DNA Binding Proteins

Science (American Association for the Advancement of Science), 2000-12, Vol.290 (5500), p.2306-2309

2000

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

Cell reports (Cambridge), 2012-12, Vol.2 (6), p.1670-1683

2012

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ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

Nature biotechnology, 2015-04, Vol.33 (4), p.395-401

2015

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Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle

Cell, 2001-09, Vol.106 (6), p.697-708

2001

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Seven myths of how transcription factors read the cis-regulatory code

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

TATA and paused promoters active in differentiated tissues have distinct expression characteristics

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing

Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing

Paused RNA polymerase II inhibits new transcriptional initiation

RNA polymerase is poised for activation across the genome

Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

Capicua controls Toll/IL-1 signaling targets independently of RTK regulation

Activated Signal Transduction Kinases Frequently Occupy Target Genes

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures

Identification of transcription factor binding sites from ChIP-seq data at high resolution

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

Molecular evolution of the Yap/Yorkie proto-oncogene and elucidation of its core transcriptional program

A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing

RNA polymerase II pausing during development

Genome-Wide Location and Function of DNA Binding Proteins

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

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle

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