Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network

(2020) Isabella V Soluri et al.   eLife

Dynamics of Free and Chromatin-Bound Histone H3 during Early Embryogenesis

(2019) Yuki Shindo et al.   CURRENT BIOLOGY

Regulatory principles governing the maternal-to-zygotic transition: insights from Drosophila melanogaster

(2019) Danielle C. Hamm et al.   Open Biology

Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation

(2019) Stephen L. McDaniel et al.   MOLECULAR CELL

The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output

(2019) Shigehiro Yamada et al.   CURRENT BIOLOGY

ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm

(2019) Marta Bozek et al.   GENOME RESEARCH

The maternal-to-zygotic transition revisited

(2019) Nadine L. Vastenhouw et al.   DEVELOPMENT

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns

(2019) Jamie C. Kwasnieski et al.   GENOME RESEARCH

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Distinct Roles of Broadly Expressed Repressors Support Dynamic Enhancer Action and Change in Time

(2019) Theodora Koromila et al.   Cell Reports

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop

(2019) Merve Deniz Abdusselamoglu et al.   eLife

Evidence for the temporal regulation of insect segmentation by a conserved sequence of transcription factors

(2018) Erik Clark et al.   DEVELOPMENT

A feed-forward relay integrates the regulatory activities of Bicoid and Orthodenticle via sequential binding to suboptimal sites

(2018) Rhea R. Datta et al.   GENES & DEVELOPMENT

A Developmental Program Truncates Long Transcripts to Temporally Regulate Cell Signaling

(2018) Jeremy E. Sandler et al.   DEVELOPMENTAL CELL

Mechanisms regulating zygotic genome activation

(2018) Katharine N. Schulz et al.   NATURE REVIEWS GENETICS

3 minutes to precisely measure morphogen concentration

(2018) Tanguy Lucas et al.   PLoS Genetics

Different modes of enhancer-specific regulation by Runt and Even-skipped during Drosophila segmentation

(2017) Saiyu Hang et al.   MOLECULAR BIOLOGY OF THE CELL

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Broadly expressed repressors integrate patterning across orthogonal axes in embryos

(2017) Theodora Koromila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development

(2017) Arbel Moshe et al.   Epigenetics & Chromatin

The Zic family homologue Odd-paired regulates Alk expression in Drosophila

(2017) Patricia Mendoza-García et al.   PLoS Genetics

The Heidelberg Screen for Pattern Mutants of Drosophila: A Personal Account

(2016) Eric Wieschaus et al.   Annual Review of Cell and Developmental Biology

Quantitative Single-Embryo Profile of Drosophila Genome Activation and the Dorsal-Ventral Patterning Network

(2016) J. E. Sandler et al.   GENETICS

Drosophilapoised enhancers are generated during tissue patterning with the help of repression

(2016) Nina Koenecke et al.   GENOME RESEARCH

Timing the Drosophila Mid-Blastula Transition: A Cell Cycle-Centered View

(2016) Kai Yuan et al.   TRENDS IN GENETICS

Bicoid gradient formation and function in the Drosophila pre-syncytial blastoderm

(2016) Zehra Ali-Murthy et al.   eLife

Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network

(2016) Erik Clark et al.   eLife

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

The Transgenic RNAi Project at Harvard Medical School: Resources and Validation

(2015) L. A. Perkins et al.   GENETICS

Zelda overcomes the high intrinsic nucleosome barrier at enhancers duringDrosophilazygotic genome activation

(2015) Yujia Sun et al.   GENOME RESEARCH

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the earlyDrosophilaembryo

(2015) Katharine N. Schulz et al.   GENOME RESEARCH

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Structure-function analysis of theDrosophila melanogasterCaudal transcription factor provides insights into core promoter-preferential activation.

(2015) Hila Shir-Shapira et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

(2014) Sun Melody Foo et al.   CURRENT BIOLOGY

Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila

(2014) Z. Xu et al.   GENES & DEVELOPMENT

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

(2014) J. P. Bothma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis

(2013) Elodie Darbo et al.   BMC GENOMICS

Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle

(2013) B Gurudatta et al.   CELL CYCLE

The ZIC gene family encodes multi-functional proteins essential for patterning and morphogenesis

(2013) Rob Houtmeyers et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos

(2013) Tanguy Lucas et al.   CURRENT BIOLOGY

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning

(2013) Hernan G. Garcia et al.   CURRENT BIOLOGY

UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents

(2013) Y. Hu et al.   GENETICS

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

(2013) M. Leichsenring et al.   SCIENCE

The Drosophila eve Insulator Homie Promotes eve Expression and Protects the Adjacent Gene from Repression by Polycomb Spreading

(2013) Miki Fujioka et al.   PLoS Genetics

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

(2013) Kai Chen et al.   eLife

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A System of Repressor Gradients Spatially Organizes the Boundaries of Bicoid-Dependent Target Genes

(2012) Hongtao Chen et al.   CELL

Precision of Hunchback Expression in the Drosophila Embryo

(2012) Michael W. Perry et al.   CURRENT BIOLOGY

Depleting Gene Activities in Early Drosophila Embryos with the "Maternal-Gal4-shRNA" System

(2012) M. V. Staller et al.   GENETICS

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

(2012) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

(2011) A. Ozdemir et al.   GENOME RESEARCH

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo

(2011) M. W. Perry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq

(2011) Susan E. Lott et al.   PLOS BIOLOGY

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

(2011) Chung-Yi Nien et al.   PLoS Genetics

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

Developmental Control of Late Replication and S Phase Length

(2010) Antony W. Shermoen et al.   CURRENT BIOLOGY

Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors

(2010) Lisa Prazak et al.   DEVELOPMENTAL BIOLOGY

Grainyhead and Zelda compete for binding to the promoters of the earliest-expressed Drosophila genes

(2010) Melissa M. Harrison et al.   DEVELOPMENTAL BIOLOGY

Odd paired transcriptional activation of decapentaplegic in the Drosophila eye/antennal disc is cell autonomous but indirect

(2010) Aditya Sen et al.   DEVELOPMENTAL BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

The Pluripotency Regulator Zic3 Is a Direct Activator of the Nanog Promoter in ESCs

(2010) Linda Shushan Lim et al.   STEM CELLS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition

(2009) X. Lu et al.   DEVELOPMENT

The maternal-to-zygotic transition: a play in two acts

(2009) W. Tadros et al.   DEVELOPMENT

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

(2008) Vivek Sarojkumar Chopra et al.   DEVELOPMENTAL BIOLOGY

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

(2008) Marcus B. Noyes et al.   NUCLEIC ACIDS RESEARCH

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY