CBP and Gcn5 drive zygotic genome activation independently of their catalytic activity

The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation

(2022) Liyun Miao et al.   MOLECULAR CELL

Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals

(2022) Aditya Sankar et al.   NATURE GENETICS

CBP /p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos

(2022) Meng Wang et al.   EMBO JOURNAL

Noncanonical imprinting: intergenerational epigenetic inheritance mediated by Polycomb complexes

(2022) Azusa Inoue   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2021) Vivekanandan Ramalingam et al.   Molecular Systems Biology

HP1 drives de novo 3D genome reorganization in early Drosophila embryos

(2021) Fides Zenk et al.   NATURE

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

(2021) Marissa M Gaskill et al.   eLife

CLAMP and Zelda function together to promote Drosophila zygotic genome activation

(2021) Jingyue Duan et al.   eLife

CLAMP regulates zygotic genome activation in Drosophila embryos

(2021) Megan M Colonnetta et al.   GENETICS

Histone variant H2A.Z regulates zygotic genome activation

(2021) Dafne Ibarra-Morales et al.   Nature Communications

What do the structures of GCN5-containing complexes teach us about their function?

(2020) Dominique Helmlinger et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Gcn5 complexes in Drosophila as a model for metazoa

(2020) Eliana F. Torres-Zelada et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

pyGenomeTracks: reproducible plots for multivariate genomic data sets

(2020) Lucille Lopez-Delisle et al.   BIOINFORMATICS

Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation

(2020) Maria Samata et al.   CELL

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

(2020) Theodora Koromila et al.   eLife

Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation

(2020) Marc A. J. Morgan et al.   NATURE GENETICS

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

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

Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation

(2019) Mary Leatham-Jensen et al.   PLoS Genetics

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

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

Ash1 counteracts Polycomb repression independent of histone H3 lysine 36 methylation

(2019) Eshagh Dorafshan et al.   EMBO REPORTS

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

(2019) Vivek Bhardwaj et al.   BIOINFORMATICS

The RNA Polymerase II Core Promoter in Drosophila

(2019) Long Vo Ngoc et al.   GENETICS

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

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

(2018) Patrick J. Murphy et al.   CELL

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone H3K4 methylation-dependent and -independent functions of Set1A/COMPASS in embryonic stem cell self-renewal and differentiation

(2017) Christie C. Sze et al.   GENES & DEVELOPMENT

Enzymatic modules of the SAGA chromatin-modifying complex play distinct roles in Drosophila gene expression and development

(2017) Xuanying Li et al.   GENES & DEVELOPMENT

Polycomb and Trithorax Group Genes inDrosophila

(2017) Judith A. Kassis et al.   GENETICS

CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II

(2017) Ann Boija et al.   MOLECULAR CELL

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability

(2017) Ryan Rickels et al.   NATURE GENETICS

Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

(2017) Fides Zenk et al.   SCIENCE

Polycomb and Trithorax Group Genes inDrosophila

(2017) Judith A. Kassis et al.   GENETICS

Direct interrogation of the role of H3K9 in metazoan heterochromatin function

(2016) Taylor J.R. Penke et al.   GENES & DEVELOPMENT

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

(2016) John Arne Dahl et al.   NATURE

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

Interrogating the Function of Metazoan Histones using Engineered Gene Clusters

(2015) Daniel J. McKay et al.   DEVELOPMENTAL CELL

Global and Specific Responses of the Histone Acetylome to Systematic Perturbation

(2015) Christian Feller et al.   MOLECULAR CELL

Absence of canonical marks of active chromatin in developmentally regulated genes

(2015) Sílvia Pérez-Lluch et al.   NATURE GENETICS

Histone H3 Serine 28 Is Essential for Efficient Polycomb-Mediated Gene Repression in Drosophila

(2015) Philip Yuk Kwong Yung et al.   Cell Reports

Regulation of Transcription by Long Noncoding RNAs

(2014) Roberto Bonasio et al.   Annual Review of Genetics

The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription

(2014) Jacques Bonnet et al.   GENES & DEVELOPMENT

Histone acetyltransferase Enok regulates oocyte polarization by promoting expression of the actin nucleation factorspire

(2014) Fu Huang et al.   GENES & DEVELOPMENT

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition

(2014) Xiao-Yong Li et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The Embryonic Linker Histone H1 Variant of Drosophila, dBigH1, Regulates Zygotic Genome Activation

(2013) Salvador Pérez-Montero et al.   DEVELOPMENTAL CELL

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

(2013) A. Saunders et al.   GENES & DEVELOPMENT

A Histone Mutant Reproduces the Phenotype Caused by Loss of Histone-Modifying Factor Polycomb

(2013) A. R. Pengelly et al.   SCIENCE

An Essential Role for Zygotic Expression in the Pre-Cellular Drosophila Embryo

(2013) Zehra Ali-Murthy et al.   PLoS Genetics

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

(2013) Kai Chen et al.   eLife

Transcription in the Absence of Histone H3.2 and H3K4 Methylation

(2012) Martina Hödl et al.   CURRENT BIOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

STAT Is an Essential Activator of the Zygotic Genome in the Early Drosophila Embryo

(2011) Amy Tsurumi et al.   PLoS Genetics

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

Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation

(2010) Qihuang Jin et al.   EMBO JOURNAL

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing

(2009) F. Tie et al.   DEVELOPMENT

A novel histone fold domain-containing protein that replaces TAF6 in Drosophila SAGA is required for SAGA-dependent gene expression

(2009) V. M. Weake et al.   GENES & DEVELOPMENT

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Hsiao-Lan Liang et al.   NATURE