Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation

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

(2022) Aditya Sankar et al.   NATURE GENETICS

Loss of TIP60 (KAT5) abolishes H2AZ lysine 7 acetylation and causes p53, INK4A, and ARF-independent cell cycle arrest

(2022) Johannes Wichmann et al.   Cell Death & Disease

Direct cell reprogramming: approaches, mechanisms and progress

(2021) Haofei Wang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Tip60 activates Hoxa9 and Meis1 expression through acetylation of H2A.Z, promoting MLL-AF10 and MLL-ENL acute myeloid leukemia

(2021) Kazutsune Yamagata et al.   LEUKEMIA

Efficient generation of dopaminergic induced neuronal cells with midbrain characteristics

(2021) Yi Han Ng et al.   Stem Cell Reports

The transcription factor code in iPSC reprogramming

(2021) Weixian Deng et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Decoding the function of bivalent chromatin in development and cancer

(2021) Dhirendra Kumar et al.   GENOME RESEARCH

The H2A.Z-nucleosome code in mammals: emerging functions

(2021) Yolanda Colino-Sanguino et al.   TRENDS IN GENETICS

Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells

(2020) Donnchadh S. Dunican et al.   BMC BIOLOGY

Pro-neuronal activity of Myod1 due to promiscuous binding to neuronal genes

(2020) Qian Yi Lee et al.   NATURE CELL BIOLOGY

Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation

(2020) Delphine Douillet et al.   NATURE GENETICS

H2A.Z is dispensable for both basal and activated transcription in post-mitotic mouse muscles

(2020) Edwige Belotti et al.   NUCLEIC ACIDS RESEARCH

TIP60 in Aging and Neurodegeneration

(2020) Zhiquan Li et al.   AGEING RESEARCH REVIEWS

De Novo KAT5 Variants Cause a Syndrome with Recognizable Facial Dysmorphisms, Cerebellar Atrophy, Sleep Disturbance, and Epilepsy

(2020) Jonathan Humbert et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Pioneer Transcription Factors Initiating Gene Network Changes

(2020) Kenneth S. Zaret   Annual Review of Genetics

UniProt: the universal protein knowledgebase in 2021

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The histone variant H2A.Z in gene regulation

(2019) Benedetto Daniele Giaimo et al.   Epigenetics & Chromatin

Genetic mapping of cell type specificity for complex traits

(2019) Kyoko Watanabe et al.   Nature Communications

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

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

DNA repair complex licenses acetylation of H2A.Z.1 by KAT2A during transcription

(2019) M. Semer et al.   Nature Chemical Biology

TIP60/KAT5 is required for neuronal viability in hippocampal CA1

(2019) Inga Urban et al.   Scientific Reports

Lysine acetyltransferase 8 is involved in cerebral development and syndromic intellectual disability

(2019) Lin Li et al.   JOURNAL OF CLINICAL INVESTIGATION

The Bivalent Genome: Characterization, Structure, and Regulation

(2019) Enrique Blanco et al.   TRENDS IN GENETICS

EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations

(2018) Zuguang Gu et al.   BMC GENOMICS

bHLH transcription factors in neural development, disease, and reprogramming

(2018) Daniel J. Dennis et al.   BRAIN RESEARCH

Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer

(2018) Chih-Chao Hsu et al.   GENES & DEVELOPMENT

Restoring Tip60 HAT/HDAC2 Balance in the Neurodegenerative Brain Relieves Epigenetic Transcriptional Repression and Reinstates Cognition

(2018) Priyalakshmi Panikker et al.   JOURNAL OF NEUROSCIENCE

Histone variant H2A.Z deposition and acetylation directs the canonical Notch signaling response

(2018) Benedetto Daniele Giaimo et al.   NUCLEIC ACIDS RESEARCH

A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons

(2018) Erik Södersten et al.   Nature Communications

Subcellular localisation modulates ubiquitylation and degradation of Ascl1

(2018) Sébastien Gillotin et al.   Scientific Reports

How selective are pharmacological inhibitors of cell cycle-regulating cyclin-dependent kinases?

(2018) Radek Jorda et al.   JOURNAL OF MEDICINAL CHEMISTRY

Dynamic control of neural stem cells by bHLH factors

(2018) Ryoichiro Kageyama et al.   NEUROSCIENCE RESEARCH

TIP55, a splice isoform of the KAT5 acetyltransferase, is essential for developmental gene regulation and organogenesis

(2018) Diwash Acharya et al.   Scientific Reports

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

The BioGRID interaction database: 2019 update

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Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

(2017) Moritz Mall et al.   NATURE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Chromatin-state discovery and genome annotation with ChromHMM

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(2017) Serif Senturk et al.   Nature Communications

Functional mapping and annotation of genetic associations with FUMA

(2017) Kyoko Watanabe et al.   Nature Communications

KAT-Independent Gene Regulation by Tip60 Promotes ESC Self-Renewal but Not Pluripotency

(2017) Diwash Acharya et al.   Cell Reports

Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons

(2017) Orly L. Wapinski et al.   Cell Reports

TFCP2 Is Required for YAP-Dependent Transcription to Stimulate Liver Malignancy

(2017) Xiao Zhang et al.   Cell Reports

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Novel complex of HAT protein TIP60 and nuclear receptor PXR promotes cell migration and adhesion

(2017) Karishma Bakshi et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

ATP-dependent chromatin remodeling during mammalian development

(2016) Swetansu K. Hota et al.   DEVELOPMENT

EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation

(2016) Suman K. Pradhan et al.   MOLECULAR CELL

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Return to quiescence of mouse neural stem cells by degradation of a proactivation protein

(2016) Noelia Urbán et al.   SCIENCE

Comparative Proteomics Reveals Strain-Specific β-TrCP Degradation via Rotavirus NSP1 Hijacking a Host Cullin-3-Rbx1 Complex

(2016) Siyuan Ding et al.   PLoS Pathogens

A dynamic mode of mitotic bookmarking by transcription factors

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A general method to improve fluorophores for live-cell and single-molecule microscopy

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Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders

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Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

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K‐Lysine acetyltransferase 2a regulates a hippocampal gene expression network linked to memory formation

(2014) Roman M Stilling et al.   EMBO JOURNAL

Epigenetic Control of Learning and Memory in Drosophila by Tip60 HAT Action

(2014) Songjun Xu et al.   GENETICS

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

(2014) P. J. Balwierz et al.   GENOME RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Regulation of histone H3K4 methylation in brain development and disease

(2014) E. Shen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Dynamic Interactions between TIP60 and p300 Regulate FOXP3 Function through a Structural Switch Defined by a Single Lysine on TIP60

(2014) Yan Xiao et al.   Cell Reports

Generation of Induced Neuronal Cells by the Single Reprogramming Factor ASCL1

(2014) Soham Chanda et al.   Stem Cell Reports

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

(2013) Y. Liao et al.   BIOINFORMATICS

Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons

(2013) Orly L. Wapinski et al.   CELL

Epigenetics of Reprogramming to Induced Pluripotency

(2013) Bernadett Papp et al.   CELL

Chromatin modulators as facilitating factors in cellular reprogramming

(2013) Luis Luna-Zurita et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells

(2013) Deqing Hu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells

(2013) Yingsha Zhang et al.   NEURON

Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest

(2012) Alvaro Rada-Iglesias et al.   Cell Stem Cell

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

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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

H2A.Z-dependent crosstalk between enhancer and promoter regulates Cyclin D1 expression

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Function of the Active Site Lysine Autoacetylation in Tip60 Catalysis

(2012) Chao Yang et al.   PLoS One

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

(2012) Manching Ku et al.   GENOME BIOLOGY

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Mapping the NPHP-JBTS-MKS Protein Network Reveals Ciliopathy Disease Genes and Pathways

(2011) Liyun Sang et al.   CELL

MYST protein acetyltransferase activity requires active site lysine autoacetylation

(2011) Hua Yuan et al.   EMBO JOURNAL

Tip60 regulates myoblast differentiation by enhancing the transcriptional activity of MyoD via their physical interactions

(2011) Jung-Woong Kim et al.   FEBS Journal

Recognition of enhancer element–specific histone methylation by TIP60 in transcriptional activation

(2011) Kwang Won Jeong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

MYST-family histone acetyltransferases: beyond chromatin

(2010) Vasileia Sapountzi et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

NuA4-dependent Acetylation of Nucleosomal Histones H4 and H2A Directly Stimulates Incorporation of H2A.Z by the SWR1 Complex

(2010) Mohammed Altaf et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

HBO1 Is Required for H3K14 Acetylation and Normal Transcriptional Activity during Embryonic Development

(2010) A. J. Kueh et al.   MOLECULAR AND CELLULAR 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

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

Epigenetic reprogramming and induced pluripotency

(2009) K. Hochedlinger et al.   DEVELOPMENT

Homozygous disruption of thetip60gene causes early embryonic lethality

(2009) Yaofei Hu et al.   DEVELOPMENTAL DYNAMICS

Histone H3 methylation links DNA damage detection to activation of the tumour suppressor Tip60

(2009) Yingli Sun et al.   NATURE CELL BIOLOGY

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

(2009) Da Wei Huang et al.   Nature Protocols

High-throughput generation of tagged stable cell lines for proteomic analysis

(2009) Jorge Z. Torres et al.   PROTEOMICS

An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity

(2008) Thomas G. Fazzio et al.   CELL

A Drug-Inducible System for Direct Reprogramming of Human Somatic Cells to Pluripotency

(2008) Dirk Hockemeyer et al.   Cell Stem Cell

Mof (MYST1 or KAT8) Is Essential for Progression of Embryonic Development Past the Blastocyst Stage and Required for Normal Chromatin Architecture

(2008) T. Thomas et al.   MOLECULAR AND CELLULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

The Adipogenic Acetyltransferase Tip60 Targets Activation Function 1 of Peroxisome Proliferator-Activated Receptor γ

(2007) Olivier van Beekum et al.   ENDOCRINOLOGY