High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites

Pioneer Transcription Factors Initiating Gene Network Changes

(2020) Kenneth S. Zaret   Annual Review of Genetics

Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo

(2020) Can Sönmezer et al.   MOLECULAR CELL

Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening

(2019) Alexandre Mayran et al.   Nature Communications

Pioneer transcription factors shape the epigenetic landscape

(2018) Alexandre Mayran et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate

(2018) Alexandre Mayran et al.   NATURE GENETICS

ATAC Primer Tool for targeted analysis of accessible chromatin

(2018) Kathryn E Yost et al.   NATURE METHODS

The mechanistic basis for chromatin regulation by pioneer transcription factors

(2018) Makiko Iwafuchi-Doi   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a

(2018) Kun-Yong Kim et al.   Nature Communications

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate

(2018) Jose Luis Sardina et al.   Cell Stem Cell

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function

(2016) Yeqing A. Yang et al.   NUCLEIC ACIDS RESEARCH

The effects of cytosine methylation on general transcription factors

(2016) Jianshi Jin et al.   Scientific Reports

Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes

(2015) Quan Peng et al.   BMC GENOMICS

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates

(2015) Hao Wu et al.   NUCLEIC ACIDS RESEARCH

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis

(2015) Chia-Feng Liu et al.   NUCLEIC ACIDS RESEARCH

DNMT3L interacts with transcription factors to target DNMT3L/DNMT3B to specific DNA sequences: Role of the DNMT3L/DNMT3B/p65-NFκB complex in the (de-)methylation of TRAF1

(2014) Romain Pacaud et al.   BIOCHIMIE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

(2014) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

(2014) Hao Feng et al.   NUCLEIC ACIDS RESEARCH

A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation

(2014) Julie Dubois-Chevalier et al.   NUCLEIC ACIDS RESEARCH

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

(2014) Arnaud R Krebs et al.   eLife

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

(2013) Y. Liao et al.   BIOINFORMATICS

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

(2013) Cornelia G. Spruijt et al.   CELL

CG methylated microarrays identify a novel methylated sequence bound by the CEBPB ATF4 heterodimer that is active in vivo

(2013) I. K. Mann et al.   GENOME RESEARCH

Sox-Oct motifs contribute to maintenance of the unmethylated H19 ICR in YAC transgenic mice

(2013) Ryuuta Sakaguchi et al.   HUMAN MOLECULAR GENETICS

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency

(2013) Yael Costa et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Oct4/Sox2 Binding Sites Contribute to Maintaining Hypomethylation of the Maternal Igf2/H19 Imprinting Control Region

(2013) David L. Zimmerman et al.   PLoS One

SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

(2013) Michael A. Lodato et al.   PLoS Genetics

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions

(2013) Angelika Feldmann et al.   PLoS Genetics

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation

(2013) Lorenzo de la Rica et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Induction of DNA Demethylation Depending on Two Sets of Sox2 and Adjacent Oct3/4 Binding Sites (Sox-Oct Motifs) within the MouseH19/Insulin-like Growth Factor 2 (Igf2) Imprinted Control Region

(2012) Naohiro Hori et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Kinetics of DNA methylation inheritance by the Dnmt1-including complexes during the cell cycle

(2012) Eric Hervouet et al.   Cell Division

ADP-ribose polymers localized on Ctcf–Parp1–Dnmt1 complex prevent methylation of Ctcf target sites

(2011) Michele Zampieri et al.   BIOCHEMICAL JOURNAL

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

CREB in adult neurogenesis - master and partner in the development of adult-born neurons?

(2011) Katharina Merz et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

(2011) A. A. Serandour et al.   GENOME RESEARCH

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

GADD45α inhibition of DNMT1 dependent DNA methylation during homology directed DNA repair

(2011) Bongyong Lee et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences

(2010) Christian Rohde et al.   BMC BIOINFORMATICS

General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to De novo DNA Methylation in Cancer Cells

(2010) C. Gebhard et al.   CANCER RESEARCH

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Polycomb Proteins Remain Bound to Chromatin and DNA during DNA Replication In Vitro

(2009) Nicole J. Francis et al.   CELL

Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells

(2009) J. Xu et al.   GENES & DEVELOPMENT

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Global MYCN Transcription Factor Binding Analysis in Neuroblastoma Reveals Association with Distinct E-Box Motifs and Regions of DNA Hypermethylation

(2009) Derek M. Murphy et al.   PLoS One

pCREB is Involved in Neural Induction of Mouse Embryonic Stem Cells by RA

(2008) Zhi-Yan Shan et al.   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

N-Myc Regulates a Widespread Euchromatic Program in the Human Genome Partially Independent of Its Role as a Classical Transcription Factor

(2008) R. Cotterman et al.   CANCER RESEARCH

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL