Sensitivity of transcription factors to DNA methylation

CTCF: a Swiss-army knife for genome organization and transcription regulation

(2019) Luca Braccioli et al.   Essays in Biochemistry

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity

(2019) Zhixiong Sun et al.   Nature Communications

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites

(2018) Chenhuan Xu et al.   SCIENCE

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

(2018) Satyanarayan Rao et al.   Epigenetics & Chromatin

Specific or not specific recruitment of DNMTs for DNA methylation, an epigenetic dilemma

(2018) Eric Hervouet et al.   Clinical Epigenetics

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

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

Principles of DNA methylation and their implications for biology and medicine

(2018) Yuval Dor et al.   LANCET

Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38

(2018) Nicholas O. Hudson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

(2018) Quy Xiao Xuan Lin et al.   NUCLEIC ACIDS RESEARCH

Dynamics and Context-Dependent Roles of DNA Methylation

(2017) Christina Ambrosi et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

(2017) Hideharu Hashimoto et al.   MOLECULAR CELL

MeDReaders: a database for transcription factors that bind to methylated DNA

(2017) Guohua Wang et al.   NUCLEIC ACIDS RESEARCH

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

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

(2017) Yimeng Yin et al.   SCIENCE

A screening system to identify transcription factors that induce binding site-directed DNA demethylation

(2017) Takahiro Suzuki et al.   Epigenetics & Chromatin

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

(2017) Judith F. Kribelbauer et al.   Cell Reports

Measuring quantitative effects of methylation on transcription factor–DNA binding affinity

(2017) Zheng Zuo et al.   Science Advances

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

(2016) Ronan C. O’Malley et al.   CELL

Role of TET enzymes in DNA methylation, development, and cancer

(2016) Kasper Dindler Rasmussen et al.   GENES & DEVELOPMENT

Transcription factors as readers and effectors of DNA methylation

(2016) Heng Zhu et al.   NATURE REVIEWS GENETICS

ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells

(2016) Vincenzo Riso et al.   NUCLEIC ACIDS RESEARCH

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

FBXL10 protects Polycomb-bound genes from hypermethylation

(2015) Mathieu Boulard et al.   NATURE GENETICS

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Methyl-CpG-binding domain proteins: readers of the epigenome

(2015) Qian Du et al.   Epigenomics

Role of DNA Methylation in Modulating Transcription Factor Occupancy

(2015) Matthew T. Maurano et al.   Cell Reports

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Pioneer transcription factors in cell reprogramming

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

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

A KRAS-directed transcriptional silencing pathway that mediates the CpG island methylator phenotype

(2014) Ryan W Serra et al.   eLife

ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection

(2013) Hannah K. Long et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family

(2013) Tuncay Baubec et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

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

(2013) Cornelia G. Spruijt et al.   CELL

Oncogenic RAS directs silencing of tumor suppressor genes through ordered recruitment of transcriptional repressors

(2013) N. Wajapeyee et al.   GENES & DEVELOPMENT

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

Cross-talk between Site-specific Transcription Factors and DNA Methylation States

(2013) Adam Blattler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Is there a telltale RH fingerprint in zinc fingers that recognizes methylated CpG dinucleotides?

(2013) Joel P. Mackay et al.   TRENDS IN BIOCHEMICAL SCIENCES

Response to Mackay et al.

(2013) Xiaodong Cheng et al.   TRENDS IN BIOCHEMICAL SCIENCES

A common mode of recognition for methylated CpG

(2013) Yiwei Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

ZBTB33 binds unmethylated regions of the genome associated with actively expressed genes

(2013) Adam Blattler et al.   Epigenetics & Chromatin

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

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

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

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

CpG methylation of half-CRE sequences creates C/EBP  binding sites that activate some tissue-specific genes

(2010) V. Rishi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues

(2010) G. Velasco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

A Maternal-Zygotic Effect Gene, Zfp57, Maintains Both Maternal and Paternal Imprints

(2008) Xiajun Li et al.   DEVELOPMENTAL CELL