Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution

Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes

(2014) Jason T. Huff et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Evolutionary Changes in Vertebrate Genome Signatures with Special Focus on Coelacanth

(2014) Y. Iwasaki et al.   DNA RESEARCH

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes

(2014) Raghunath Chatterjee et al.   Epigenetics & Chromatin

Repair of naturally occurring mismatches can induce mutations in flanking DNA

(2014) Jia Chen et al.   eLife

Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding

(2013) Ximiao He et al.   BMC GENOMICS

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

LINE1 and Alu repetitive element DNA methylation in tumors and white blood cells from epithelial ovarian cancer patients

(2013) Stacey N. Akers et al.   GYNECOLOGIC ONCOLOGY

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

c-Jun/c-Fos heterodimers regulate cellular genes via a newly identified class of methylated DNA sequence motifs

(2013) M. Gustems et al.   NUCLEIC ACIDS RESEARCH

CpG methylation recruits sequence specific transcription factors essential for tissue specific gene expression

(2012) Raghunath Chatterjee et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

MBD4 and TDG: Multifaceted DNA glycosylases with ever expanding biological roles

(2012) Ashley B. Sjolund et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Cooperative Transcription Factor Complexes in Control

(2012) G. J. Martinez et al.   SCIENCE

CG methylation

(2012) Charles Vinson et al.   Epigenomics

Overlapping ETS and CRE Motifs ( G / C CGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

(2012) Raghunath Chatterjee et al.   G3-Genes Genomes Genetics

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

The Dinucleotide CG as a Genomic Signalling Module

(2011) Adrian Bird   JOURNAL OF MOLECULAR BIOLOGY

Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

(2011) Daisy Monica Makapedua et al.   Marine Genomics

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

Cancer epigenetics reaches mainstream oncology

(2011) Manuel Rodríguez-Paredes et al.   NATURE MEDICINE

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

(2010) Desiree Tillo et al.   PLoS One

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

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

G+C content dominates intrinsic nucleosome occupancy

(2009) Desiree Tillo et al.   BMC BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I

(2009) C. M. Whittle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Methylation-Dependent Binding of the Epstein-Barr Virus BZLF1 Protein to Viral Promoters

(2009) Sarah J. Dickerson et al.   PLoS Pathogens

All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

(2008) Julian M Rozenberg et al.   BMC GENOMICS

Comparative Analysis of CpG Islands in Four Fish Genomes

(2008) Leng Han et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

Genome-scale relationships between cytosine methylation and dinucleotide abundances in animals

(2008) Martin W. Simmen   GENOMICS

Choose your partners: dimerization in eukaryotic transcription factors

(2008) Grigoris D. Amoutzias et al.   TRENDS IN BIOCHEMICAL SCIENCES

CpG island density and its correlations with genomic features in mammalian genomes

(2008) Leng Han et al.   GENOME BIOLOGY