CTCF confers local nucleosome resiliency after DNA replication and during mitosis

Transcription factor activity and nucleosome organization in mitosis

(2019) Nicola Festuccia et al.   GENOME RESEARCH

CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

(2019) Marlies E. Oomen et al.   GENOME RESEARCH

The molecular logic of Nanog-induced self-renewal in mouse embryonic stem cells

(2019) Victor Heurtier et al.   Nature Communications

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

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

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

Transcription Restart Establishes Chromatin Accessibility after DNA Replication

(2019) Kathleen R. Stewart-Morgan et al.   MOLECULAR CELL

Chromatin domains rich in inheritance

(2018) Danny Reinberg et al.   SCIENCE

A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes

(2018) Sheila S Teves et al.   eLife

Genome-wide Rules of Nucleosome Phasing in Drosophila

(2018) Sandro Baldi et al.   MOLECULAR CELL

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs

(2018) Jeremy Dufourt et al.   Nature Communications

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

(2018) Aleksandra Pękowska et al.   Cell Systems

The Epigenetic Paradox of Pluripotent ES Cells

(2017) Nicola Festuccia et al.   JOURNAL OF MOLECULAR BIOLOGY

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing

(2017) Greta Pintacuda et al.   MOLECULAR CELL

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

(2017) André L Martins et al.   NUCLEIC ACIDS RESEARCH

Julia: A Fresh Approach to Numerical Computing

(2017) Jeff Bezanson et al.   SIAM REVIEW

Mitotic phosphorylation of CCCTC-binding factor (CTCF) reduces its DNA binding activity

(2017) Takeshi Sekiya et al.   FEBS Open Bio

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

Transcriptional Regulators Compete with Nucleosomes Post-replication

(2016) Srinivas Ramachandran et al.   CELL

Cycling through developmental decisions: how cell cycle dynamics control pluripotency, differentiation and reprogramming

(2016) Abdenour Soufi et al.   DEVELOPMENT

Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

(2016) Nicola Festuccia et al.   NATURE CELL BIOLOGY

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

(2016) Nick D.L. Owens et al.   Cell Reports

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

(2016) Nicola Wiechens et al.   PLoS Genetics

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

(2015) Abdenour Soufi et al.   CELL

Lagging-strand replication shapes the mutational landscape of the genome

(2015) Martin A. M. Reijns et al.   NATURE

Dynamic Regulation of Transcription Factors by Nucleosome Remodeling

(2015) Ming Li et al.   BIOPHYSICAL JOURNAL

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

(2014) Vladimir B. Teif et al.   GENOME RESEARCH

Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

(2014) Constance Alabert et al.   NATURE CELL BIOLOGY

Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes

(2013) J. M. Caravaca et al.   GENES & DEVELOPMENT

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

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

Aurora B and Cdk1 mediate Wapl activation and release of acetylated cohesin from chromosomes by phosphorylating Sororin

(2013) T. Nishiyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome Remodeling and Epigenetics

(2013) P. B. Becker et al.   Cold Spring Harbor Perspectives in Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Intrinsic coupling of lagging-strand synthesis to chromatin assembly

(2012) Duncan J. Smith et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Genome-wide nucleosome positioning during embryonic stem cell development

(2012) Vladimir B Teif et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Global mitotic phosphorylation of C2H2zinc finger protein linker peptides

(2011) Raed Rizkallah et al.   CELL CYCLE

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Analysis of protein dynamics at active, stalled, and collapsed replication forks

(2011) B. M. Sirbu et al.   GENES & DEVELOPMENT

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA mediated chromatin pull-down for the study of chromatin replication

(2011) Anna E. Kliszczak et al.   Scientific Reports

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing

(2010) N. A. Kent et al.   NUCLEIC ACIDS RESEARCH

Nucleosome-mediated cooperativity between transcription factors

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Mediators of reprogramming: transcription factors and transitions through mitosis

(2008) Dieter Egli et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics