Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells

Featuring the nucleosome surface as a therapeutic target

(2015) Isabel Torres Gomes da Silva et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

CD24 tracks divergent pluripotent states in mouse and human cells

(2015) Nika Shakiba et al.   Nature Communications

Dppa3 expression is critical for generation of fully reprogrammed iPS cells and maintenance of Dlk1-Dio3 imprinting

(2015) Xingbo Xu et al.   Nature Communications

Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers

(2014) Yu Tao et al.   BMC BIOLOGY

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

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

Genome-wide characterization of the routes to pluripotency

(2014) Samer M. I. Hussein et al.   NATURE

Divergent reprogramming routes lead to alternative stem-cell states

(2014) Peter D. Tonge et al.   NATURE

Small RNA changes en route to distinct cellular states of induced pluripotency

(2014) Jennifer L. Clancy et al.   Nature Communications

Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming

(2014) Jason A. West et al.   Nature Communications

An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator

(2014) Dong-Sung Lee et al.   Nature Communications

Ribosomal RNA Gene Transcription Mediated by the Master Genome Regulator Protein CCCTC-binding Factor (CTCF) Is Negatively Regulated by the Condensin Complex

(2013) Kaimeng Huang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

(2013) Rupa Sridharan et al.   NATURE CELL BIOLOGY

Vitamin C modulates TET1 function during somatic cell reprogramming

(2013) Jiekai Chen et al.   NATURE GENETICS

Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation

(2012) Zhaoyu Li et al.   CELL

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs

(2012) Jiekai Chen et al.   NATURE GENETICS

Genome-wide nucleosome positioning during embryonic stem cell development

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

Concise Review: Chromatin and Genome Organization in Reprogramming

(2012) Alva Biran et al.   STEM CELLS

The Histone Demethylases Jhdm1a/1b Enhance Somatic Cell Reprogramming in a Vitamin-C-Dependent Manner

(2011) Tao Wang et al.   Cell Stem Cell

CpG islands and the regulation of transcription

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

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Mechanisms for Vascular Cell Adhesion Molecule-1 Activation of ERK1/2 during Leukocyte Transendothelial Migration

(2011) Hiam Abdala-Valencia et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Vitamin C Enhances the Generation of Mouse and Human Induced Pluripotent Stem Cells

(2010) Miguel Angel Esteban et al.   Cell Stem Cell

A Mesenchymal-to-Epithelial Transition Initiates and Is Required for the Nuclear Reprogramming of Mouse Fibroblasts

(2010) Ronghui Li et al.   Cell Stem Cell

Parallel gateways to pluripotency: open chromatin in stem cells and development

(2010) Fong Ming Koh et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Open chromatin in pluripotency and reprogramming

(2010) Alexandre Gaspar-Maia et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nucleosome positioning, gene regulation and disease

(2010) Arnold Stein   Epigenomics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

(2009) Da Wei Huang et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

GeneTrack--a genomic data processing and visualization framework

(2008) I. Albert et al.   BIOINFORMATICS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Patterning of mouse embryonic stem cell-derived pan-mesoderm by Activin A/Nodal and Bmp4 signaling requires Fibroblast Growth Factor activity

(2008) Erik Willems et al.   DIFFERENTIATION

Promotion of Reprogramming to Ground State Pluripotency by Signal Inhibition

(2008) Jose Silva et al.   PLOS BIOLOGY