Interplay between chromatin modifications and paused RNA polymerase II in dynamic transition between stalled and activated genes

Paused RNA Polymerase II as a Developmental Checkpoint

(2011) Michael Levine   CELL

A Hierarchical Combination of Factors Shapes the Genome-wide Topography of Yeast Meiotic Recombination Initiation

(2011) Jing Pan et al.   CELL

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Genome-wide analysis reveals novel molecular features of mouse recombination hotspots

(2011) Fatima Smagulova et al.   NATURE

CTCF-binding elements mediate control of V(D)J recombination

(2011) Chunguang Guo et al.   NATURE

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Structural basis of RNA polymerase II backtracking, arrest and reactivation

(2011) Alan C. M. Cheung et al.   NATURE

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Treatment of breast cancer cells with DNA demethylating agents leads to a release of Pol II stalling at genes with DNA-hypermethylated regions upstream of TSS

(2011) Yongguang Tao et al.   NUCLEIC ACIDS RESEARCH

G4 motifs correlate with promoter-proximal transcriptional pausing in human genes

(2011) J. Eddy et al.   NUCLEIC ACIDS RESEARCH

Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences

(2011) Y. Tao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization

(2011) T. Gkikopoulos et al.   SCIENCE

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

TIF1γ Controls Erythroid Cell Fate by Regulating Transcription Elongation

(2010) Xiaoying Bai et al.   CELL

Activation-Induced Cytidine Deaminase Targets DNA at Sites of RNA Polymerase II Stalling by Interaction with Spt5

(2010) Rushad Pavri et al.   CELL

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts

(2010) D. Enderle et al.   GENOME RESEARCH

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells

(2010) Diego Pasini et al.   NATURE

Chromatin remodelling during development

(2010) Lena Ho et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators

(2010) David Landeira et al.   NATURE CELL BIOLOGY

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

(2010) Jing Jin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Lsh Mediated RNA Polymerase II Stalling at HoxC6 and HoxC8 Involves DNA Methylation

(2010) Yongguang Tao et al.   PLoS One

NELF Potentiates Gene Transcription in the Drosophila Embryo

(2010) Xiaoling Wang et al.   PLoS One

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

Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex

(2010) A. Missra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells

(2009) Jamy C. Peng et al.   CELL

Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation

(2009) Diana C. Hargreaves et al.   CELL

Jumonji Modulates Polycomb Activity and Self-Renewal versus Differentiation of Stem Cells

(2009) Xiaohua Shen et al.   CELL

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

Regulation of Hox Gene Activity by Transcriptional Elongation in Drosophila

(2009) Vivek S. Chopra et al.   CURRENT BIOLOGY

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

Stalled Hox promoters as chromosomal boundaries

(2009) V. S. Chopra et al.   GENES & DEVELOPMENT

The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands

(2009) H. Takeshima et al.   GENOME RESEARCH

Human Negative Elongation Factor Activates Transcription and Regulates Alternative Transcription Initiation

(2009) Jianlong Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The logic of chromatin architecture and remodelling at promoters

(2009) Bradley R. Cairns   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

(2009) K. Adelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synchronous and Stochastic Patterns of Gene Activation in theDrosophilaEmbryo

(2009) Alistair N. Boettiger et al.   SCIENCE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

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

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Lsh Participates in DNA Methylation and Silencing of Stem Cell Genes

(2009) Sichuan Xi et al.   STEM CELLS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Poised RNA Polymerase II Gives Pause for Thought

(2008) Thanasis Margaritis et al.   CELL

Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci

(2008) Steven J. Petesch et al.   CELL

Postrecruitment Regulation of RNA Polymerase II Directs Rapid Signaling Responses at the Promoters of Estrogen Target Genes

(2008) M. Kininis et al.   MOLECULAR AND CELLULAR BIOLOGY

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

Poised Polymerases: On Your Mark…Get Set…Go!

(2008) David H. Price   MOLECULAR CELL

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

(2008) D. A. Hendrix et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE