Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

Evidence of selection for an accessible nucleosomal array in human

(2016) Guénola Drillon et al.   BMC GENOMICS

C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis

(2015) Chris van Oevelen et al.   Stem Cell Reports

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin

(2014) Philipp Korber et al.   NUCLEIC ACIDS RESEARCH

Chromatin and DNA sequences in defining promoters for transcription initiation

(2013) Ferenc Müller et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Genome-Wide Organization of Eukaryotic Preinitiation Complex Is Influenced by Nonconsensus Protein-DNA Binding

(2013) Ariel Afek et al.   BIOPHYSICAL JOURNAL

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

(2013) Shannon M. Lauberth et al.   CELL

Canonical nucleosome organization at promoters forms during genome activation

(2013) Y. Zhang et al.   GENOME RESEARCH

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

(2013) Chirag Nepal et al.   GENOME RESEARCH

Structural visualization of key steps in human transcription initiation

(2013) Yuan He et al.   NATURE

Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence

(2013) Jyotsana J. Parmar et al.   NUCLEIC ACIDS RESEARCH

Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements

(2013) Sterling Sawaya et al.   PLoS One

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

(2013) William S Kruesi et al.   eLife

Nucleosome DNA Bendability Matrix(C. elegans)

(2012) I. Gabdank et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Genome-wide nucleosome positioning during embryonic stem cell development

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

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

(2012) René Dreos et al.   NUCLEIC ACIDS RESEARCH

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

Human genes with CpG island promoters have a distinct transcription-associated chromatin organization

(2012) Tanya Vavouri et al.   GENOME BIOLOGY

Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification

(2011) Tadasu Nozaki et al.   BMC GENOMICS

New insights into the function of transcription factor TFIID from recent structural studies

(2011) Gabor Papai et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide

(2011) S. S. Teves et al.   GENES & DEVELOPMENT

CpG islands and the regulation of transcription

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

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast

(2011) J. B. Zaugg et al.   GENOME RESEARCH

Variety of genomic DNA patterns for nucleosome positioning

(2011) I. Ioshikhes et al.   GENOME RESEARCH

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Cracking the chromatin code: Precise rule of nucleosome positioning

(2011) Edward N. Trifonov   Physics of Life Reviews

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

Nucleosome sequence preferences influence in vivo nucleosome organization

(2010) Noam Kaplan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

G+C content dominates intrinsic nucleosome occupancy

(2009) Desiree Tillo et al.   BMC BIOINFORMATICS

Recent advances in understanding the structure and function of general transcription factor TFIID

(2009) Emilie Cler et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The logic of chromatin architecture and remodelling at promoters

(2009) Bradley R. Cairns   NATURE

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

(2009) Yair Field et al.   NATURE GENETICS

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

(2009) Yong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

(2009) Elizabeth A Rach et al.   GENOME BIOLOGY

The RNA polymerase II core promoter — the gateway to transcription

(2008) Tamar Juven-Gershon et al.   CURRENT OPINION IN CELL BIOLOGY

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Structural Insight into the Recognition of the H3K4me3 Mark by the TFIID Subunit TAF3

(2008) Hugo van Ingen et al.   STRUCTURE