Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors

(2019) Haruhiko Ehara et al.   SCIENCE

Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation

(2019) Razvan V Chereji et al.   GENOME RESEARCH

Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation

(2019) Jacques Bonnet et al.   DEVELOPMENTAL CELL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors

(2018) Matthew J. Rossi et al.   GENOME RESEARCH

Widespread and precise reprogramming of yeast protein–genome interactions in response to heat shock

(2018) Vinesh Vinayachandran et al.   GENOME RESEARCH

Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription

(2018) Slawomir Kubik et al.   MOLECULAR CELL

Spt6 Association with RNA Polymerase II Directs mRNA Turnover During Transcription

(2018) Raghuvar Dronamraju et al.   MOLECULAR CELL

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Fine-Resolution Mapping of TF Binding and Chromatin Interactions

(2018) Jenia Gutin et al.   Cell Reports

Chromosome Dynamics in Response to DNA Damage

(2018) Andrew Seeber et al.   Annual Review of Genetics

RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast

(2018) Sandipan Brahma et al.   MOLECULAR CELL

Structure of transcribing RNA polymerase II-nucleosome complex

(2018) Lucas Farnung et al.   Nature Communications

Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation

(2017) Yoo Jin Joo et al.   GENES & DEVELOPMENT

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays

(2017) Michal Levo et al.   MOLECULAR CELL

MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers

(2017) Răzvan V. Chereji et al.   MOLECULAR CELL

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters

(2017) Arnaud R. Krebs et al.   MOLECULAR CELL

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex

(2017) Youwei Xu et al.   Nature Communications

Mechanisms of ATP-Dependent Chromatin Remodeling Motors

(2016) Coral Y. Zhou et al.   Annual Review of Biophysics

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

(2016) Charles Girardot et al.   BMC BIOINFORMATICS

Transcriptional Regulators Compete with Nucleosomes Post-replication

(2016) Srinivas Ramachandran et al.   CELL

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization

(2016) Jason D. True et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection

(2016) Cedric R. Clapier et al.   MOLECULAR CELL

Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing

(2016) Ross T. Fennessy et al.   NUCLEIC ACIDS RESEARCH

Maintenance of Epigenetic Information

(2016) Geneviève Almouzni et al.   Cold Spring Harbor Perspectives in Biology

Dynamics of Nucleosome Positioning Maturation following Genomic Replication

(2016) Pauline Vasseur et al.   Cell Reports

Molecular mechanisms of ribosomal protein gene coregulation

(2015) Rohit Reja et al.   GENES & DEVELOPMENT

Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

(2015) Corinna Lieleg et al.   MOLECULAR AND CELLULAR BIOLOGY

Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast

(2015) Slawomir Kubik et al.   MOLECULAR CELL

Histone exchange, chromatin structure and the regulation of transcription

(2015) Swaminathan Venkatesh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism

(2015) Timothy J Parnell et al.   eLife

Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo

(2015) Poshen B Chen et al.   BMC GENOMICS

Regulating the Chromatin Landscape: Structural and Mechanistic Perspectives

(2014) Blaine Bartholomew   Annual Review of Biochemistry

Comparative analysis of methods for genome-wide nucleosome cartography

(2014) Luis Quintales et al.   BRIEFINGS IN BIOINFORMATICS

Nucleosome positioning in yeasts: methods, maps, and mechanisms

(2014) Corinna Lieleg et al.   CHROMOSOMA

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

(2014) Britta Knight et al.   GENES & DEVELOPMENT

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

(2014) Clifford A. Meyer et al.   NATURE REVIEWS GENETICS

Fuzziness and noise in nucleosomal architecture

(2014) Oscar Flores et al.   NUCLEIC ACIDS RESEARCH

The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening

(2014) Sanja Musladin et al.   NUCLEIC ACIDS RESEARCH

Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity

(2014) E. C. Small et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast

(2013) C. M. DeGennaro et al.   MOLECULAR AND CELLULAR BIOLOGY

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

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

(2013) G. Moyle-Heyrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

(2013) Evgeniy A. Ozonov et al.   PLoS Computational Biology

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons

(2012) Jason M Rizzo et al.   BMC MOLECULAR BIOLOGY

Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers

(2012) Kuangyu Yen et al.   CELL

reSETting chromatin during transcription elongation

(2012) Michaela Smolle et al.   Epigenetics

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

A map of nucleosome positions in yeast at base-pair resolution

(2012) Kristin Brogaard et al.   NATURE

Chromatin architectures at fission yeast transcriptional promoters and replication origins

(2012) Robert M. Givens et al.   NUCLEIC ACIDS RESEARCH

The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes

(2011) Christian J Wippo et al.   EMBO JOURNAL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes

(2011) Hope A. Cole et al.   NUCLEIC ACIDS RESEARCH

Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes

(2011) Jason M. Rizzo et al.   NUCLEIC ACIDS RESEARCH

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

A Complete Set of Nascent Transcription Rates for Yeast Genes

(2010) Vicent Pelechano et al.   PLoS One

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

(2010) Noam Kaplan et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

NA-Seq: A Discovery Tool for the Analysis of Chromatin Structure and Dynamics during Differentiation

(2009) Gaetano Gargiulo et al.   DEVELOPMENTAL CELL

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

(2009) A. Weiner et al.   GENOME RESEARCH

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

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

A translational signature for nucleosome positioning in vivo

(2009) Micaela Caserta et al.   NUCLEIC ACIDS RESEARCH

Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?

(2009) Arnold Stein et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

(2008) Gwenael Badis et al.   MOLECULAR CELL

A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae

(2008) Grace Marie Jones et al.   NATURE METHODS