Linking Core Promoter Classes to Circadian Transcription

The core promoter: At the heart of gene expression

(2015) Yehuda M. Danino et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2015) Bérénice A. Benayoun et al.   CELL

Circadian mRNA expression: insights from modeling and transcriptomics

(2015) Sarah Lück et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Highly Efficient Genome Editing via CRISPR/Cas9 to Create Clock Gene Knockout Cells

(2015) Sandra Korge et al.   JOURNAL OF BIOLOGICAL RHYTHMS

In the Driver’s Seat

(2015) Alejandro Montenegro-Montero et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone exchange, chromatin structure and the regulation of transcription

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

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

(2015) Vanja Haberle et al.   NUCLEIC ACIDS RESEARCH

Core promoters in transcription: old problem, new insights

(2015) Ananda L. Roy et al.   TRENDS IN BIOCHEMICAL SCIENCES

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

CLOCK:BMAL1 is a pioneer-like transcription factor

(2014) J. S. Menet et al.   GENES & DEVELOPMENT

A Mouse Geneticist's Practical Guide to CRISPR Applications

(2014) P. Singh et al.   GENETICS

Detecting Rhythms in Time Series with RAIN

(2014) Paul F. Thaben et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

(2014) Christopher M. Weber et al.   MOLECULAR CELL

ANP32E is a histone chaperone that removes H2A.Z from chromatin

(2014) Arnaud Obri et al.   NATURE

Universality of core promoter elements?

(2014) Matthias Siebert et al.   NATURE

Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays

(2014) Brendan Osberg et al.   NUCLEIC ACIDS RESEARCH

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

(2014) G. dos Santos et al.   NUCLEIC ACIDS RESEARCH

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

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

Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

(2014) Sarah Lück et al.   Cell Reports

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

(2014) Mathieu Quinodoz et al.   GENOME BIOLOGY

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

(2013) Andreas H. Ehrensberger et al.   CELL

Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals

(2013) Telmo Henriques et al.   MOLECULAR CELL

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

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Nascent-Seq analysis ofDrosophilacycling gene expression

(2013) Joseph Rodriguez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular architecture of the mammalian circadian clock

(2013) Carrie L. Partch et al.   TRENDS IN CELL BIOLOGY

Nucleosome Remodeling and Epigenetics

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

Mechanism for 12 Hr Rhythm Generation by the Circadian Clock

(2013) Pål O. Westermark et al.   Cell Reports

Regulation of a Mammalian Gene Bearing a CpG Island Promoter and a Distal Enhancer

(2013) Georgina Berrozpe et al.   Cell Reports

The Circadian Clock Coordinates Ribosome Biogenesis

(2013) Céline Jouffe et al.   PLOS BIOLOGY

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The COMPASS Family of Histone H3K4 Methylases: Mechanisms of Regulation in Development and Disease Pathogenesis

(2012) Ali Shilatifard   Annual Review of Biochemistry

Coupling polymerase pausing and chromatin landscapes for precise regulation of transcription

(2012) Daniel A. Gilchrist et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2012) Zhaoyu Li et al.   CELL

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

(2012) Gangqing Hu et al.   Cell Stem Cell

Combinatorial complexity in chromatin structure and function: revisiting the histone code

(2012) Oliver J Rando   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells

(2012) T. Clouaire et al.   GENES & DEVELOPMENT

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators

(2012) D. J. Huebert et al.   MOLECULAR AND CELLULAR BIOLOGY

Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β

(2012) Han Cho et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

(2012) Gwendal Le Martelot et al.   PLOS BIOLOGY

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

(2012) Manching Ku et al.   GENOME BIOLOGY

Genome-wide “Re”-Modeling of Nucleosome Positions

(2011) Ronen Sadeh et al.   CELL

Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression

(2011) K. C. Abruzzi et al.   GENES & DEVELOPMENT

CpG islands and the regulation of transcription

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

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Transcription factor TFIIF is not required for initiation by RNA polymerase II, but it is essential to stabilize transcription factor TFIIB in early elongation complexes

(2011) P. Cabart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosomes and the accessibility problem

(2011) Xin Wang et al.   TRENDS IN GENETICS

Genomic and chromatin signals underlying transcription start-site selection

(2011) Eivind Valen et al.   TRENDS IN GENETICS

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

(2011) Elizabeth A. Rach et al.   PLoS Genetics

Circadian Control of Global Gene Expression Patterns

(2010) Colleen J. Doherty et al.   Annual Review of Genetics

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

The TFIIB Tip Domain Couples Transcription Initiation to Events Involved in RNA Processing

(2010) Khiem Tran et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

The histone methyltransferase MLL1 permits the oscillation of circadian gene expression

(2010) Sayako Katada et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Grasping trimethylation of histone H3 at lysine 4

(2010) Michiel Vermeulen et al.   Epigenomics

Assessing Computational Methods of Cis-Regulatory Module Prediction

(2010) Jing Su et al.   PLoS Computational Biology

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation

(2009) Diana C. Hargreaves et al.   CELL

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

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

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

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

(2009) Caroline C. Friedel et al.   NUCLEIC ACIDS RESEARCH

Regulation of Clock-Controlled Genes in Mammals

(2009) Katarzyna Bozek et al.   PLoS One

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Clock-dependent and independent transcriptional control of the two isoforms from the mouseRorγgene

(2008) Valérie Mongrain et al.   GENES TO CELLS

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

Dominant and Redundant Functions of TFIID Involved in the Regulation of Hepatic Genes

(2008) Antonis Tatarakis et al.   MOLECULAR CELL

Nuclear Hormone Receptors for Heme: REV-ERBα and REV-ERBβ Are Ligand-Regulated Components of the Mammalian Clock

(2008) Thomas P. Burris   MOLECULAR ENDOCRINOLOGY

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

(2008) Leighton J. Core et al.   SCIENCE

Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm

(2008) Jun Yan et al.   PLoS Computational Biology