Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions

Clock-dependent chromatin topology modulates circadian transcription and behavior

(2018) Jérôme Mermet et al.   GENES & DEVELOPMENT

Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription

(2018) Yong Hoon Kim et al.   SCIENCE

Diurnal transcriptome atlas of a primate across major neural and peripheral tissues

(2018) Ludovic S. Mure et al.   SCIENCE

Regulation of circadian clock transcriptional output by CLOCK:BMAL1

(2018) Alexandra J. Trott et al.   PLoS Genetics

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs

(2017) Jake Yeung et al.   GENOME RESEARCH

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

Gut microbiota directs PPARγ‐driven reprogramming of the liver circadian clock by nutritional challenge

(2016) Mari Murakami et al.   EMBO REPORTS

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

Circadian physiology of metabolism

(2016) Satchidananda Panda   SCIENCE

Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors

(2015) Jason Piper et al.   BMC GENOMICS

The Liver Clock Controls Cholesterol Homeostasis through Trib1 Protein-mediated Regulation of PCSK9/Low Density Lipoprotein Receptor (LDLR) Axis

(2015) Di Ma et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discrete functions of nuclear receptor Rev-erb  couple metabolism to the clock

(2015) Y. Zhang et al.   SCIENCE

CLOCK:BMAL1 is a pioneer-like transcription factor

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

Smooth-muscle BMAL1 participates in blood pressure circadian rhythm regulation

(2014) Zhongwen Xie et al.   JOURNAL OF CLINICAL INVESTIGATION

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

(2014) Myong-Hee Sung et al.   MOLECULAR CELL

Tissue-specific clocks in Arabidopsis show asymmetric coupling

(2014) Motomu Endo et al.   NATURE

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver

(2013) Logan J Everett et al.   BMC GENOMICS

Reprogramming of the Circadian Clock by Nutritional Challenge

(2013) Kristin L. Eckel-Mahan et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

A Mummified Duck-Billed Dinosaur with a Soft-Tissue Cock’s Comb

(2013) Phil R. Bell et al.   CURRENT BIOLOGY

C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements

(2013) Lars Grøntved et al.   EMBO JOURNAL

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites

(2013) Jason Gertz et al.   MOLECULAR CELL

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Cycles in spatial and temporal chromosomal organization driven by the circadian clock

(2013) Lorena Aguilar-Arnal et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular architecture of the mammalian circadian clock

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

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

(2012) V. Theodorou et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

(2012) N. Koike et al.   SCIENCE

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

(2012) Jerome S Menet et al.   eLife

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

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

(2011) Guillaume Rey et al.   PLOS BIOLOGY

Identification of interacting transcription factors regulating tissue gene expression in human

(2010) Zihua Hu et al.   BMC GENOMICS

CLOCK Regulates Circadian Rhythms of Hepatic Glycogen Synthesis through Transcriptional Activation ofGys2

(2010) Ryosuke Doi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Vascular PPARγ Controls Circadian Variation in Blood Pressure and Heart Rate through Bmal1

(2008) Ningning Wang et al.   Cell Metabolism

Modeling an Evolutionary Conserved Circadian Cis-Element

(2008) Eric R. Paquet et al.   PLoS Computational Biology