Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells

Not All H3K4 Methylations Are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification

(2017) Deqing Hu et al.   MOLECULAR CELL

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler

(2017) Kalyan K. Sinha et al.   SCIENCE

Traceless Synthesis of Asymmetrically Modified Bivalent Nucleosomes

(2016) Carolin C. Lechner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Single-Molecule Studies in Live Cells

(2016) Ji Yu   Annual Review of Physical Chemistry

Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions

(2016) Erin E. Swinstead et al.   CELL

Transcriptional Regulators Compete with Nucleosomes Post-replication

(2016) Srinivas Ramachandran et al.   CELL

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes

(2016) Peter van Galen et al.   MOLECULAR CELL

FACT Remodels the Tetranucleosomal Unit of Chromatin Fibers for Gene Transcription

(2016) Wei Li et al.   MOLECULAR CELL

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution

(2016) Assaf Weiner et al.   NATURE BIOTECHNOLOGY

A two-state activation mechanism controls the histone methyltransferase Suv39h1

(2016) Manuel M Müller et al.   Nature Chemical Biology

Dense transcript profiling in single cells by image correlation decoding

(2016) Ahmet F Coskun et al.   NATURE METHODS

Single-cell multimodal profiling reveals cellular epigenetic heterogeneity

(2016) Lih Feng Cheow et al.   NATURE METHODS

Analysis of computational footprinting methods for DNase sequencing experiments

(2016) Eduardo G Gusmao et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

A decade of transcription factor-mediated reprogramming to pluripotency

(2016) Kazutoshi Takahashi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-molecule decoding of combinatorially modified nucleosomes

(2016) E. Shema et al.   SCIENCE

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes

(2016) Sergei Rudnizky et al.   Nature Communications

Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin

(2016) Kyoko Hiragami-Hamada et al.   Nature Communications

Mechanisms of Nucleosome Dynamics In Vivo

(2016) Steven Henikoff   Cold Spring Harbor Perspectives in Medicine

Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin

(2016) Chao Yu Zhen et al.   eLife

Library construction for next-generation sequencing: Overviews and challenges

(2016) Steven R. Head et al.   BIOTECHNIQUES

Dynamic Chromatin Regulation from a Single Molecule Perspective

(2015) Beat Fierz   ACS Chemical Biology

Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility

(2015) Thuy T.M. Ngo et al.   CELL

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

(2015) Davide Cacchiarelli et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

Imaging Live-Cell Dynamics and Structure at the Single-Molecule Level

(2015) Zhe Liu et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

(2015) Takashi Nagano et al.   Nature Protocols

Single-cell epigenomics: techniques and emerging applications

(2015) Omer Schwartzman et al.   NATURE REVIEWS GENETICS

Targeting Polycomb systems to regulate gene expression: modifications to a complex story

(2015) Neil P. Blackledge 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

Getting up to speed with transcription elongation by RNA polymerase II

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

A novel hybrid single molecule approach reveals spontaneous DNA motion in the nucleosome

(2015) Sijie Wei et al.   NUCLEIC ACIDS RESEARCH

Nucleosomes undergo slow spontaneous gaping

(2015) Thuy T.M. Ngo et al.   NUCLEIC ACIDS RESEARCH

Restricted epigenetic inheritance of H3K9 methylation

(2015) P. N. C. B. Audergon et al.   SCIENCE

Long-Range Chromatin Interactions

(2015) Job Dekker et al.   Cold Spring Harbor Perspectives in Biology

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

(2015) Davide Normanno et al.   Nature Communications

Multivalency governs HP1α association dynamics with the silent chromatin state

(2015) Sinan Kilic et al.   Nature Communications

ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

(2015) Gabriel E. Zentner et al.   Nature Communications

Dam it's good! DamID profiling of protein-DNA interactions

(2015) Gabriel N. Aughey et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Regulating the Chromatin Landscape: Structural and Mechanistic Perspectives

(2014) Blaine Bartholomew   Annual Review of Biochemistry

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Subnucleosomal Structures and Nucleosome Asymmetry across a Genome

(2014) Ho Sung Rhee et al.   CELL

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

(2014) Edith Heard et al.   CELL

Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes

(2014) P. Lhoumaud et al.   EMBO JOURNAL

Human Heterochromatin Protein 1α Promotes Nucleosome Associations That Drive Chromatin Condensation

(2014) Abdelhamid M. Azzaz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Analysis of the heterochromatin protein 1 (HP1) interactome in Drosophila

(2014) Hyun-Wook Ryu et al.   Journal of Proteomics

DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence

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

Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing

(2014) Jun Liang et al.   MOLECULAR CELL

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells

(2014) Zohar Shipony et al.   NATURE

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

High-resolution digital profiling of the epigenome

(2014) Gabriel E. Zentner et al.   NATURE REVIEWS GENETICS

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

The conformational state of the nucleosome entry–exit site modulates TATA box-specific TBP binding

(2014) Aaron R. Hieb et al.   NUCLEIC ACIDS RESEARCH

Epigenetic inheritance uncoupled from sequence-specific recruitment

(2014) K. Ragunathan et al.   SCIENCE

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

(2014) F. Song et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Transcribing through the nucleosome

(2014) Sheila S. Teves et al.   TRENDS IN BIOCHEMICAL SCIENCES

Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus

(2014) Ignacio Izeddin et al.   eLife

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

(2013) Geeta J. Narlikar et al.   CELL

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization

(2013) Amos Tanay et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Histone H3K27 Trimethylation Inhibits H3 Binding and Function of SET1-Like H3K4 Methyltransferase Complexes

(2013) D.-H. Kim et al.   MOLECULAR AND CELLULAR BIOLOGY

Division of Labor between the Chromodomains of HP1 and Suv39 Methylase Enables Coordination of Heterochromatin Spread

(2013) Bassem Al-Sady et al.   MOLECULAR CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

(2013) Nico Battich et al.   NATURE METHODS

High-resolution mapping of transcription factor binding sites on native chromatin

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

(2013) J Christof M Gebhardt et al.   NATURE METHODS

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

(2013) Housheng Hansen He et al.   NATURE METHODS

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

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Measuring Chromatin Interaction Dynamics on the Second Time Scale at Single-Copy Genes

(2013) K. Poorey et al.   SCIENCE

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Asymmetrically Modified Nucleosomes

(2012) Philipp Voigt et al.   CELL

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Chromatin as an expansive canvas for chemical biology

(2012) Beat Fierz et al.   Nature Chemical Biology

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

(2012) Karolin Luger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Perceiving the epigenetic landscape through histone readers

(2012) Catherine A Musselman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamics of inherently bounded histone modification domains

(2012) C. Hodges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural dynamics of nucleosomes at single-molecule resolution

(2012) John S. Choy et al.   TRENDS IN BIOCHEMICAL SCIENCES

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Antagonism between MES-4 and Polycomb Repressive Complex 2 Promotes Appropriate Gene Expression in C. elegans Germ Cells

(2012) Laura J. Gaydos et al.   Cell Reports

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

(2011) Oren Ram et al.   CELL

High-Resolution Genome-wide Mapping of the Primary Structure of Chromatin

(2011) Zhenhai Zhang et al.   CELL

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Pioneer transcription factors: establishing competence for gene expression

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

Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins

(2011) H. Wang et al.   GENOME RESEARCH

Dynamics of Nucleosome Invasion by DNA Binding Proteins

(2011) Hannah S. Tims et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Constraints in Collaborative Competition of Transcription Factors against the Nucleosome

(2011) Georgette Moyle-Heyrman et al.   JOURNAL OF MOLECULAR BIOLOGY

Chromodomain-Mediated Oligomerization of HP1 Suggests a Nucleosome-Bridging Mechanism for Heterochromatin Assembly

(2011) Daniele Canzio et al.   MOLECULAR CELL

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

Chromatin Dynamics

(2010) Michael R. Hübner et al.   Annual Review of Biophysics

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Chemically Controlled Protein Assembly: Techniques and Applications

(2010) Adrian Fegan et al.   CHEMICAL REVIEWS

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Chromatin structure and the inheritance of epigenetic information

(2010) Raphaël Margueron et al.   NATURE REVIEWS GENETICS

Histone variants — ancient wrap artists of the epigenome

(2010) Paul B. Talbert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nucleosome accessibility governed by the dimer/tetramer interface

(2010) Vera Böhm et al.   NUCLEIC ACIDS RESEARCH

Nucleosome-mediated cooperativity between transcription factors

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

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

Spontaneous Mutation Accumulation Studies in Evolutionary Genetics

(2009) Daniel L. Halligan et al.   Annual Review of Ecology Evolution and Systematics

Multiscale Analysis of Dynamics and Interactions of Heterochromatin Protein 1 by Fluorescence Fluctuation Microscopy

(2009) Katharina P. Müller et al.   BIOPHYSICAL JOURNAL

10 Years of Tension on Chromatin: Results from Single Molecule Force Spectroscopy

(2009) Fan-Tso Chien et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Role of the polycomb protein EED in the propagation of repressive histone marks

(2009) Raphael Margueron et al.   NATURE

Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber

(2009) Maarten Kruithof et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamics and function of compact nucleosome arrays

(2009) Michael G Poirier et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

(2009) Michael A Hall et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mapping accessible chromatin regions using Sono-Seq

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

Spontaneous Access to DNA Target Sites in Folded Chromatin Fibers

(2008) Michael G. Poirier et al.   JOURNAL OF MOLECULAR BIOLOGY

HP1-β mobilization promotes chromatin changes that initiate the DNA damage response

(2008) Nabieh Ayoub et al.   NATURE

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS

High-density mapping of single-molecule trajectories with photoactivated localization microscopy

(2008) Suliana Manley et al.   NATURE METHODS

A practical guide to single-molecule FRET

(2008) Rahul Roy et al.   NATURE METHODS

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

(2008) Keir C Neuman et al.   NATURE METHODS

Genome-wide approaches to studying chromatin modifications

(2008) Dustin E. Schones et al.   NATURE REVIEWS GENETICS