Mapping chromatin modifications at the single cell level

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

(2019) Wai Lim Ku et al.   NATURE METHODS

The cis-Regulatory Atlas of the Mouse Immune System

(2019) Hideyuki Yoshida et al.   CELL

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Design, Construction, and Validation of Histone-Binding Effectors in Vitro and in Cells

(2018) Stefan J. Tekel et al.   BIOCHEMISTRY

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

(2018) Peggie Cheung et al.   CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

Single-Cell DNA Methylation Profiling: Technologies and Biological Applications

(2018) Ino D. Karemaker et al.   TRENDS IN BIOTECHNOLOGY

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Cell-type-specific brain methylomes profiled via ultralow-input microfluidics

(2018) Sai Ma et al.   Nature Biomedical Engineering

High-Resolution Single-Cell DNA Methylation Measurements Reveal Epigenetically Distinct Hematopoietic Stem Cell Subpopulations

(2018) Tony Hui et al.   Stem Cell Reports

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

A chromatin integration labelling method enables epigenomic profiling with lower input

(2018) Akihito Harada et al.   NATURE CELL BIOLOGY

Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution

(2018) Efrat Shema et al.   NATURE GENETICS

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells

(2017) Xiaoji Wu et al.   GENES & DEVELOPMENT

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq)

(2017) Stephen J Clark et al.   Nature Protocols

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells

(2017) Lin Han et al.   NUCLEIC ACIDS RESEARCH

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic sites

(2017) Cristiana Lungu et al.   Nature Communications

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

AgIn: measuring the landscape of CpG methylation of individual repetitive elements

(2016) Yuta Suzuki et al.   BIOINFORMATICS

Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas

(2016) Yu Hou et al.   CELL RESEARCH

DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation

(2016) Matthias Farlik et al.   Cell Stem Cell

Next stop for the CRISPR revolution: RNA-guided epigenetic regulators

(2016) Suhani Vora et al.   FEBS Journal

Repetitive DNA methylome analysis by small-scale and single-cell shotgun bisulfite sequencing

(2016) Hisato Kobayashi et al.   GENES TO CELLS

A Genetically Encoded Probe for Live-Cell Imaging of H4K20 Monomethylation

(2016) Yuko Sato et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2016) Alistair N. Boettiger et al.   NATURE

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

(2016) Dylan Mooijman et al.   NATURE BIOTECHNOLOGY

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

(2016) Assaf Weiner et al.   NATURE BIOTECHNOLOGY

Complex transcriptional modulation with orthogonal and inducible dCas9 regulators

(2016) Yuchen Gao et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

The molecular hallmarks of epigenetic control

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

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

Lateral Thinking: How Histone Modifications Regulate Gene Expression

(2016) Moyra Lawrence et al.   TRENDS IN GENETICS

Tracing Dynamic Changes of DNA Methylation at Single-Cell Resolution

(2015) Yonatan Stelzer 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

Q-RRBS: a quantitative reduced representation bisulfite sequencing method for single-cell methylome analyses

(2015) Kangli Wang et al.   Epigenetics

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

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

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

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

(2015) Iain C Macaulay et al.   NATURE METHODS

Single-cell, locus-specific bisulfite sequencing (SLBS) for direct detection of epimutations in DNA methylation patterns

(2015) Silvia Gravina et al.   NUCLEIC ACIDS RESEARCH

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

SnapShot: Histone Modifications

(2014) He Huang et al.   CELL

Application of histone modification-specific interaction domains as an alternative to antibodies

(2014) Goran Kungulovski et al.   GENOME RESEARCH

Regulation of RNA polymerase II activation by histone acetylation in single living cells

(2014) Timothy J. Stasevich et al.   NATURE

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

(2013) M. Stevens et al.   GENOME RESEARCH

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

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

(2013) Sivakanthan Kasinathan 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

Detection of histone modifications at specific gene loci in single cells in histological sections

(2013) Delphine Gomez et al.   NATURE METHODS

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

(2013) A. H. Laszlo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

(2013) J. Schreiber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetically encoded system to track histone modification in vivo

(2013) Yuko Sato et al.   Scientific Reports

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

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

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Readers of histone modifications

(2011) Miyong Yun et al.   CELL RESEARCH

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

(2011) Hongcang Gu et al.   Nature Protocols

Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling

(2011) Yoko Hayashi-Takanaka et al.   NUCLEIC ACIDS RESEARCH

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY