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Article
Smart-RRBS for single-cell methylome and transcriptome analysis
The integration of DNA methylation and transcriptional state within single cells is of broad interest. Several single-cell dual- and multi-omics approaches have been reported that enable further investigation ...
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Article
TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers
Mammalian cells stably maintain high levels of DNA methylation despite expressing both positive (DNMT3A/B) and negative (TET1-3) regulators. Here, we analyzed the independent and combined effects of these regu...
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Article
Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia
Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer1. Chronic lymphocytic leukaemia (CLL) is a highly informative model for cancer evolution as it undergoes sub...
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Article
Open AccessCorrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
Cancer evolution is fueled by epigenetic as well as genetic diversity. In chronic lymphocytic leukemia (CLL), intra-tumoral DNA methylation (DNAme) heterogeneity empowers evolution. Here, to comprehensively st...
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Article
Capturing sequence diversity in metagenomes with comprehensive and scalable probe design
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nuc...
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Article
Author Correction: Global delay in nascent strand DNA methylation
Following online publication of this article, the Gene Expression Omnibus records corresponding to accession codes GSM2406773, MN-d6, and GSM2406772, MN-d14, listed in the data availability statement were dele...
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Article
Global delay in nascent strand DNA methylation
Cytosine methylation is widespread among organisms and essential for mammalian development. In line with early postulations of an epigenetic role in gene regulation, symmetric CpG methylation can be mitoticall...
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Article
Open AccessGenome-wide tracking of dCas9-methyltransferase footprints
In normal mammalian development cytosine methylation is essential and is directed to specific regions of the genome. Despite notable advances through map** its genome-wide distribution, studying the direct c...
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Article
Genetic determinants and epigenetic effects of pioneer-factor occupancy
Transcription factors (TFs) direct developmental transitions by binding to target DNA sequences, influencing gene expression and establishing complex gene-regultory networks. To systematically determine the mo...
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Article
Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer
Analysis of global remethylation in mouse embryos at several developmental stages identifies an epigenetic landscape that partitions extraembryonic tissues within the embryo and resembles a frequent, global de...
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Article
Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells
Long-term culture of male embryonic stem cells in naive conditions containing Mek1/2 and Gsk3a/b inhibitors leads to irreversible changes in epigenetic and genomic stability that compromise their in vivo developm...
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Article
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Genome sequencing of Zika virus samples from infected patients and Aedes aegypti mosquitoes in Florida shows that the virus was probably introduced into the United States on multiple occasions, and that the Carib...
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Article
Zika virus evolution and spread in the Americas
One hundred and ten Zika virus genomes from ten countries and territories involved in the Zika virus epidemic reveal rapid expansion of the epidemic within Brazil and multiple introductions to other regions.
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Article
Virus genomes reveal factors that spread and sustained the Ebola epidemic
The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the reg...
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Article
Open AccessTargeted bisulfite sequencing of the dynamic DNA methylome
The ability to measure DNA methylation precisely and efficiently continues to drive our understanding of this modification in development and disease. Whole genome bisulfite sequencing has the advantage of the...
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Article
Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells
Alexander Meissner and colleagues use CRISPR/Cas9 genome editing to inactivate the DNA methyltransferases DNMT1, DNMT3A and DNMT3B in human embryonic stem cells (ESCs). They find an essential role for DNMT1 in hu...
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Article
Simultaneous generation of many RNA-seq libraries in a single reaction
RNAtag-seq barcodes transcripts prior to cDNA synthesis, thereby allowing pooled library generation from many input samples.
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Article
Open AccessTranscription factor binding dynamics during human ES cell differentiation
Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome-wid...
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Article
Dissecting neural differentiation regulatory networks through epigenetic footprinting
The integrative analysis of epigenetic footprints along consecutive stages of neural progenitors derived from human ES cells reveals regulatory mechanisms that orchestrate stage-specific differentiation.
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Article
Open AccessEnhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targe...
