-
Protocol
Genome-Wide Map** of Active Regulatory Elements Using ATAC-seq
Active cis-regulatory elements (cREs) in eukaryotes are characterized by nucleosomal depletion and, accordingly, higher accessibility. This property has turned out to be immensely useful for identifying cREs geno...
-
Protocol
Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq
The ability to analyze the transcriptomic and epigenomic states of individual single cells has in recent years transformed our ability to measure and understand biological processes. Recent advancements have f...
-
Article
Aging disrupts circadian gene regulation and function in macrophages
Aging is characterized by an increased vulnerability to infection and the development of inflammatory diseases, such as atherosclerosis, frailty, cancer and neurodegeneration. Here, we find that aging is assoc...
-
Protocol
Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq
A hallmark feature of active cis-regulatory elements (CREs) in eukaryotes is their nucleosomal depletion and, accordingly, higher to enzymatic treatment. This property has been the basis of a number of seque...
-
Protocol
Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq
The ATAC-seq assay has emerged as the most useful, versatile, and widely adaptable method for profiling accessible chromatin regions and tracking the activity of cis-regulatory elements (cREs) in eukaryotes. Than...
-
Article
Long-range single-molecule map** of chromatin accessibility in eukaryotes
Map** open chromatin regions has emerged as a widely used tool for identifying active regulatory elements in eukaryotes. However, existing approaches, limited by reliance on DNA fragmentation and short-read ...
-
Article
Reduced CTL motility and activity in avascular tumor areas
Patchy infiltration of tumors by cytotoxic T cells (CTLs) predicts poorer prognosis for cancer patients. The factors limiting intratumoral CTL dissemination, though, are poorly understood. To study CTL dissemi...
-
Article
Chromatin accessibility and the regulatory epigenome
Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome refle...
-
Article
Correction: Corrigendum: Derivation of novel human ground state naive pluripotent stem cells
Nature 504, 282–286 (2013); doi:10.1038/nature12745 The reduced representation bisulphite sequencing (RRBS) data generated and analysed in this Letter were not originally uploaded to the Gene Expression Omnibu...
-
Article
Correction: Corrigendum: Deterministic direct reprogramming of somatic cells to pluripotency
Nature 502, 65–70 (2013); doi:10.1038/nature12587 In this Article, the reduced representation bisulphite sequencing (RRBS) data obtained and analysed were not initially uploaded to the Gene Expression Omnibus ...
-
Article
Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells
Using a new method to estimate DNA methylation turnover rate, embryonic stem cells are shown to lack clonal transmission of methylation but still maintain a stable epigenetic state, whereas somatic cells trans...
-
Article
Derivation of novel human ground state naive pluripotent stem cells
It is known that human embryonic stem (ES) cells are more similar to mouse primed epiblast stem cells than to naive mouse ES cells; here culture conditions are determined that allow human ES and induced plurip...
-
Article
Deterministic direct reprogramming of somatic cells to pluripotency
Somatic cells can be inefficiently and stochastically reprogrammed into induced pluripotent stem (iPS) cells by exogenous expression of Oct4 (also called Pou5f1), Sox2, Klf4 and Myc (hereafter referred to as O...
