71 Result(s)
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Bradley E Bernstein
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Article
Open AccessSystematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells
Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to...
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Open AccessEpigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids
In all terrestrial vertebrates, the parathyroid glands are critical regulators of calcium homeostasis and the sole source of parathyroid hormone (PTH). Hyperparathyroidism and hypoparathyroidism are clinically...
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Open AccessExposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro
Microglia, the macrophages of the brain parenchyma, are key players in neurodegenerative diseases such as Alzheimer’s disease. These cells adopt distinct transcriptional subtypes known as states. Understanding...
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Open AccessUltraviolet radiation shapes dendritic cell leukaemia transformation in the skin
Tumours most often arise from progression of precursor clones within a single anatomical niche. In the bone marrow, clonal progenitors can undergo malignant transformation to acute leukaemia, or differentiate ...
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Open AccessChromatin complex dependencies reveal targeting opportunities in leukemia
Chromatin regulators are frequently mutated in human cancer and are attractive drug targets. They include diverse proteins that share functional domains and assemble into related multi-subunit complexes. To in...
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Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements
Epigenomic maps identify gene regulatory elements by their chromatin state. However, prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate the interdependence of elements in...
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Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations
The combination of single-cell transcriptomics with mitochondrial DNA variant detection can be used to establish lineage relationships in primary human cells, but current methods are not scalable to interrogat...
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Open AccessAuthor Correction: Perspectives on ENCODE
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Open AccessAuthor Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
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Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells
The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast n...
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Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity
Epigenetic dysregulation is a defining feature of tumorigenesis that is implicated in immune escape1,2. Here, to identify factors that modulate the immune sensitivity of cancer cells, we performed in vivo CRISPR–...
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Article
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance
Appropriate use and interpretation of serological tests for assessments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure, infection and potential immunity require accurate data on assay...
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Open AccessDetecting sample swaps in diverse NGS data types using linkage disequilibrium
As the number of genomics datasets grows rapidly, sample mislabeling has become a high stakes issue. We present CrosscheckFingerprints (Crosscheck), a tool for quantifying sample-relatedness and detecting inco...
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Open AccessSingle-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance
Tumors can evolve and adapt to therapeutic pressure by acquiring genetic and epigenetic alterations that may be transient or stable. A precise understanding of how such events contribute to intratumoral hetero...
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Perspectives on ENCODE
The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of develo** a comprehensive map of functional elements in the human genome. These included genes, biochemical regions...
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Article
Open AccessExpanded encyclopaedias of DNA elements in the human and mouse genomes
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the ...
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Open AccessChromatin accessibility promotes hematopoietic and leukemia stem cell activity
Chromatin organization is a highly orchestrated process that influences gene expression, in part by modulating access of regulatory factors to DNA and nucleosomes. Here, we report that the chromatin accessibil...
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Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs
Epigenetic aberrations are widespread in cancer, yet the underlying mechanisms and causality remain poorly understood1–3. A subset of gastrointestinal stromal tumours (GISTs) lack canonical kinase mutations but i...
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Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo
Development and differentiation are associated with profound changes to histone modifications, yet their in vivo function remains incompletely understood. Here, we generated mouse models expressing inducible h...
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Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
