Single-Cell DNA Methylation Profiling: Technologies and Biological Applications

Karemaker, Ino D; Vermeulen, Michiel

doi:10.1016/j.tibtech.2018.04.002

Cited by 141 publications

(102 citation statements)

References 63 publications

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“…Beyond basic scRNA-seq and scDNA-seq experiments, various assays have been proposed to measure chromatin accessibility [37,38], DNA methylation [39], protein levels [40], protein binding, and also for performing multiple simultaneous measurements [41,42] in single cells. The corresponding increase in experimental choices means another possible inflation of feature spaces.…”

Section: Scaling To Higher Dimensionalities: More Cells More Featurementioning

confidence: 99%

Eleven grand challenges in single-cell data science

et al. 2020

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The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.

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Section: Scaling To Higher Dimensionalities: More Cells More Featurementioning

confidence: 99%

Eleven grand challenges in single-cell data science

et al. 2020

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“…Current methods for detecting DNA modifications at the single cell level are either directusing bisulfite conversion, methylation sensitive restriction enzymes, or third-generation sequencingor indirectusing fluorescent reporters sensitive to DNA methylation (for a recent review, see Karemaker and Vermeulen, 2018). These methods primarily focus on 5mC and 5hmC, the two most common DNA modifications, but a subset could be adapted to detect other modifications.…”

Section: Single Cell Measurements Of Dna Modificationsmentioning

confidence: 99%

Mapping chromatin modifications at the single cell level

Ludwig

Bintu

2019

Development

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Understanding chromatin regulation holds enormous promise for controlling gene regulation, predicting cellular identity, and developing diagnostics and cellular therapies. However, the dynamic nature of chromatin, together with cell-to-cell heterogeneity in its structure, limits our ability to extract its governing principles. Single cell mapping of chromatin modifications, in conjunction with expression measurements, could help overcome these limitations. Here, we review recent advances in single cell-based measurements of chromatin modifications, including optimization to reduce DNA loss, improved DNA sequencing, barcoding, and antibody engineering. We also highlight several applications of these techniques that have provided insights into cell-type classification, mapping modification co-occurrence and heterogeneity, and monitoring chromatin dynamics.

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“…Importantly, single-cell methods for DNA methylation profiling have also recently been developed, which will undoubtedly provide important answers about DNA methylation dynamics especially regarding heterogeneous systems. I refer the reader to a more extensive review about these methods [76].…”

Section: Boxmentioning

confidence: 99%

DNA (Hydroxy)Methylation in T Helper Lymphocytes

Monticelli

2019

Trends in Biochemical Sciences

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Upon recognition of an antigen, the differentiation of antigen-inexperienced naïve T lymphocytes into subsets able to effectively coordinate host defense is controlled by a network of transcription factors and regulatory molecules. In the cell nucleus, these factors act in the context of epigenetic modifications that influence DNA accessibility and ultimately gene expression. This review discusses recent findings about the role of DNA methylation (and its oxidized derivatives) in modulating differentiation and functions of T helper lymphocytes of the adaptive immune system.

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Single-Cell DNA Methylation Profiling: Technologies and Biological Applications

Cited by 141 publications

References 63 publications

Eleven grand challenges in single-cell data science

Eleven grand challenges in single-cell data science

Mapping chromatin modifications at the single cell level

DNA (Hydroxy)Methylation in T Helper Lymphocytes

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