Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)

Carter, Benjamin C.; Ku, Wai Lim; Kang, Jee Youn; Hu, Gangqing; Perrie, Jonathan; Tang, Qingsong; Zhao, Keji

doi:10.1038/s41467-019-11559-1

Cited by 113 publications

(53 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[ 90,93 ] Thus, mapping gene expression patterns onto spatial coordinates can reveal how specific factors present in vivo govern the determination of stem cell fate. [ 88 ] Recent advances in single‐cell sequencing (sc‐seq) methods have enabled unbiased, high‐throughput molecular profiling across several layers of biological information (e.g., immunophenotype, [ 94–96 ] epigenetic modifications, [ 97 ] chromatin accessibility, [ 98,99 ] transcriptome, [ 100,101 ] and genome [ 102 ] ) that resolve the heterogeneity in cell state and identity within cellular communities. [ 103 ] However, the dissociation protocols required to produce single‐cell suspensions discard the spatial context of molecular profiles.…”

Section: Spatial Molecular Profiling Of Intercellular Communicationmentioning

confidence: 99%

Engineered Tools to Study Intercellular Communication

et al. 2020

View full text Add to dashboard Cite

All multicellular organisms rely on intercellular communication networks to coordinate physiological functions. As members of a dynamic social network, each cell receives, processes, and redistributes biological information to define and maintain tissue homeostasis. Uncovering the molecular programs underlying these processes is critical for prevention of disease and aging and development of therapeutics. The study of intercellular communication requires techniques that reduce the scale and complexity of in vivo biological networks while resolving the molecular heterogeneity in “omic” layers that contribute to cell state and function. Recent advances in microengineering and high‐throughput genomics offer unprecedented spatiotemporal control over cellular interactions and the ability to study intercellular communication in a high‐throughput and mechanistic manner. Herein, this review discusses how salient engineered approaches and sequencing techniques can be applied to understand collective cell behavior and tissue functions.

show abstract

Section: Spatial Molecular Profiling Of Intercellular Communicationmentioning

confidence: 99%

Engineered Tools to Study Intercellular Communication

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Epigenome: DNA-associated protein binding sites Ai et al, 2019;Carter et al, 2019;Grosselin et al, 2019;Kaya-Okur et al, 2019; Single-cell DNA methylation (scDNA methylation) Epigenome: transcription activity Reviewed by Karemaker and Vermeulen, 2018 Single-cell Hi-C (scHi-C) Epigenome: 3D chromatin organization Nagano et al, 2013;Ramani et al, 2017;Zhou et al, 2019 Single-molecule fluorescence in situ hybridization (smFISH)…”

Section: Development Of the Human Pancreasmentioning

confidence: 99%

Understanding generation and regeneration of pancreatic β cells from a single-cell perspective

2020

Development

View full text Add to dashboard Cite

Understanding the mechanisms that underlie the generation and regeneration of β cells is crucial for developing treatments for diabetes. However, traditional research methods, which are based on populations of cells, have limitations for defining the precise processes of β-cell differentiation and trans-differentiation, and the associated regulatory mechanisms. The recent development of single-cell technologies has enabled re-examination of these processes at a single-cell resolution to uncover intermediate cell states, cellular heterogeneity and molecular trajectories of cell fate specification. Here, we review recent advances in understanding βcell generation and regeneration, in vivo and in vitro, from single-cell technologies, which could provide insights for optimization of diabetes therapy strategies.

show abstract

“…However, these numbers are still high and prohibit the profiling of rare material. If cell number is very limited, other methods such as uliChIP-seq ( Brind’Amour et al., 2015 ), CUT&RUN ( Skene and Henikoff, 2017 ), STAR ChIP ( Zhang et al., 2016 ), CUT&TAG ( Kaya-Okur et al., 2019 ), ACT-seq ( Carter et al., 2019 ), itChIP-seq ( Ai et al., 2019 ) can be used.…”

Section: Limitationsmentioning

confidence: 99%

Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation

Sharrocks

et al. 2020

STAR Protocols

View full text Add to dashboard Cite

Summary Mapping the genomic locations of chromatin-associated proteins, such as transcription factors and histone modifications, is key to understanding the mechanisms of transcriptional regulation. ChIPmentation offers a simple and robust way of investigating the genomic binding sites of a protein using relatively low-input material. Here, we present a detailed protocol for the key steps that lead to a successful ChIPmentation experiment, as well as a quick analysis pipeline to examine the data. For complete details on the use and execution of this protocol, please refer to Schmidl et al. (2015) . For example data produced by this protocol, please refer to Henriksson et al. (2019) and Zhang et al. (2019) .

show abstract

Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)

Cited by 113 publications

References 22 publications

Engineered Tools to Study Intercellular Communication

Engineered Tools to Study Intercellular Communication

Understanding generation and regeneration of pancreatic β cells from a single-cell perspective

Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation

Contact Info

Product

Resources

About