μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells

Altemose, Nicolas; Maslan, Annie; Rios-Martinez, Carolina; Lai, Andre; White, Jonathan A.; Streets, Aaron

doi:10.1016/j.cels.2020.08.015

Cited by 20 publications

(18 citation statements)

References 63 publications

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“…High-quality deep RNA-seq can be achieved due to the small reaction volume (200–300 pL for each droplet). Streets’ group integrated protein imaging and DNA sequencing to study the interaction between Lamin-B1 protein and lamina-associate domains (LADs) [ 40 ]. The protein-DNA interaction was measured by the DNA adenine methyltransferase identification (DamID), which identifies the methyl groups deposited near the protein-DNA contact sites at the adenine bases ( m6 A).…”

Section: Microvalvementioning

confidence: 99%

Microfluidic Compartmentalization Platforms for Single Cell Analysis

et al. 2022

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Many cellular analytical technologies measure only the average response from a cell population with an assumption that a clonal population is homogenous. The ensemble measurement often masks the difference among individual cells that can lead to misinterpretation. The advent of microfluidic technology has revolutionized single-cell analysis through precise manipulation of liquid and compartmentalizing single cells in small volumes (pico- to nano-liter). Due to its advantages from miniaturization, microfluidic systems offer an array of capabilities to study genomics, transcriptomics, and proteomics of a large number of individual cells. In this regard, microfluidic systems have emerged as a powerful technology to uncover cellular heterogeneity and expand the depth and breadth of single-cell analysis. This review will focus on recent developments of three microfluidic compartmentalization platforms (microvalve, microwell, and microdroplets) that target single-cell analysis spanning from proteomics to genomics. We also compare and contrast these three microfluidic platforms and discuss their respective advantages and disadvantages in single-cell analysis.

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Section: Microvalvementioning

confidence: 99%

Microfluidic Compartmentalization Platforms for Single Cell Analysis

et al. 2022

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“…Since DamID was first developed (Vogel et al, 2007), a wide range of derivative technologies have been established (see (Aughey et al, 2019)). This includes the possibility to perform live-cell imaging of DamID-marked chromatin regions (Altemose et al, 2020;Borsos et al, 2019;Kind et al, 2013), targeted DamID (TaDa) for tissue-specific profiling without cell isolation or dissection (Marshall & Brand, 2017;Southall et al, 2013), proteomics on DamIDmarked genomic regions (Wong et al, 2021), single-cell experiments (Altemose et al, 2020;Borsos et al, 2019;Kind et al, 2015;Rooijers et al, 2019), and protocols for performing DamID in living mouse preimplantation embryos (Borsos et al, 2019;Pal et al, 2021).…”

Section: Advantages Of Damid For Studying Histone Ptms During Embryogenesismentioning

confidence: 99%

“…Since this approach is an adaptation that can be applied to any DamID protocol, it provides all advantages that the DamID toolbox has to offer and makes them available to the study of chromatin modifications. This includes the possibility to perform (live) imaging of Dammethylated DNA (Altemose et al, 2020;Borsos et al, 2019;Kind et al, 2013), tissue-specific study of model organisms without cell isolation via Targeted DamID (TaDa) (Southall et al, 2013), DamID-directed proteomics (Wong et al, 2021), multi-modal single-molecule sequencing (Cheetham et al, 2021), (multi-modal) single-cell sequencing studies (Altemose et al, 2020;Borsos et al, 2019;Kind et al, 2015;Rooijers et al, 2019), and the processing of samples with extremely little starting material (Borsos et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Single-cell profiling of transcriptome and histone modifications with EpiDamID

Rang

Luca

Vries

et al. 2021

Preprint

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Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, including various combinations of transcriptome, genome and epigenome. However, comprehensive profiling of the histone post-translational modifications that influence gene expression at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of genetically engineered proteins. By fusing Dam to single-chain variable fragment antibodies, engineered chromatin reader domains, or endogenous chromatin-binding proteins, we render the DamID technology and all its implementations compatible with the genome-wide identification of histone post-translational modifications. Importantly, this enables the joint analysis of chromatin marks and transcriptome in a variety of biological systems at the single-cell level. In this study, we use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. We further demonstrate the applicability of this method to in vivo systems by mapping H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specifically in the notochord. Overall, EpiDamID is a new addition to a vast existing toolbox for obtaining systematic insights into the role of chromatin states during dynamic cellular processes.

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“…This technique has been used to generate single cell laminar interaction maps. 23 By comparing data across cells, lamina-associated domains within the genome can be divided into constitutive and variable domains on the basis of the number of cells in which a locus is associated with the lamina. Lamina association can be used to probe cell type, as constitutive lamina-associated domains are associated with low gene expression.…”

Section: Spatial Resolution Of Subnuclear Featuresmentioning

confidence: 99%

Single cell biology—a Keystone Symposia report

Cable¹,

Elowitz

Domingos

et al. 2021

Annals of the New York Academy of Sciences

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Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.

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μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells

Cited by 20 publications

References 63 publications

Microfluidic Compartmentalization Platforms for Single Cell Analysis

Microfluidic Compartmentalization Platforms for Single Cell Analysis

Single-cell profiling of transcriptome and histone modifications with EpiDamID

Single cell biology—a Keystone Symposia report

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