2020
DOI: 10.1016/j.cels.2020.08.015
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μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells

Abstract: Highlights d New microfluidic device images and sorts single cells then performs single-cell DamID d Improved m6 A-Tracer method images protein-DNA interactions with less background d mDamID identifies LADs that vary between single cells and across cell types d Imaging can be used to select cells with greater DamID sequencing signal to noise

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Cited by 17 publications
(18 citation statements)
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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%
“…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%
“…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%
“…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%