2020
DOI: 10.1101/2020.11.17.385476
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Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy

Abstract: Proper regulation of genome architecture and activity is essential for the development and function of multicellular organisms. Histone modifications, acting in combination, specify these activity states at individual genomic loci. However, the methods used to study these modifications often require either a large number of cells or are limited to targeting one histone mark at a time. Here, we developed a new method called Single Cell Evaluation of Post-TRanslational Epigenetic Encoding (SCEPTRE) that uses Exp… Show more

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Cited by 6 publications
(7 citation statements)
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“…The concept that modification states of proteins modulate their interaction affinities is well established in the study of cytoskeletal polymers ( Howard, 2001 ; Mitchison, 1992 ; Phillips et al, 2012 ) but could provide a fresh perspective on the relationship between chromatin modifications and chromatin structure. Further testing of the methylation-compaction model will require direct interrogation of chromatin states at individual gene loci in single cells, work that will be aided by new methods to simultaneously visualize histone modification states and chromatin folding at single gene loci in single cells ( Kundu et al, 2017 ; Xu et al, 2018 ; Woodworth et al, 2020 ).…”
Section: Discussionmentioning
confidence: 99%
“…The concept that modification states of proteins modulate their interaction affinities is well established in the study of cytoskeletal polymers ( Howard, 2001 ; Mitchison, 1992 ; Phillips et al, 2012 ) but could provide a fresh perspective on the relationship between chromatin modifications and chromatin structure. Further testing of the methylation-compaction model will require direct interrogation of chromatin states at individual gene loci in single cells, work that will be aided by new methods to simultaneously visualize histone modification states and chromatin folding at single gene loci in single cells ( Kundu et al, 2017 ; Xu et al, 2018 ; Woodworth et al, 2020 ).…”
Section: Discussionmentioning
confidence: 99%
“…In addition, chromatin modeling can facilitate the interpretation of the chromatin motion at the local level and in the long range. More importantly, the chromatin motion data could be integrated with the chromatin conformation data, which is captured through HiC, to develop a unified model of the chromatin (Huang et al, 2020; Woodworth et al, 2021). Such a model would take into account the chromatin motion with the chromatin conformational change, and will allow for the study of casual relationships between chromatin motion and other subcellular activities, such as epigenetic modification, transcription, DNA replication, DNA damage and repair.…”
Section: Discussionmentioning
confidence: 99%
“…In addition, chromatin modeling can facilitate the interpretation of the chromatin motion at the local level and in the long range. More importantly, the chromatin motion data could be integrated with the chromatin conformation data, which is captured through HiC, to develop a unified model of the chromatin (Huang et al, 2020;Woodworth et al, 2021). DATA AVAILABILITY STATEMENT…”
Section: Chromatin Motion and Transcriptionmentioning
confidence: 99%
“…The affordable DIY SDCM that we present here had strong performance in terms of spatial resolution, utility with various objective lenses, and application to a number of routine and challenging applications for biological imaging. Our own group has already used this DIY SDCM for imaging thin tissue sections and expanded cultured cells [40,41] although we have not previously described the DIY SDCM itself.…”
Section: Discussionmentioning
confidence: 99%