CRISPR-Tag: an Efficient DNA Tagging System in Living Cells

Chen, Baohui; Zou, Wei

doi:10.1101/280495

Cited by 3 publications

(1 citation statement)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Such visualization could ultimately be informative to study transcriptional activation. We and others (Fang et al 2018;Kraus et al 2017;Neguembor et al 2018;Chen et al 2013;Chen et al 2018) have developed methods to image specific genomic sites, opening up the possibility to visualize DNA density and compaction at clutches located in specific regulatory regions in order to correlate function with the structure of DNA.…”

Section: Discussionmentioning

confidence: 99%

Nanoscale decompaction of nucleosomal DNA revealed through multi-color super-resolution microscopy

Otterstrom

Vicario

et al. 2018

Preprint

View full text Add to dashboard Cite

Super-resolution imaging of histones and DNA reveals that DNA is compacted by groups of nucleosomes -clutches -at the nanoscale level and clutch compaction of DNA is affected by histone tail acetylation especially in highly folded regions containing several nearby clutches. AbstractChromatin organization plays an important role in regulating gene expression. Previously, we showed that chromatin is organized in the form of nucleosome groups or clutches. The size and nucleosome packing density of clutches decreased in hyperacetylated cells having more open chromatin. While hyperacetylation is thought to disrupt histone-DNA and inter-nucleosome interactions, its impact on higher order DNA compaction by groups of nucleosomes in vivo is not clear. To elucidate this question, we carried out two-color super-resolution imaging of histones and DNA in cells treated with the Histone Deacetylase (HDAC) inhibitor Trichostatin A (TSA). We showed that a lower percentage of DNA was associated to clutches in hyperacetylated cells, suggesting a decrease in nucleosome occupancy. We further identified the presence of "clutch" DNA within a nanoscale distance around the clutches. Upon histone hyperacetylation, the radius of the clutch DNA decreased leading to DNA release from the clutches, consistent with disruption of DNA-histone interactions. Finally, the most dramatic decompaction was observed for groups of clutches in close spatial proximity, suggesting that neighboring clutches influence each other´s DNA compaction.

show abstract

Section: Discussionmentioning

confidence: 99%

Nanoscale decompaction of nucleosomal DNA revealed through multi-color super-resolution microscopy

Otterstrom

Vicario

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

Single-cell approaches to understand genome organisation throughout the cell cycle

McClelland

2019

Essays in Biochemistry

View full text Add to dashboard Cite

Mammalian genomes are ordered at several scales, ranging from nucleosomes (beads on a string), to topologically associated domains (TADs), laminar associated domains (LADs), and chromosome territories. These are described briefly below and we refer the reader to some recent comprehensive reviews on genome architecture summarising the current state of knowledge of the organisational principles of the nucleus [1,2]. Biological observations from populations of millions of individual cells can reveal consensus behaviour. New methods to study and interpret biological data at the single-cell level have recently been instrumental in revealing new understanding of cell-to-cell variation and novel biology. Here we will summarise the recent advances in single-cell technology that have provided insights into the behaviour of the mammalian genome during a cell cycle. We will focus on the interphase domain structure of chromosomes, including TADs and LADs, and how chromosome architecture changes during the cell cycle. The role of genome architecture relating to gene expression has been reviewed elsewhere [3].

show abstract

CRISPR interference as low burden logic inverters in synthetic circuits: characterization and tuning

Bellato

Chiacchiera

Salibi

et al. 2020

Preprint

View full text Add to dashboard Cite

The rational design of complex biological systems through the interconnection of single functional building blocks is hampered by many unpredictability sources; this is mainly due to the tangled context-dependency behavior of those parts once placed into an intrinsically complex living system. Among others, the finite amount of translational resources in prokaryotic cells leads to load effects in heterologous protein expression. As a result, hidden interactions among protein synthesis rates arise, leading to unexpected and counterintuitive behaviors. To face this issue in rational design of synthetic circuits in bacterial cells, CRISPR interference is here evaluated as genetic logic inverters with low translational resource usage, compared with traditional transcriptional regulators. This system has been studied and characterized in several circuit configurations. Each module composing the circuit architecture has been optimized in order to meet the desired specifications, and its reduced metabolic load has been eventually demonstrated via in-vivo assays.

show abstract

CRISPR-Tag: an Efficient DNA Tagging System in Living Cells

Cited by 3 publications

References 18 publications

Nanoscale decompaction of nucleosomal DNA revealed through multi-color super-resolution microscopy

Nanoscale decompaction of nucleosomal DNA revealed through multi-color super-resolution microscopy

Single-cell approaches to understand genome organisation throughout the cell cycle

CRISPR interference as low burden logic inverters in synthetic circuits: characterization and tuning

Contact Info

Product

Resources

About