The prevention and resolution of DNA replication–transcription conflicts in eukaryotic cells

Wu, Wei; Hickson, Ian; Liu, Ying

doi:10.1007/s42764-020-00012-z

Cited by 7 publications

(6 citation statements)

References 152 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Transcription and DNA replication in a cell’s S phase are in inherent conflict, which can be a source of DNA damage and genome instability 46 . It would in this regard be of interest to further explore whether cells in S phase respond weaker to transcriptional stimulations as a general strategy to temporarily decouple DNA replication and transcription 47 .…”

Section: Discussionmentioning

confidence: 99%

Live-seq enables temporal transcriptomic recording of single cells

Chen

Guillaume‐Gentil

Rainer

et al. 2022

Nature

122

100

View full text Add to dashboard Cite

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity1. However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy2,3, thus allowing to couple a cell’s ground-state transcriptome to its downstream molecular or phenotypic behaviour. To benchmark Live-seq, we used cell growth, functional responses and whole-cell transcriptome read-outs to demonstrate that Live-seq can accurately stratify diverse cell types and states without inducing major cellular perturbations. As a proof of concept, we show that Live-seq can be used to directly map a cell’s trajectory by sequentially profiling the transcriptomes of individual macrophages before and after lipopolysaccharide (LPS) stimulation, and of adipose stromal cells pre- and post-differentiation. In addition, we demonstrate that Live-seq can function as a transcriptomic recorder by preregistering the transcriptomes of individual macrophages that were subsequently monitored by time-lapse imaging after LPS exposure. This enabled the unsupervised, genome-wide ranking of genes on the basis of their ability to affect macrophage LPS response heterogeneity, revealing basal Nfkbia expression level and cell cycle state as important phenotypic determinants, which we experimentally validated. Thus, Live-seq can address a broad range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.

show abstract

Section: Discussionmentioning

confidence: 99%

Live-seq enables temporal transcriptomic recording of single cells

Chen

Guillaume‐Gentil

Rainer

et al. 2022

Nature

122

100

View full text Add to dashboard Cite

show abstract

“…[15] The two most important functions of DNA in the cell are replication and transcription. [22] Replication and transcription are very important for the continuity of the cells. [23] DNA begins its replication and transcription processes when it receives the signal by binding a special regulatory protein to a specific region.…”

Section: Resultsmentioning

confidence: 99%

“…[15] . The two most important functions of DNA in the cell are replication and transcription [22] . Replication and transcription are very important for the continuity of the cells [23] .…”

Section: Resultsmentioning

confidence: 99%

Fabrication and Characterization of Saffron Stamen Aqueous Extract Controlled Release System as Potential Topical Treatment of Thermal Burn Wounds

et al. 2021

View full text Add to dashboard Cite

In our study, we aimed the preparation of Saffron stamen aqueous extract (SSAE) loaded chitosan nanoparticles (CNPs) to be used topically for thermal burns. First, biological activity tests such as DNA binding, DNA cleavage and antibacterial activity were performed to determine the effectiveness of SSAE to be encapsulated. Additionally, a genotoxicity test was performed for the reliability of SSAE. Ionic gelation method was used for encapsulation, and SSAE-loaded CNPs were obtained. Average particle size, zeta potential, polydispersity index (PdI), morphology, and releasing kinetics of the SSAE-loaded CNPs and blank CNPs were determined. DNA binding showed that SSAE interacted with DNA electrostatically. It was determined that all doses of SSAE used in hydrolytic and oxidative DNA cleavage experiments cleave DNA. As a result of the Ames / Salmonella test, it was found that 1,25 mg SSAE was not genotoxic. Then, this concentration was used in nanoparticle synthesis. As a result of DLS analysis, it was determined that SSAE-loaded CNPs have an average size of 57.61 � 1.234 nm, 0.175 � 0.008 PdI, and + 14 � 0.755 mV zeta potential. Encapsulation efficiency and loading capacity of SSAE-loaded CNPs calculated as 71.76 % and 2,64 % respectively. As a result of releasing kinetics, it was determined that 79.54 % of SSAE was released after 168 hours. Antibacterial results revealed that SSAE loaded CNPs were more effective against bacteria than blank SSAE.

show abstract

“…It would in this regard be of interest to further explore whether cells in S phase respond weaker to transcriptional stimulations as a general strategy to temporarily decouple DNA replication and transcription 54 .…”

Section: Discussionmentioning

confidence: 99%

“…Transcription and DNA replication in a cell’s S phase are in inherent conflict, which can be a source of DNA damage and genome instability 53 . It would in this regard be of interest to further explore whether cells in S phase respond weaker to transcriptional stimulations as a general strategy to temporarily decouple DNA replication and transcription 54 .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide molecular recording using Live-seq

Chen

Guillaume‐Gentil

Dainese

et al. 2021

Preprint

View full text Add to dashboard Cite

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity in health and disease. However, scRNA-seq requires lysing cells, which makes it impossible to link the individual cells to downstream molecular and phenotypic states. Here, we established Live-seq, an approach for single-cell transcriptome profiling that preserves cell viability during RNA extraction using fluidic force microscopy. Based on cell division, functional responses and whole-cell transcriptome read-outs, we show that Live-seq does not induce major cellular perturbations and therefore can function as a transcriptomic recorder. We demonstrate this recording capacity by preregistering the transcriptomes of individual macrophage-like RAW 264.7 cells that were subsequently subjected to time-lapse imaging after lipopolysaccharide (LPS) exposure. This enabled the unsupervised, genome-wide ranking of genes based on their ability to impact macrophage LPS response heterogeneity, revealing basal NFKBIA expression level and cell cycle state as major phenotypic determinants. Furthermore, we show that Live-seq can be used to sequentially profile the transcriptomes of individual macrophages before and after stimulation with LPS, thus enabling the direct mapping of a cell's trajectory. Live-seq can address a broad range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.

show abstract

The prevention and resolution of DNA replication–transcription conflicts in eukaryotic cells

Cited by 7 publications

References 152 publications

Live-seq enables temporal transcriptomic recording of single cells

Live-seq enables temporal transcriptomic recording of single cells

Fabrication and Characterization of Saffron Stamen Aqueous Extract Controlled Release System as Potential Topical Treatment of Thermal Burn Wounds

Genome-wide molecular recording using Live-seq

Contact Info

Product

Resources

About