scholarly journals Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

2020 ◽  
Author(s):  
Hajnalka L. Pálinkás ◽  
Angéla Békési ◽  
Gergely Róna ◽  
Lőrinc Pongor ◽  
Gergely Tihanyi ◽  
...  
Keyword(s):  
Drug Treatment ◽  
Human Cancer ◽  
Super Resolution ◽  
Cancer Cell Line ◽  
Distribution Patterns ◽  
Genome Wide ◽  
Sequencing Method ◽  
Anti Cancer ◽  
Resolution Imaging ◽  
Spatio Temporal

ABSTRACTNumerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug-treatment in human cancer cell-line HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards more active/functional segments. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can also be applied to study the dynamic spatio-temporal nature of genomic uracil.

scholarly journals Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Hajnalka L Pálinkás ◽  
Angéla Békési ◽  
Gergely Róna ◽  
Lőrinc Pongor ◽  
Gábor Papp ◽  
...  
Keyword(s):  
Human Cancer ◽  
Super Resolution ◽  
Cancer Cell Line ◽  
Distribution Patterns ◽  
Genome Wide ◽  
Sequencing Method ◽  
Anti Cancer ◽  
Drug Treatments ◽  
Resolution Imaging ◽  
Spatio Temporal

Numerous anti-cancer drugs perturb thymidylate biosynthesis and lead to genomic uracil incorporation contributing to their antiproliferative effect. Still, it is not yet characterized if uracil incorporations have any positional preference. Here, we aimed to uncover genome-wide alterations in uracil pattern upon drug treatments in human cancer cell line models derived from HCT116. We developed a straightforward U-DNA sequencing method (U-DNA-Seq) that was combined with in situ super-resolution imaging. Using a novel robust analysis pipeline, we found broad regions with elevated probability of uracil occurrence both in treated and non-treated cells. Correlation with chromatin markers and other genomic features shows that non-treated cells possess uracil in the late replicating constitutive heterochromatic regions, while drug treatment induced a shift of incorporated uracil towards segments that are normally more active/functional. Data were corroborated by colocalization studies via dSTORM microscopy. This approach can be applied to study the dynamic spatio-temporal nature of genomic uracil.

scholarly journals Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase

PLoS Genetics ◽  
2020 ◽  
Vol 16 (6) ◽  
pp. e1008595 ◽  
Author(s):  
Johan A. Slotman ◽  
Maarten W. Paul ◽  
Fabrizia Carofiglio ◽  
H. Martijn de Gruiter ◽  
Tessa Vergroesen ◽  
...  
Keyword(s):  
Dna Repair ◽  
Meiotic Prophase ◽  
Super Resolution ◽  
Distribution Patterns ◽  
Dynamic Distribution ◽  
Resolution Imaging

scholarly journals Super-resolution microscopy can identify specific protein distribution patterns in platelets incubated with cancer cells

Nanoscale ◽  
2019 ◽  
Vol 11 (20) ◽  
pp. 10023-10033 ◽  
Author(s):  
Jan Bergstrand ◽  
Lei Xu ◽  
Xinyan Miao ◽  
Nailin Li ◽  
Ozan Öktem ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Dictionary Learning ◽  
Super Resolution ◽  
Distribution Patterns ◽  
Specific Protein ◽  
Protein Distribution ◽  
Activated Platelets ◽  
Resolution Imaging ◽  
Super Resolution Microscopy

Super-resolution imaging of P-selectin in platelets together with dictionary learning allow specifically activated platelets to be identified in an automatic objective manner.

scholarly journals Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Rajarshi P. Ghosh ◽  
Barbara J. Meyer
Keyword(s):  
Single Molecule ◽  
Genome Organization ◽  
Spatial Organization ◽  
Super Resolution ◽  
Annual Review ◽  
Publication Date ◽  
Cellular Processes ◽  
Regulatory Processes ◽  
Genome Wide ◽  
Resolution Imaging

Nuclei are central hubs for information processing in eukaryotic cells. The need to fit large genomes into small nuclei imposes severe restrictions on genome organization and the mechanisms that drive genome-wide regulatory processes. How a disordered polymer such as chromatin, which has vast heterogeneity in its DNA and histone modification profiles, folds into discernibly consistent patterns is a fundamental question in biology. Outstanding questions include how genomes are spatially and temporally organized to regulate cellular processes with high precision and whether genome organization is causally linked to transcription regulation. The advent of next-generation sequencing, super-resolution imaging, multiplexed fluorescent in situ hybridization, and single-molecule imaging in individual living cells has caused a resurgence in efforts to understand the spatiotemporal organization of the genome. In this review, we discuss structural and mechanistic properties of genome organization at different length scales and examine changes in higher-order chromatin organization during important developmental transitions. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Dynamics as a cause for the nanoscale organization of the genome

2020 ◽  
Author(s):  
R. Barth ◽  
G. Fourel ◽  
H. A. Shaban
Keyword(s):  
Local Density ◽  
Super Resolution ◽  
Active Motion ◽  
Chromatin Dynamics ◽  
Small Areas ◽  
Functional Implications ◽  
Causality Inference ◽  
A Cell ◽  
Resolution Imaging ◽  
Spatio Temporal

AbstractChromatin ‘blobs’ were recently identified by live super-resolution imaging as pervasive, but transient and dynamic structural entities consisting of a few associating nucleosomes. The origin and functional implications of these blobs are, however, unknown. Following these findings, we explore whether causal relationships exist between parameters characterizing the chromatin blob dynamics and structure, by adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals that chromatin dynamics is a key determinant of both blob area and local density. However, such causality can only be demonstrated in small areas (10 – 20%) of the nucleus, highlighting that chromatin dynamics and structure at the nanoscale is dominated by stochasticity. Pixels for which the inter-blob distance can be effectively demonstrated to depend on chromatin dynamics appears as clump in the nucleus, and display both a higher blob density and higher local dynamics as compared with the rest of the nucleus. Furthermore, we show that the theory of active semiflexible polymers can be invoked to provide potential mechanisms leading to the organization of chromatin into blobs. Based on active motion-inducing effectors, this framework qualitatively recapitulates experimental observations and predicts that chromatin blobs might be formed stochastically by a collapse of local polymer segments consisting of a few nucleosomes. Our results represent a first step towards elucidating the mechanisms that govern the dynamic and stochastic organization of chromatin in a cell nucleus.

Terahertz Integration and Spatio-Temporal Super-Resolution Imaging on LiNbO3 Chip

2019 ◽  
Vol 46 (5) ◽  
pp. 0508003
Author(s):  
张琦 Zhang Qi ◽  
吴强 Wu Qiang ◽  
张斌 Zhang Bin ◽  
潘崇佩 Pan Chongpei ◽  
王日德 Wang Ride ◽  
...  
Keyword(s):  
Super Resolution ◽  
Resolution Imaging ◽  
Spatio Temporal

scholarly journals Quantitative Super-Resolution Imaging for the Analysis of GPCR Oligomerization

Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1503
Author(s):  
Megan D. Joseph ◽  
Elena Tomas Tomas Bort ◽  
Richard P. Grose ◽  
Peter J. McCormick ◽  
Sabrina Simoncelli
Keyword(s):  
Single Molecule ◽  
Protein Targeting ◽  
Purinergic Receptor ◽  
Pancreatic Cancer Cell Line ◽  
Super Resolution ◽  
Cancer Cell Line ◽  
Oligomeric State ◽  
P2y2 Receptors ◽  
Resolution Imaging ◽  
G Protein Coupled

G-protein coupled receptors (GPCRs) are known to form homo- and hetero- oligomers which are considered critical to modulate their function. However, studying the existence and functional implication of these complexes is not straightforward as controversial results are obtained depending on the method of analysis employed. Here, we use a quantitative single molecule super-resolution imaging technique named qPAINT to quantify complex formation within an example GPCR. qPAINT, based upon DNA-PAINT, takes advantage of the binding kinetics between fluorescently labelled DNA imager strands to complementary DNA docking strands coupled to protein targeting antibodies to quantify the protein copy number in nanoscale dimensions. We demonstrate qPAINT analysis via a novel pipeline to study the oligomerization of the purinergic receptor Y2 (P2Y2), a rhodopsin-like GPCR, highly expressed in the pancreatic cancer cell line AsPC-1, under control, agonistic and antagonistic conditions. Results reveal that whilst the density of P2Y2 receptors remained unchanged, antagonistic conditions displayed reduced percentage of oligomers, and smaller numbers of receptors in complexes. Yet, the oligomeric state of the receptors was not affected by agonist treatment, in line with previous reports. Understanding P2Y2 oligomerization under agonistic and antagonistic conditions will contribute to unravelling P2Y2 mechanistic action and therapeutic targeting.

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