Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Visualization of the Nucleolus Using Ethynyl Uridine.

ABSTRACT: Thanks to recent innovative methodologies, key cellular processes such as replication or transcription can be visualized directly in situ in intact tissues. Many studies use so-called click iT chemistry where nascent DNA can be tracked by 5-ethynyl-2'-deoxyuridine (EdU), and nascent RNA by 5-ethynyl uridine (EU). While the labeling of replicating DNA by EdU has already been well established and further exploited in plants, the use of EU to reveal nascent RNA has not been developed to such an extent. In this article, we present a protocol for labeling of nucleolar RNA transcripts using EU and show that EU effectively highlights the nucleolus. The method is advantageous, because the need to prepare transgenic plants expressing fluorescently tagged nucleolar components when the nucleolus has to be visualized can be avoided.

SUBMITTER: Dvorackova M

PROVIDER: S-EPMC5820300 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Visualization of the Nucleolus Using Ethynyl Uridine.

Dvořáčková Martina M Fajkus Jiří J

Frontiers in plant science 20180216

Thanks to recent innovative methodologies, key cellular processes such as replication or transcription can be visualized directly <i>in situ</i> in intact tissues. Many studies use so-called click iT chemistry where nascent DNA can be tracked by 5-ethynyl-2'-deoxyuridine (EdU), and nascent RNA by 5-ethynyl uridine (EU). While the labeling of replicating DNA by EdU has already been well established and further exploited in plants, the use of EU to reveal nascent RNA has not been developed to such ...[more]

PMID: 29503656

Similar Datasets

Mechanism for controlled assembly of transcriptional condensates by Aire [5'-ethynyl uridine RNA-seq]

Project description:Transcriptional condensates play a crucial role in gene expression and regulation, yet their assembly mechanisms remain poorly understood. We here report a multi-layered mechanism for condensate assembly by Autoimmune regulator (Aire), an essential transcriptional regulator (TR) that orchestrates gene expression reprogramming for central T-cell tolerance. Aire condensates assemble on enhancers, stimulating local transcriptional activities and connecting disparate inter-chromosomal loci. This functional condensate formation hinges upon the coordination between three Aire domains: polymerization domain CARD, histone binding domain PHD1 and C-terminal tail (CTT). Specifically, CTT binds coactivators CBP/p300, recruiting Aire to CBP/p300-rich enhancers and promoting CARD-mediated condensate assembly. Conversely, PHD1 binds to the ubiquitous histone mark H3K4me0, keeping Aire dispersed throughout the genome until Aire nucleates on enhancers. Our findings showed that the balance between PHD1-mediated suppression and CTT-mediated stimulation of Aire polymerization is crucial to form transcriptionally active condensates at target sites, providing new insights into controlled polymerization of TRs.

2024-07-08 | GSE267527 | GEO

Practical Synthesis of Ethynyl(phenyl)-?3-Iodane Using Calcium Carbide as an Ethynyl Group Source.

Project description:Stannylation of calcium carbide followed by Sn-hypervalent iodine(III) exchange reaction cleanly afforded the electrophilic ethynylating agent ethynyl(phenyl)-?3-iodane in high yield. This two-step method uses very inexpensive materials and is readily operable without any special precautions.

| S-EPMC7010717 | biostudies-literature

Mapping nucleolus-associated chromatin interactions using nucleolus Hi-C reveals pattern of heterochromatin interactions.

Project description:As the largest substructures in the nucleus, nucleoli are the sites of ribosome biogenesis. Increasing evidence indicates that nucleoli play a key role in the organization of 3D genome architecture, but systematic studies of nucleolus-associated chromatin interactions are lacking. Here, we developed a nucleolus Hi-C (nHi-C) experimental technique to enrich nucleolus-associated chromatin interactions. Using the nHi-C experiment, we identify 264 high-confidence nucleolus-associated domains (hNADs) that form strong heterochromatin interactions associated with the nucleolus and consist of 24% of the whole genome in HeLa cells. Based on the global hNAD inter-chromosomal interactions, we find five nucleolar organizer region (NOR)-bearing chromosomes formed into two clusters that show different interaction patterns, which is concordant with their epigenetic states and gene expression levels. hNADs can be divided into three groups that display distinct cis/trans interaction signals, interaction frequencies associated with nucleoli, distance from the centromeres, and overlap percentage with lamina-associated domains (LADs). Nucleolus disassembly caused by Actinomycin D (ActD) significantly decreases the strength of hNADs and affects compartment/TAD strength genome-wide. In summary, our results provide a global view of heterochromatin interactions organized around nucleoli and demonstrate that nucleoli act as an inactive inter-chromosomal hub to shape both compartments and TADs.

| S-EPMC9867699 | biostudies-literature

Prebiotic Phosphorylation of Uridine using Diamidophosphate in Aerosols.

Project description:One of the most challenging fundamental problems in establishing prebiotically plausible routes for phosphorylation reactions using phosphate is that they are thermodynamically unfavorable in aqueous conditions. Diamidophosphate (DAP), a potentially prebiotically relevant compound, was shown to phosphorylate nucleosides in aqueous medium, albeit at a very slow rate (days/weeks). Here, we demonstrate that performing these reactions within an aerosol environment, a suitable model for the early Earth ocean-air interface, yields higher reaction rates when compared to bulk solution, thus overcoming these rate limitations. As a proof-of-concept, we demonstrate the effective conversion (~6.5-10%) of uridine to uridine-2',3'-cyclophosphate in less than 1 h. These results suggest that aerosol environments are a possible scenario in which prebiotic phosphorylation could have occurred despite unfavorable rates in bulk solution.

| S-EPMC6753121 | biostudies-literature

Mechanism for controlled assembly of transcriptional condensates by Aire [5'-ethynyl uridine RNA-seq]

Project description:Mechanism for controlled assembly of transcriptional condensates by Aire [5'-ethynyl uridine RNA-seq]

| PRJNA1111781 | ENA

Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

Project description:We used DamID to map nucleolus interactions in human cells using a 4x tandem repeat of the nucleolar targeting sequence of AP3D1 (Scott, 2010) ("4xAP3"). These interactions are mapped in various human cell lines, including human K562 cells

2020-12-18 | GSE148609 | GEO

Intracellular detection of cytosine incorporation in genomic DNA by using 5-ethynyl-2'-deoxycytidine.

Project description:5-Ethynyl-2'-deoxycytidine triphosphate (EdCTP) was synthesized as a probe to be used in conjunction with fluorescent labeling to facilitate the analysis of the in vivo dynamics of DNA-centered processes (DNA replication, repair and cytosine demethylation). Kinetic analysis showed that EdCTP is accepted as a substrate by Klenow exo(-) and DNA polymerase β. Incorporation of 5-ethynyl-2'-deoxycytidine (EdC) into DNA by these enzymes is, at most, modestly less efficient than native dC. EdC-containing DNA was visualized by using a click reaction with a fluorescent azide, following polymerase incorporation and T4 DNA ligase mediated ligation. Subsequent experiments in mouse male germ cells and zygotes demonstrated that EdC is a specific and reliable reporter of DNA replication, in vivo.

| S-EPMC3341615 | biostudies-literature

9-Ethynyl-9H-carbazole.

Project description:The title compound, C(14)H(9)N, is the second crystallographically characterized example of an ynamine with an H atom in the C-terminal position. There are two independent mol-ecules (A and B) in the asymmetric unit. The structures of both mol-ecules are essentially planar (r.m.s. deviation = 0.0312 and 0.0152?Å). The N-C(sp) bond lengths are 1.353?(4) and 1.350?(4)?Å, and those of the acetyl-ene bonds are 1.189?(4) and 1.190?(4)?Å. The C(sp)-H bond lengths are 0.95?(5) and 0.97?(4)?Å. These geometries are consistent with those of the previously reported ynamine characterized by crystallography. In the crystal, the mol-ecules stack along the c axis, forming two kinds of columnar structures. The acetyl-ene C atoms of mol-ecule A have a short contact [3.341?(4)?Å and 3.396?(4)?Å] with an adjacent mol-ecule A at the C-C bond of the fused part, which originates in ?-? stacking inter-action; no remarkable spatial contact is recognized within the stacking of mol-ecule B.

| S-EPMC3297888 | biostudies-other

A novel multicolor immunostaining method using ethynyl deoxyuridine for analysis of in situ immunoproliferative response.

Project description:Immune responses are generally accompanied by antigen presentation and proliferation and differentiation of antigen-specific lymphocytes (immunoproliferation), but analysis of these events in situ on tissue sections is very difficult. We have developed a new method of simultaneous multicolor immunofluorescence staining for immunohistology and flow cytometry using a thymidine analogue, 5-ethynyl-2'-deoxyuridine (EdU). Because of the small size of azide dye using click chemistry and elimination of DNA denaturation steps, EdU staining allowed for immunofluorescence staining of at least four colors including two different markers on a single-cell surface, which is impossible with the standard 5-bromo-2'-deoxyuridine method. By using two rat models, successfully detected parameters were the cluster of differentiation antigens including phenotypic and functional markers of various immune cells, histocompatibility complex antigens, and even some nuclear transcription factors. Proliferating cells could be further sorted and used for RT-PCR analysis. This method thus enables functional in situ time-kinetic analysis of immunoproliferative responses in a distinct domain of the lymphoid organs, which are quantitatively confirmed by flow cytometry.

| S-EPMC4534512 | biostudies-literature

4-(Dimethyl-amino)phenyl ethynyl telluride.

Project description:The title compound, C(10)H(11)NTe, is the first organyl ethynyl telluride, R-Te-C C-H, to be structurally characterized. In the L-shaped mol-ecule, the aryl moiety, viz. Me(2)NC(6)H(4)Te, is almost perpendicular to the Te-C C-H fragment. The Te-Csp(2) bond [2.115 (3) Å] is significantly longer than the Te-Csp bond [2.041 (4) Å]. The Te-C C group is approximately linear [Te-C-C = 178.5 (4)° and C C = 1.161 (5) Å], while the coordination at the Te atom is angular [C-Te-C = 95.92 (14)°]. In the crystal structure, there are Csp-H⋯N hydrogen bonds which are perpendicular to the CNMe(2) group; the N atom displays some degree of pyramidalization. Centrosymmetrically related pairs of mol-ecules are linked by Te⋯π(ar-yl) inter-actions, with Te⋯Cg = 3.683 (4) Å and Csp-Te⋯Cg = 159.1 (2)° (Cg is the centroid of the benzene ring). These inter-actions lead to the formation of zigzag ribbons which run along c and are approximately parallel to (110).

| S-EPMC2968982 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data