Name: sa-&#946;-galactosidase-based screening assay for the identification of senotherapeutic drugs
Uploaded: 2019-06-28T14:30:00
Description: Watch this Scientific Journal Video about SA-Î²-Galactosidase-Based Screening Assay for the Identification of Senotherapeutic Drugs at JoVE.com

This work was supported by NIH Grants AG043376 (Project 2 and Core A, PDR; Project 1 and Core B, LJN) and AG056278 (Project 3 and Core A, PDR; and Project 2, LJN) and a grant from the Glenn Foundation (LJN).

Animal use was approved by the Scripps Florida Institutional Animal Care and Use Committee.
1. Generation of senescent murine embryonic fibroblast (MEF) &#8211; 12-15 days
<ol>
	<li>Isolate wild type and Ercc1-/- MEFs from pregnant female mice at embryonic day 13 (E13) as described previously33. 
	NOTE: All following steps are carried out in a tissue culture hood under aseptic conditions and using sterile instruments.</li>
	<li>Resect the embr...

SA-&#946;-Gal is a well-defined biomarker for cellular senescence originally discovered by Dimri&#160;et al. (1995) showing that senescent human fibroblasts have increased activity of SA-&#946;-Gal when assayed at pH 623 compared to proliferating cells. Meanwhile, in vitro and in vivo assay for SA-&#946;-Gal have been established for different cell types and tissues25,39,40. The fluorescence base...

Cellular senescence was described for the first time by Leonard Hayflick and Paul Moorhead, who showed that normal cells had a limited ability to proliferate in culture1. Senescent cells fail to proliferate despite the presence of nutrients, growth factors and lack of contact inhibition, but remain metabolically active2. This phenomenon is known as replicative senescence and was mainly attributed to the telomere shortening, at least in human cells3. Further studies have shown that cells can also be induced to undergo senescence in response to other stimuli, such as oncogenic stress (oncogene induced senescence, OIS), DNA damage, cytotoxic drugs, or irradiation (stress induced senescence, SIS)4,5,6. In response to DNA damage, including telomere erosion, cells either senesce, start uncontrolled cell growth, or undergo apoptosis if the damage cannot be repaired. In this case, cell senescence seems to be beneficial as it acts in a tumor suppressive manner2. In contrast, senescence is increased with aging due to the accumulation of cellular damage including DNA damage. Since senescent cells can secrete cytokines, metalloproteinases and growth factors, termed the senescence-associated secretory phenotype (SASP), this age-dependent increase in cellular senescence and SASP contributes to decreased tissue homeostasis and subsequently aging. Also, this age-dependent increase in the senescence burden is known to induce metabolic diseases, stress sensitivity, progeria syndromes, and impaired healing7,8 and is, in part, responsible for the numerous age-related diseases, such as atherosclerosis, osteoarthritis, muscular degeneration, ulcer formation, and Alzheimer&#39;s disease9,10,11,12,13. Eliminating senescent cells can help to prevent or delay tissue dysfunction and extend healthspan14. This has been shown in transgenic mouse models14,15,16 as well as by using senolytic drugs and drug combinations that were discovered through both drug screening efforts and bioinformatic analysis of pathways induced specifically in senescent cells17,18,19,20,21,22. Identifying more optimal senotherapeutic drugs, able to more effectively reduce the senescent cell burden, is an important next step in the development of therapeutic approaches for healthy aging.
Senescent cells show characteristic phenotypic and molecular features, both in culture and in vivo. These senescence markers could be either the cause or the result of senescence induction or a byproduct of molecular changes in these cells. However, no single marker is found specifically in senescent cells. Currently, senescence-associated &#946;-galactosidase (SA-&#946;-Gal) detection is one of the best-characterized and established single-cell based methods to measure senescence in vitro and in vivo. SA-&#946;-Gal is a lysosomal hydrolase with an optimal enzymatic activity at pH 4. Measuring its activity at pH 6 is possible because senescent cells show increased lysosomal activity23,24. For living cells, increased lysosomal pH is obtained by lysosomal alkalinization with the vacuolar H+-ATPase inhibitor Bafilomycin A1 or the endosomal acidification inhibitor chloroquine25,26. 5-Dodecanoylaminofluorescein Di-&#946;-D-galactopyranoside (C12FDG) is used as substrate in living cells as it retains the cleaved product in the cells due to its 12 carbon lipophilic moiety25. Importantly, SA-&#946;-Gal activity itself is not directly connected with any pathway identified in senescent cells and is not necessary to induce senescence. With this assay, senescent cells can be identified even in the heterogeneous cell populations and aging tissues, such as skin biopsies from older individuals. It also has been used to show a correlation between cell senescence and aging23 as it is a reliable marker for senescent cell detection in several organisms and conditions27,28,29,30. Here, a high throughput SA-&#946;-Gal screening assay based on the fluorescent substrate C12FDG using primary mouse embryonic fibroblasts (MEFs) with robustly oxidative stress induced cell senescence is described and its advantages and disadvantages are discussed. Although this assay can be performed with different cell types, the use of Ercc1-deficient, DNA repair impaired MEFs allows for more rapid induction of senescence under conditions of oxidative stress. In mice, reduced expression of the DNA repair endonuclease ERCC1-XPF causes impaired DNA repair, accelerated accumulation of endogenous DNA damage, elevated ROS, mitochondrial dysfunction, increased senescent cell burden, loss of stem cell function and premature aging, similar to natural aging31,32. Similarly, Ercc1-deficient MEFs undergo senescence more rapidly in culture17. An important feature of the senescent MEF assay is that each well has a mixture of senescent and non-senescent cells, allowing for the clear demonstration of senescent cell-specific effects. However, although we believe that the use of oxidative stress in primary cells to induce senescence is more physiologic, this assay also can be used with cell lines where senescence is induced with DNA damaging agents like etoposide or irradiation.

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			<td height="40" style="height:40px;width:216px;">DMEM&#160;</td>
			<td style="width:201px;">Corning</td>
			<td style="width:344px;">10-013-CV</td>
			<td style="width:167px;">medium</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Ham&#39;s F10</td>
			<td>Gibco</td>
			<td>12390-035</td>
			<td style="width:167px;">medium</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">fetal bovine serum</td>
			<td>Tissue Culture Biologics</td>
			<td>101</td>
			<td style="width:167px;">serum</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">1x non-essential amino acids</td>
			<td>Corning</td>
			<td>25-025-Cl</td>
			<td style="width:167px;">amino-acids</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">bafilomycin A1&#160;</td>
			<td>Sigma</td>
			<td>B1793</td>
			<td style="width:167px;">lysosomal inhibitor</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">C12FDG</td>
			<td>Setareh Biotech</td>
			<td>7188</td>
			<td style="width:167px;">b-Gal substrate</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Hoechst 33342&#160;</td>
			<td>Life Technologies</td>
			<td>H1399</td>
			<td style="width:167px;">DNA intercalation agent</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">17DMAG</td>
			<td>Selleck Chemical LLC</td>
			<td>50843</td>
			<td style="width:167px;">HSP90 inhibitor</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">InCell6000 Cell Imaging System</td>
			<td>GE Healthcare</td>
			<td></td>
			<td style="width:167px;">High Content Imaging System</td>
		</tr>
	</tbody>
</table>

sa-&#946;-galactosidase-based screening assay for the identification of senotherapeutic drugs

Cell senescence is one of the hallmarks of aging known to negatively influence a healthy lifespan. Drugs able to kill senescent cells specifically in cell culture, termed senolytics, can reduce the senescent cell burden in vivo and extend healthspan. Multiple classes of senolytics have been identified to date including HSP90 inhibitors, Bcl-2 family inhibitors, piperlongumine, a FOXO4 inhibitory peptide and the combination of Dasatinib/Quercetin. Detection of SA-&#946;-Gal at an increased lysosomal pH is one of the best characterized markers for the detection of senescent cells. Live cell measurements of senescence-associated &#946;-galactosidase (SA-&#946;-Gal) activity using the fluorescent substrate C12FDG in combination with the determination of the total cell number using a DNA intercalating Hoechst dye opens the possibility to screen for senotherapeutic drugs that either reduce overall SA-&#946;-Gal activity by killing of senescent cells (senolytics) or by suppressing SA-&#946;-Gal and other phenotypes of senescent cells (senomorphics). Use of a high content fluorescent image acquisition and analysis platform allows for the rapid, high throughput screening of drug libraries for effects on SA-&#946;-Gal, cell morphology and cell number.

SA-&#946;-Gal activity can be detected in cells that are induced to senesce by various ways from replicative exhaustion, genotoxic and oxidative stress, to oncogene activation23,25,38. In the current model using Ercc1-deficient mouse embryonic fibroblast cells, normoxic growth conditions (20% O2) were sufficient to induce cell senescence after cultivating them for a few passag...

Watch this Scientific Journal Video about SA-Î²-Galactosidase-Based Screening Assay for the Identification of Senotherapeutic Drugs at JoVE.com

SA-&amp;#946;-Galactosidase-Based Screening Assay for the Identification of Senotherapeutic Drugs

Cellular senescence is the key factor in the development of chronic age-related pathologies. Identification of therapeutics that target senescent cells show promise for extending healthy aging. Here, we present a novel assay to screen for the identification of senotherapeutics based on measurement of senescence associated &#946;-Galactosidase activity in single cells.

SA-&#946;-Galactosidase-Based Screening Assay for the Identification of Senotherapeutic Drugs

Cell senescence is one of the hallmarks of aging known to negatively influence a healthy lifespan. Drugs able to kill senescent cells specifically in cell ...

We describe here for the first time a method that allows high-throughput drug screening for senotherapeutic compounds that have been shown to be beneficial in aging-related diseases. In fact, several clinical trials with drugs tested in this essence are currently ongoing. The main advantage of this technique is to distinguish between two types of senotherapeutic drugs, senolytics and senomorphics, by using the well-established detection of SA-beta-Galactosidase in senescent cells.This technique is an important screening tool for novel senotherapeutic compounds. In fact, several compounds that have been identified with the help of this screen are featured in various high-profile publications, and are currently in clinical trial. This technique is extremely versatile, and may be adapted to several high-throughput screens.In fact, it's possible to multiplex screens, and screen for compounds that suppress senescence via the activation or inhibition of one of several pathways. Mince each embryo into one millimeter pieces and pipe it up and down several times. Next, add 10 milliliters of growth medium to the tissues of each embryo.Plate them in a 10 centimeter culture dish, and incubate at 37 degrees Celsius in 3%oxygen and 5%carbon dioxide for two to three days. And incubate the rest of each embryo with 0.25%trypsin EDTA mixture for 10 minutes. To trypsinize cells, first, carefully remove the growth medium and wash the cells with 10 milliliters of 1X PBS twice.Then, add two milliliters of a 025 trypsin EDTA solution to the cells, and incubate them at 37 degrees Celsius for two to three minutes. Next, inspect the cells under a microscope to make sure that the cells are detached from the surface. Add the same amount of growth medium to terminate the trypsin digestion, and transfer the cells to a conical tube.Then, centrifuge the cells at 200 times G for three minutes. Discard the supernatant, and add fresh growth medium to re-suspend the cells. Next, count the cells and seed them in new plates at the projected cell density.For non-senescent subcultivation, first, split confluent cells at a one-to-four ratio. Then incubate cells at 37 degrees Celsius in 3%oxygen and 5%carbon dioxide to extend for another passage. Next, to induce cell senescence, seed split confluent cells from passage one at a ratio of one to four and incubate them at 37 degrees Celsius in 20%oxygen and 5%carbon dioxide environment for three days.To monitor cellular senescence, with an advanced Coulter Cell Counter system, measure the gradual increase in cell diameter and cell volume during each trypsinization step. To begin beta-Gal screening assay, seed 5, 000 senescent cells or 3, 000 non-senescent cells per well in 96 well plates. Then, add 100 microliters of growth medium to each well and incubate cells at 37 degrees Celsius and 20%oxygen and 5%carbon dioxide for six hours.Next, add drug dilutions to MEF cells and incubate the cells at 37 degrees Celsius in 20%oxygen and 5%carbon dioxide for 24 to 48 hours. After incubation, remove the drug solution and wash cells with 100 microliters of 1X PBS. To induce lysosomal alkalinization, pre-treat cells with 90 microliters of bafilomycin A1 solution, diluted in fresh cell culture medium at a final concentration of 100 nanomolar.Then, incubate cells at 37 degrees Celsius in 20%oxygen and 5%carbon dioxide environment for an hour. For fluorescence analysis of SA-beta-Gal activity, make a fresh working solution of C12FDG diluted in growth medium, at a final concentration of 100 micromolar. Then, add 10 microliters of the working solution to the culture medium at a final concentration of 10 micromolar, and incubate cells at 37 degrees Celsius in 20%oxygen and 5%carbon dioxide for two hours.Wash cells with 100 microliters of 1X PBS. Next, add two microliters of a 100 micrograms-per-milliliter Hoechst 33342 dye at a final concentration of two micrograms per milliliter. Incubate the cells at 37 degrees Celsius, 20%oxygen, and 5%carbon dioxide for 20 minutes.After incubation, remove the media, add 100 microliters of fresh growth medium, and proceed to imaging. In this study, a high-content fluorescent image acquisition and analysis platform allowed for identification of senolytic drugs, such as 17-DMAG, that reduced the overall SA-beta-Gal activities in murine embryonic fibroblast cell cultures containing senescent cells in passage five. The software-generated quantitative analyses of mixtures of senescent and non-senescent cells allow for the clear demonstration of senescent cell-specific effects, and the elimination of background beta-galactosidase activity by bafilomycin A.Make sure all necessary cell controls are included, especially untreated senescent cells and senescent cells treated with a positive control.This essay includes working with primary cells under oxidative stress, which can lead to variation that need to be monitored. This procedure is the first step in the detection of senotherapeutic drugs. Additional cell viability and cell senescent essays need to be performed to confirm the screening results.Several new senolytic drugs have been detected using this essay, including the first senolytic drug combination dasatinib quercetin, heat shock protein 90 inhibitors, Bcl-2 family inhibitors, and the polyphenol fisetin.

sa-galactosidase-based-screening-assay-for-identification

Research

JoVE Journal

Biology

RhoC GTPase Activation Assay

RhoC GTPase has 91% homology to RhoA GTPase. Because of its prevalence in cells, many reagents and techniques for RhoA GTPase have been developed. However, RhoC GTPase is expressed in metastatic cancer cells at relatively low levels. Therefore, few RhoC-specific reagents have been developed. We have adapted a Rho activation assay to detect RhoC GTPase. This technique utilizes a GST-Rho binding domain fusion protein to pull out active RhoC GTPase. In addition, we can harvest total protein at the beginning of the assay to determine levels of total (GTP and GDP bound) RhoC GTPase. This allows for the determination of active versus total RhoC GTPase in the cell. Several commercial versions of this procedure have been developed however, the commercial kits are optimized for RhoA GTPase and typically do not work well for RhoC GTPase. Parts of the assay have been modified as well as development of a RhoC-specific antibody.

This protocol utilizes a pull down assay to determine the levels of active RhoC GTPase within cells.

RhoC GTPase has 91% homology to RhoA GTPase.  Because of its prevalence in cells, many reagents and techniques for RhoA GTPase have been developed.  ...

Identification and Analysis of Mouse Erythroid Progenitors using the CD71/TER119 Flow-cytometric Assay

The study of erythropoiesis aims to understand how red cells are formed from earlier hematopoietic and erythroid progenitors. Specifically, the rate of red cell formation is regulated by the hormone erythropoietin (Epo), whose synthesis is triggered by tissue hypoxia. A threat to adequate tissue oxygenation results in a rapid increase in Epo, driving an increase in erythropoietic rate, a process known as the erythropoietic stress response. The resulting increase in the number of circulating red cells improves tissue oxygen delivery. An efficient erythropoietic stress response is therefore critical to the survival and recovery from physiological and pathological conditions such as high altitude, anemia, hemorrhage, chemotherapy or stem cell transplantation. 
The mouse is a key model for the study of erythropoiesis and its stress response. Mouse definitive (adult-type) erythropoiesis takes place in the fetal liver between embryonic days 12.5 and 15.5, in the neonatal spleen, and in adult spleen and bone marrow. Classical methods of identifying erythroid progenitors in tissue rely on the ability of these cells to give rise to red cell colonies when plated in Epo-containing semi-solid media. Their erythroid precursor progeny are identified based on morphological criteria. Neither of these classical methods allow access to large numbers of differentiation-stage-specific erythroid cells for molecular study. Here we present a flow-cytometric method of identifying and studying differentiation-stage-specific erythroid progenitors and precursors, directly in the context of freshly isolated mouse tissue. The assay relies on the cell-surface markers CD71, Ter119, and on the flow-cytometric 'forward-scatter' parameter, which is a function of cell size. The CD71/Ter119 assay can be used to study erythroid progenitors during their response to erythropoietic stress in vivo, for example, in anemic mice or mice housed in low oxygen conditions. It may also be used to study erythroid progenitors directly in the tissues of genetically modified adult mice or embryos, in order to assess the specific role of the modified molecular pathway in erythropoiesis.

A flow-cytometric method for identification and molecular analysis of differentiation-stage-specific murine erythroid progenitors and precursors, directly in freshly &#x2013;harvested mouse bone marrow, spleen or fetal liver. The assay relies on cell-surface markers CD71, Ter119, and cell size.

The study of erythropoiesis aims to understand how red cells are formed from earlier hematopoietic and erythroid progenitors. Specifically, the rate of ...

Fluorescence-microscopy Screening and Next-generation Sequencing: Useful Tools for the Identification of Genes Involved in Organelle Integrity

This protocol describes a fluorescence microscope-based screening of Arabidopsis seedlings and describes how to map recessive mutations that alter the subcellular distribution of a specific tagged fluorescent marker in the secretory pathway. Arabidopsis is a powerful biological model for genetic studies because of its genome size, generation time, and conservation of molecular mechanisms among kingdoms. The array genotyping as an approach to map the mutation in alternative to the traditional method based on molecular markers is advantageous because it is relatively faster and may allow the mapping of several mutants in a really short time frame. This method allows the identification of proteins that can influence the integrity of any organelle in plants. Here, as an example, we propose a screen to map genes important for the integrity of the endoplasmic reticulum (ER). Our approach, however, can be easily extended to other plant cell organelles (for example see1,2), and thus represents an important step toward understanding the molecular basis governing other subcellular structures.

A fundamental quest in cell biology is to define the mechanisms that underlie the identity of the organelles that make eukaryotic cells. Here we propose a method to identify the genes responsible for the morphological and functional integrity of plant organelles using fluorescence microscopy and next-generation sequencing tools.

This protocol describes a fluorescence microscope-based screening of Arabidopsis seedlings and describes how to map recessive mutations that alter the ...

A Fluorescent Screening Assay for Identifying Modulators of GIRK Channels

G protein-gated inward rectifier K+ (GIRK) channels function as cellular mediators of a wide range of hormones and neurotransmitters and are expressed in the brain, heart, skeletal muscle and endocrine tissue1,2. GIRK channels become activated following the binding of ligands (neurotransmitters, hormones, drugs, etc.) to their plasma membrane-bound, G protein-coupled receptors (GPCRs). This binding causes the stimulation of G proteins (Gi and Go) which subsequently bind to and activate the GIRK channel. Once opened the GIRK channel allows the movement of K+ out of the cell causing the resting membrane potential to become more negative. As a consequence, GIRK channel activation in neurons decreases spontaneous action potential formation and inhibits the release of excitatory neurotransmitters. In the heart, activation of the GIRK channel inhibits pacemaker activity thereby slowing the heart rate.
GIRK channels represent novel targets for the development of new therapeutic agents for the treatment neuropathic pain, drug addiction, cardiac arrhythmias and other disorders3. However, the pharmacology of these channels remains largely unexplored. Although a number of drugs including anti-arrhythmic agents, antipsychotic drugs and antidepressants block the GIRK channel, this inhibition is not selective and occurs at relatively high drug concentrations3.
Here, we describe a real-time screening assay for identifying new modulators of GIRK channels. In this assay, neuronal AtT20 cells, expressing GIRK channels, are loaded with membrane potential-sensitive fluorescent dyes such as bis-(1,3-dibutylbarbituric acid) trimethine oxonol [DiBAC4(3)] or HLB 021-152 (Figure 1). The dye molecules become strongly fluorescent following uptake into the cells (Figure 1). Treatment of the cells with GPCR ligands stimulates the GIRK channels to open. The resulting K+ efflux out of the cell causes the membrane potential to become more negative and the fluorescent signal to decrease (Figure 1). Thus, drugs that modulate K+ efflux through the GIRK channel can be assayed using a fluorescent plate reader. Unlike other ion channel screening assays, such atomic absorption spectrometry4 or radiotracer analysis5, the GIRK channel fluorescent assay provides a fast, real-time and inexpensive screening procedure.

A real-time screening procedure for identifying drugs that interact with G protein-gated inward rectifier K+ (GIRK) channels is described. The assay utilizes membrane potential-sensitive fluorescent dyes to measure GIRK channel activity. This technique is adaptable for use on a number of cell lines.

G protein-gated inward rectifier K+ (GIRK) channels function as cellular mediators of a wide range of hormones and neurotransmitters and are expressed in ...

Identification of Post-translational Modifications of Plant Protein Complexes

Plants adapt quickly to changing environments due to elaborate perception and signaling systems. During pathogen attack, plants rapidly respond to infection via the recruitment and activation of immune complexes. Activation of immune complexes is associated with post-translational modifications (PTMs) of proteins, such as phosphorylation, glycosylation, or ubiquitination. Understanding how these PTMs are choreographed will lead to a better understanding of how resistance is achieved.
Here we describe a protein purification method for nucleotide-binding leucine-rich repeat (NB-LRR)-interacting proteins and the subsequent identification of their post-translational modifications (PTMs). With small modifications, the protocol can be applied for the purification of other plant protein complexes. The method is based on the expression of an epitope-tagged version of the protein of interest, which is subsequently partially purified by immunoprecipitation and subjected to mass spectrometry for identification of interacting proteins and PTMs.
This protocol demonstrates that: i). Dynamic changes in PTMs such as phosphorylation can be detected by mass spectrometry; ii). It is important to have sufficient quantities of the protein of interest, and this can compensate for the lack of purity of the immunoprecipitate; iii). In order to detect PTMs of a protein of interest, this protein has to be immunoprecipitated to get a sufficient quantity of protein.

We describe here a protocol for the purification and characterization of plant protein complexes. We demonstrate that by immunoprecipitating a single protein within a complex, so we can identify its post-translational modifications and its interacting partners.

Plants adapt quickly to changing environments due to elaborate perception and signaling systems. During pathogen attack, plants rapidly respond to ...

RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes

Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been made in identifying the components of the editosome complex that catalyze RNA editing. However, it is still not clear how those proteins work together. Chemical compounds obtained from a high-throughput screen against the editosome may block or affect one or more steps in the editing cycle. Therefore, the identification of new chemical compounds will generate valuable molecular probes for dissecting the editosome function and assembly. In previous studies, in vitro editing assays were carried out using radio-labeled RNA. These assays are time consuming, inefficient and unsuitable for high-throughput purposes. Here, a homogenous fluorescence-based &#8220;mix and measure&#8221; hammerhead ribozyme in vitro reporter assay to monitor RNA editing, is presented. Only as a consequence of RNA editing of the hammerhead ribozyme a fluorescence resonance energy transfer (FRET) oligoribonucleotide substrate undergoes cleavage. This in turn results in separation of the fluorophore from the quencher thereby producing a signal. In contrast, when the editosome function is inhibited, the fluorescence signal will be quenched. This is a highly sensitive and simple assay that should be generally applicable to monitor in vitro RNA editing or high throughput screening of chemicals that can inhibit the editosome function.

A highly sensitive ribozyme-based assay, applicable to high-throughput screening of chemicals targeting the unique process of RNA editing in trypanosomatid pathogens, is described in this paper. Inhibitors can be used as tools for hypothesis-driven analysis of the RNA editing process and ultimately as therapeutics.

Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been ...

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays focus on transcriptional regulation, being essentially aimed at the identification of promoter-targeting molecules. As a result, post-transcriptional mechanisms are largely uncovered by gene expression targeted drug development. Here we describe a cell-based assay aimed at investigating the role of the 3&#39; untranslated region (3&#8217; UTR) in the modulation of the fate of its mRNA, and at identifying compounds able to modify it. The assay is based on the use of a luciferase reporter construct containing the 3&#8217; UTR of a gene of interest stably integrated into a disease-relevant cell line. The protocol is divided into two parts, with the initial focus on the primary screening aimed at the identification of molecules affecting luciferase activity after 24 hr of treatment. The second part of the protocol describes the counter-screening necessary to discriminate compounds modulating luciferase activity specifically through the 3&#8217; UTR. In addition to the detailed protocol and representative results, we provide important considerations about the assay development and the validation of the hit(s) on the endogenous target. The described cell-based reporter gene assay will allow scientists to identify molecules modulating protein levels via post-transcriptional mechanisms dependent on a 3&#8217; UTR.

Here we describe a cell-based reporter gene assay as a valuable tool to screen chemical libraries for compounds modulating post-transcriptional control mechanisms exerted through 3&#8217; UTR.

Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays ...

Identification of Kinase-substrate Pairs Using High Throughput Screening

We have developed a screening platform to identify dedicated human protein kinases for phosphorylated substrates which can be used to elucidate novel signal transduction pathways. Our approach features the use of a library of purified GST-tagged human protein kinases and a recombinant protein substrate of interest. We have used this technology to identify MAP/microtubule affinity-regulating kinase 2 (MARK2) as the kinase for a glucose-regulated site on CREB-Regulated Transcriptional Coactivator 2 (CRTC2), a protein required for beta cell proliferation, as well as the Axl family of tyrosine kinases as regulators of cell metastasis by phosphorylation of the adaptor protein ELMO. We describe this technology and discuss how it can help to establish a comprehensive map of how cells respond to environmental stimuli.

Protein phosphorylation is a central feature of how cells interpret and respond to information in their extracellular milieu. Here, we present a high throughput screening protocol using kinases purified from mammalian cells to rapidly identify kinases that phosphorylate a substrate(s) of interest.


We have developed a screening platform to identify dedicated human protein kinases for phosphorylated substrates which can be used to elucidate novel ...

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and silencing of genes mediate the response of plants to environmental signals and developmental cues. Therefore, insights into the mechanisms that control plant gene expression are essential to gain a deep understanding of how biological processes are regulated in plants. The chromatin immunoprecipitation (ChIP) technique described here is a procedure to identify the DNA-binding sites of proteins in genes or genomic regions of the model species Arabidopsis thaliana. The interactions with DNA of proteins of interest such as transcription factors, chromatin proteins or posttranslationally modified versions of histones can be efficiently analyzed with the ChIP protocol. This method is based on the fixation of protein-DNA interactions in vivo, random fragmentation of chromatin, immunoprecipitation of protein-DNA complexes with specific antibodies, and quantification of the DNA associated with the protein of interest by PCR techniques. The use of this methodology in Arabidopsis has contributed significantly to unveil transcriptional regulatory mechanisms that control a variety of plant biological processes. This approach allowed the identification of the binding sites of the Arabidopsis chromatin protein EBS to regulatory regions of the master gene of flowering FT. The impact of this protein in the accumulation of particular histone marks in the genomic region of FT was also revealed through ChIP analysis.

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Chromatin immunoprecipitation is a powerful technique for the identification of DNA binding sites of Arabidopsis proteins in vivo. This procedure includes chromatin cross-linking and fragmentation, immunoprecipitation with selective antibodies against the protein of interest, and qPCR analysis of bound DNA. We describe a simple ChIP assay optimized for Arabidopsis plants.

Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and ...

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)

Population and family-based genetic studies typically result in the identification of genetic variants that are statistically associated with a clinical disease or phenotype. For many diseases and traits, most variants are non-coding, and are thus likely to act by impacting subtle, comparatively hard to predict mechanisms controlling gene expression. Here, we describe a general strategic approach to prioritize non-coding variants, and screen them for their function. This approach involves computational prioritization using functional genomic databases followed by experimental analysis of differential binding of transcription factors (TFs) to risk and non-risk alleles. For both electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genetic variants, a synthetic DNA oligonucleotide (oligo) is used to identify factors in the nuclear lysate of disease or phenotype-relevant cells. For EMSA, the oligonucleotides with or without bound nuclear factors (often TFs) are analyzed by non-denaturing electrophoresis on a tris-borate-EDTA (TBE) polyacrylamide gel. For DAPA, the oligonucleotides are bound to a magnetic column and the nuclear factors that specifically bind the DNA sequence are eluted and analyzed through mass spectrometry or with a reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) followed by Western blot analysis. This general approach can be widely used to study the function of non-coding genetic variants associated with any disease, trait, or phenotype.

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

We present a strategic plan and protocol for identifying non-coding genetic variants affecting transcription factor (TF) DNA binding. A detailed experimental protocol is provided for electrophoretic mobility shift assay (EMSA) and DNA affinity precipitation assay (DAPA) analysis of genotype-dependent TF DNA binding.

Population and family-based genetic studies typically result in the identification of genetic variants that are statistically associated with a clinical ...