Damos las gracias a D. Braendle, Kurz CL y F. Sanchis Montañana-por sus contribuciones. Este proyecto fue apoyado por becas de la ANR y el Consejo Regional PACA, y la financiación institucional del INSERM y el CNRS.

<ol>
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Biol. 278, 49-59 (2005).</li><li>Pujol, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anti-fungal+innate+immunity+in+C.+elegans+is+enhanced+by+evolutionary+diversification+of+antimicrobial+peptides.">Anti-fungal innate immunity in C. elegans is enhanced by evolutionary diversification of antimicrobial peptides.</a> PLoS Pathog. 4, e1000105-e1000105 (2008).</li><li>Simmer, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome-Wide+RNAi+of+C.+elegans+Using+the+Hypersensitive+rrf-3+Strain+Reveals+Novel+Gene+Functions.">Genome-Wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions.</a> PLoS Biol. 1, e12-e12 (2003).</li><li>Couillault, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TLR-independent+control+of+innate+immunity+in+Caenorhabditis+elegans+by+the+TIR+domain+adaptor+protein+TIR-1,+an+ortholog+of+human+SARM.">TLR-independent control of innate immunity in Caenorhabditis elegans by the TIR domain adaptor protein TIR-1, an ortholog of human SARM.</a> Nat Immunol. 5, 488-494 (2004).</li><li>Morton, E., Lamitina, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+suite+of+MATLAB-based+computational+tools+for+automated+analysis+of+COPAS+Biosort+data.">A suite of MATLAB-based computational tools for automated analysis of COPAS Biosort data.</a> Biotechniques. 48, xxv-xxx (2010).</li><li>Rohlfing, A. K., Miteva, Y., Hannenhalli, S., Lamitina, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+and+physiological+activation+of+osmosensitive+gene+expression+mimics+transcriptional+signatures+of+pathogen+infection+in+C.+elegans.">Genetic and physiological activation of osmosensitive gene expression mimics transcriptional signatures of pathogen infection in C. elegans.</a> PLoS One. 5, e9010-e9010 (2010).</li><li>Lee, K. Z., Kniazeva, M., Han, M., Pujol, N., Ewbank, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+fatty+acid+synthase+fasn-1+acts+upstream+of+WNK+and+Ste20&#47;GCK-VI+kinases+to+modulate+antimicrobial+peptide+expression+in+C.+elegans+epidermis.">The fatty acid synthase fasn-1 acts upstream of WNK and Ste20&#47;GCK-VI kinases to modulate antimicrobial peptide expression in C. elegans epidermis.</a> Virulence. 1, 113-122 (2010).</li><li>Duverger, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+semi-automated+high-throughput+approach+to+the+generation+of+transposon+insertion+mutants+in+the+nematode+Caenorhabditis+elegans.">A semi-automated high-throughput approach to the generation of transposon insertion mutants in the nematode Caenorhabditis elegans.</a> Nucleic Acids Res. 35, e11-e11 (2007).</li><li>Pierce-Shimomura, J. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+analysis+of+crawling+and+swimming+locomotory+patterns+in+C.+elegans.">Genetic analysis of crawling and swimming locomotory patterns in C. elegans.</a> Proc. Natl. Acad. Sci. U.S.A. 105, 20982-20987 (2008).</li><li>Ruzanov, P., Riddle, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deep+SAGE+analysis+of+the+Caenorhabditis+elegans+transcriptome.">Deep SAGE analysis of the Caenorhabditis elegans transcriptome.</a> Nucleic Acids Res. 38, 3252-3262 (2010).</li><li>Kurz, C. L., Ewbank, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Infection+in+a+dish:+high-throughput+analyses+of+bacterial+pathogenesis.">Infection in a dish: high-throughput analyses of bacterial pathogenesis.</a> Curr. Opin. Microbiol. 10, 10-16 (2007).</li><li>Okoli, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+antifungal+compounds+active+against+Candida+albicans+using+an+improved+high-throughput+Caenorhabditis+elegans+assay.">Identification of antifungal compounds active against Candida albicans using an improved high-throughput Caenorhabditis elegans assay.</a> PLoS One. 4, e7025-e7025 (2009).</li><li>Moy, T. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+novel+antimicrobials+using+a+live-animal+infection+model.">Identification of novel antimicrobials using a live-animal infection model.</a> Proc. Natl. Acad. Sci. U. S. A. 103, 10414-10419 (2006).</li><li>Ballestriero, F., Thomas, T., Burke, C., Egan, S., Kjelleberg, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+compounds+with+bioactivity+against+the+nematode+Caenorhabditis+elegans+by+a+screen+based+on+the+functional+genomics+of+the+marine+bacterium+Pseudoalteromonas+tunicata+D2.">Identification of compounds with bioactivity against the nematode Caenorhabditis elegans by a screen based on the functional genomics of the marine bacterium Pseudoalteromonas tunicata D2.</a> Appl. Environ. Microbiol. 76, 5710-5717 (2010).</li></ol>

El laboratorio de Ewbank colabora con la Unión Biometrica y Modul-Bio.

<p class="jove_content"&gt; El protocolo actual permite a gran escala de cribado de RNAi en<em&gt; C. elegans</em&gt; En medios sólidos, utilizando el nivel de expresión de un gen reportero fluorescente como una lectura. Se ha optimizado con herramientas automatizadas para facilitar los ensayos de alto rendimiento, lo que permite un manejo fácil y rápida de grandes cantidades de muestras, de una manera eficiente, fiable y reproducible. Otros métodos se han descrito que no depender tanto de tratamiento automatizado de muestras líquidas<sup&gt; 8</sup&gt;.</p&gt;<p class="jove_content"&gt; Uno de los aspectos clave de la organización para que el protocolo ha sido el desarrollo de un método robusto de seguimiento de la muestra mediante la adaptación del software comercial MBioLIMS al procedimiento pantalla de RNAi en colaboración con la ModulBio empresa. En cada etapa del procedimiento, las placas están identificados por códigos de barras generados en el LIMS. Como el LIMS también registra la identidad de los clones en cada pocillo en cada placa, pasando de bien a gen putativo es simple. Y más allá de esto, los enlaces de LIMS a la base de datos de WormBase comunidad, permitiendo el acceso directo a los datos moleculares y funcionales acerca de un determinado gen. El LIMS también facilita el análisis que se llevó a cabo en la placa o incluso a nivel de cromosomas y todo el genoma. Para estos análisis, los datos se almacenan en una forma que es totalmente compatible con las herramientas descritas anteriormente, tales como COPAmulti<sup&gt; 16</sup&gt;.</p&gt;<p class="jove_content"&gt; Un punto crítico experimental en el método es el ajuste de la cantidad de alimentos en relación con el número de gusanos. Para los ensayos de muchos, es esencial que los gusanos no hambre al final del experimento, pero también es importante no tener demasiada comida en el comienzo. Hemos observado que una alta densidad de alimentos disminuye la inducción de fluorescencia en el protocolo utilizando gusanos que llevan la p<em&gt; PNL-29</em&gt; :: Reportero GFP. Esto puede reflejar una disminución de la eficiencia de la infección, cuando los gusanos se cultivan en las bacterias demasiado (BS, resultados no publicados). Al mismo tiempo, las condiciones de cultivo de la bacteria ARNi también es importante, ya que esto determina si dsRNA se produce a un nivel óptimo. Algunos protocolos de RNAi a gran escala requiere la cultura de los clones de RNAi en placas de agar antes de la siembra de cultivos líquidos<sup&gt; 8</sup&gt;. Se obtuvo el silenciamiento de genes robustos omitir este paso. Hemos optado por un exceso de crecimiento de cada cultura para garantizar resultados homogéneos. El protocolo descrito en el hecho proporciona material suficiente para llevar a cabo 2 o 3 pantallas en paralelo. Con el fin de obtener los resultados más sólidos, estamos a favor, sin embargo, la realización de las pantallas en duplicado utilizando cultivos independientes de los gusanos, bacterias y esporas de hongos RNAi.</p&gt;<p class="jove_content"&gt; Otro paso crítico está relacionado al uso de medio que no sea ni muy húmedo ni muy seco. Si las placas no se seque lo suficiente, el ARNi las bacterias no se seque correctamente y los gusanos van a nadar durante el ensayo. Esto puede causar problemas. Por ejemplo, los gusanos no son eficientemente infectados por<em&gt; D. coniospora</em&gt; En el líquido (C. Couillault, resultados no publicados). Por otro lado, en placas secas, la osmolaridad de los incrementos de medio de cultivo. Esto tiene efectos directos sobre la fisiología del gusano<sup&gt; 17</sup&gt;, Incluyendo la inducción de algunos genes de péptidos antimicrobianos, tales como<em&gt; PNL 29</em&gt;<sup&gt; 18</sup&gt;. El volumen utilizado para dispensar gusanos y esporas es crítico para permitir un secado rápido y eficaz. Si hay más de 10 l de líquido se añade a las placas frescas, los pocillos puede tomar muchas horas para secar. Esto puede significar que es difícil de utilizar métodos robóticos para añadir gusanos a las placas. Por ejemplo, cada gusano es dispensado por la Biosort en alrededor de 1 l de líquido. En la actualidad distribuir los gusanos de forma manual ya que también nos permite superar la tendencia de los gusanos en la solución de los sedimentos.</p&gt;<p class="jove_content"&gt; Hemos informado anteriormente de un ajuste de la Biosort que permitió una placa de 96 pocillos a analizar en 36 minutos<sup&gt; 19</sup&gt;. IBU de la máquina fabricante ofrece ahora una modificación de la Biosort para disminuir aún más el tiempo de análisis. Con el &quot;FastReFlex&quot;, las muestras se enrutan directamente a través de la celda de flujo para el análisis, sin pasar por el filtro de burbuja trampa. Esto resulta en una reducción significativa en el tiempo para la adquisición de datos; una placa entera puede ser analizado en 22 minutos permitiendo alrededor de 20 placas a tratar por día. Si las placas no se congelaron, sin embargo, habría un intervalo de 8 horas entre las primeras y la última. Dada la relativamente corta duración del experimento, con la infección que dura sólo 18 horas, esto introduciría una variable inaceptable través de las placas. No sólo las placas de congelación antes del análisis de resolver este problema, pero también es esencial en el contexto de análisis de alto rendimiento, ya que con el protocolo actual y los robots estándar de manejo de líquidos, 2 personas puede procesar hasta 50 planchas a la semana. En la actualidad, de manera rutinaria la pantalla de 30 platos a la semana, lo que permite una pantalla de todo el genomaque se llevó a cabo una vez en menos de 2 meses.</p&gt;<p class="jove_content"&gt; Una característica interesante de este protocolo es el hecho de que utiliza agar sólido, permitiendo ensayos que no se pueden realizar en cultivo líquido. Como fisiología gusano difiere dependiendo de las condiciones de cultivo<sup&gt; 20,21</sup&gt;, Siendo capaz de realizar los ensayos en medio sólido también puede complementar habituales pantallas de base líquida. Para ciertos fenotipos (por ejemplo, movimiento), el análisis puede llevarse a cabo directamente con placas de medio 96-bien sólidos. Para la pantalla actual, sin embargo, como la Biosort no puede muestrear de placas de medio sólido, gusanos se transfiere primero a líquido antes de la congelación. Por otro lado, la Biosort COPAS permite un análisis cuantitativo multiparamétrico compatible con la medición de muchos fenotipos diferentes. Es probable que para cualquier pantalla dado que no todos los parámetros medidos será la principal lectura. No obstante, estas medidas pueden ser útiles por varias razones. Ellos permiten una para determinar si el ensayo funcionó correctamente. Por ejemplo, se puede comprobar el número y tamaño de los gusanos en cada pocillo. Sólo cuando un clon ARNi debe bloquear el crecimiento o la reproducción no debe haber una desviación de los valores esperados. Los pozos con menos de 20 gusanos o / y de los animales un 30% más pequeños (TOF) en comparación con estándaresestándar de control sin efecto sobre el crecimiento (<em&gt; Por ejemplo, las buenas prácticas agrarias (RNAi</em&gt;)) Pueden ser excluidos de los análisis posteriores. La función de estos clones se pueden abordar utilizando un protocolo alternativo en el que los gusanos están expuestos a las bacterias RNAi después de su desarrollo está muy avanzada<sup&gt; 15</sup&gt;. Los diferentes parámetros también se pueden utilizar para refinar gen candidato (golpe) la selección, por ejemplo, la limitación de accesos sólo a los que afectan a la fluorescencia verde, pero no en rojo. El método exacto elegido para seleccionar muestras dependerá del tipo de pantalla y su exacta lectura. Dada la complejidad de los datos generados a partir de un análisis cuantitativo del genoma de pantalla ancha, la colaboración con un experto en estadística que sean necesarios.</p&gt;<p class="jove_content"&gt; El protocolo se describe se puede adaptar fácilmente a otros tipos de ensayos. Por ejemplo, en la etapa de infección<em&gt; D. coniospora</em&gt; Podría ser reemplazado por cualquier otro patógeno capaz de infectar a los medios sólidos. Esto es potencialmente útil como hemos encontrado que muchos de los factores de virulencia importantes de Serratia marcescens infección en cultivo líquido no juegan un papel durante la infección en un medio sólido (E. Pradel, comunicación personal). El protocolo es también totalmente compatible con las pruebas de los compuestos químicos<sup&gt; 22-24</sup&gt;, O para identificar compuestos con actividad biológica con diferentes bibliotecas de las bacterias<sup&gt; 25</sup&gt;, Por lo que debe encontrar una utilidad general en el<em&gt; C. elegans</em&gt; Comunidad de investigación.</p

<table border="1"><tbody><tr><td> Nombre del reactivo </td><td> Empresa </td><td> Número de catálogo </td><td> Comentarios </td></tr><tr><td> Bactoagar </td><td> BD Diagnostic Systems </td><td> 214010 </td><td></td></tr><tr><td> Ampicilina </td><td> Sigma-Aldrich </td><td> A9518 </td><td></td></tr><tr><td> Bactopeptona </td><td> BD Diagnostic Systems </td><td> 211677 </td><td></td></tr><tr><td> CaCl 2 </td><td> Todo proveedor que </td><td></td><td></td></tr><tr><td> Película adhesiva AeraSeal </td><td> Dutscher </td><td> 760214 </td><td></td></tr><tr><td> Isopropílico β-D-tiogalactopiranósido (IPTG) </td><td> Thermo Scientific </td><td> AB-0481 </td><td></td></tr><tr><td> K 2 HPO 4 </td><td> Todo proveedor que </td><td></td><td></td></tr><tr><td> KH 2 PO 4 </td><td> Todo proveedor que </td><td></td><td></td></tr><tr><td> MgSO 4 </td><td> Todo proveedor que </td><td></td><td></td></tr><tr><td> NaCl </td><td> Todo proveedor que </td><td></td><td></td></tr><tr><td> Na 2 HPO 4 </td><td> Todo proveedor que </td><td></td><td></td></tr><tr><td> NaOH </td><td> Todo proveedor que </td><td></td><td></td></tr><tr><td> Placa de 96 pozos profundos </td><td> Thermo Scientific </td><td> AB-0932 </td><td></td></tr><tr><td> Placas de 96 pocillos plana </td><td> FALCON </td><td> 353072 </td><td></td></tr><tr><td> 96 placa redonda y </td><td> FALCON </td><td> 353077 </td><td></td></tr><tr><td> La tetraciclina </td><td> Sigma-Aldrich </td><td> T8032 </td><td></td></tr><tr><td> Triton X-100 </td><td> Todo proveedor que </td><td></td><td></td></tr><tr><td> TECAN robot </td><td> TECAN </td><td></td><td></td></tr><tr><td> Liquidator96 TM </td><td> RAININ </td><td></td><td></td></tr><tr><td> COPAS Biosort </td><td> Unión Biometrica </td><td></td><td></td></tr><tr><td> LIMS </td><td> Modul-Bio </td><td></td><td></td></tr></tbody></table>

quantitative and automated high-throughput genome-wide rnai screens in c. elegans

La interferencia de ARN es un poderoso método para comprender la función de genes, especialmente cuando se realiza a escala de todo el genoma y en un contexto cuantitativo. En C. elegans, la función del gen puede ser derribado sencilla y eficaz por la alimentación de los gusanos con bacterias que expresan el dsRNA correspondiente a un gen específico 1. Si bien la creación de bibliotecas de clones de RNAi cubriendo la mayor parte de la C. elegans genoma 2,3 abrió el camino para que los verdaderos estudios de genómica funcional (véase, por ejemplo 4-7), la mayoría de los métodos establecidos son laboriosos. Moy y sus colegas han desarrollado protocolos de semi-automatizados que facilitan todo el genoma de las pantallas de 8. El enfoque se basa en imágenes microscópicas y análisis de imágenes. A continuación se describe un protocolo alternativo para un alto rendimiento en todo el genoma de pantalla, basado en la manipulación robótica de clones bacterianos ARNi, el análisis cuantitativo utilizando el Biosort COPAS (Unión Biometrica (UBI)), y unsoftware integrado: el MBioLIMS (Laboratory Information Management System de Modul-Bio) una tecnología que proporciona un mayor rendimiento para la gestión de datos y el seguimiento de la muestra. El método permite que las pantallas se llevó a cabo en placas de medio sólido. Esto es particularmente importante para algunos estudios, como los que abordan las interacciones huésped-patógeno en C. elegans, ya que ciertos microbios no son eficientes gusanos infectan en cultivo líquido. Se muestra cómo el método puede ser utilizado para cuantificar la importancia de los genes en el anti-hongos inmunidad innata en C. elegans. En este caso, el método se basa en el uso de una cepa transgénica llevar una infección epidérmica inducible del gen reportero fluorescente, con GFP bajo el control del promotor del gen del péptido antimicrobiano nlp 29 y un reportero fluorescente de color rojo que se expresa constitutivamente en el epidermis. Este último proporciona un control interno para la integridad funcional de la epidermisy no específica del transgén silenciar 9. Cuando los gusanos de control están infectadas por el hongo que presentan fluorescencia verde. Derribar por RNAi un gen necesario para la expresión resultados Nlp 29 en la fluorescencia disminuida después de la infección. En la actualidad, este protocolo permite a los más de 3.000 clones de RNAi para ser probado y analizado por semana, abriendo la posibilidad de la detección del genoma completo en menos de 2 meses.

Watch this Scientific Journal Video about Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans at JoVE.com

Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans

Se describe un protocolo de uso de<em&gt; C. elegans</em&gt; Y las bibliotecas de RNAi de alimentación que permite la medición automática de múltiples parámetros, como la fluorescencia, el tamaño y la opacidad de los gusanos individuales de una población. Damos un ejemplo de una pantalla para identificar genes implicados en la anti-hongos en la inmunidad innata<em&gt; C. elegans</em&gt;.

Cuantitativos y automatizada de alto rendimiento del genoma completo de RNAi pantallas en C. elegans</em

RNA interference is a powerful method to understand gene function, especially when conducted at a whole-genome scale and in a quantitative context. In C. ...

quantitative-automated-high-throughput-genome-wide-rnai-screens-c

Research

JoVE Journal

Biology

Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans

17.5K vistas.  Université de la Méditerranée. Se describe un protocolo de uso de C. elegans Y las bibliotecas de RNAi de alimentación que permite la medición automática de múltiples parámetros, como la fluorescencia, el tamaño y la opacidad de los gusanos individuales de una población. Damos un ejemplo de una pantalla para identificar genes implicados en la anti-hongos en la inmunidad innata C. elegans.

Video: Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans

Development of automated imaging and analysis for zebrafish chemical screens.

We demonstrate the application of image-based high-content screening (HCS) methodology to identify small molecules that can modulate the FGF/RAS/MAPK pathway in zebrafish embryos. The zebrafish embryo is an ideal system for in vivo high-content chemical screens. The 1-day old embryo is approximately 1mm in diameter and can be easily arrayed into 96-well plates, a standard format for high throughput screening. During the first day of development, embryos are transparent with most of the major organs present, thus enabling visualization of tissue formation during embryogenesis. The complete automation of zebrafish chemical screens is still a challenge, however, particularly in the development of automated image acquisition and analysis. We previously generated a transgenic reporter line that expresses green fluorescent protein (GFP) under the control of FGF activity and demonstrated their utility in chemical screens 1. To establish methodology for high throughput whole organism screens, we developed a system for automated imaging and analysis of zebrafish embryos at 24-48 hours post fertilization (hpf) in 96-well plates 2. In this video we highlight the procedures for arraying transgenic embryos into multiwell plates at 24hpf and the addition of a small molecule (BCI) that hyperactivates FGF signaling 3. The plates are incubated for 6 hours followed by the addition of tricaine to anesthetize larvae prior to automated imaging on a Molecular Devices ImageXpress Ultra laser scanning confocal HCS reader. Images are processed by Definiens Developer software using a Cognition Network Technology algorithm that we developed to detect and quantify expression of GFP in the heads of transgenic embryos. In this example we highlight the ability of the algorithm to measure dose-dependent effects of BCI on GFP reporter gene expression in treated embryos.

We report the development of a system for automated imaging and analysis of zebrafish transgenic embryos in multiwell plates. This demonstrates the ability to measure dose dependent effects of a small molecule, BCI, on Fibroblast Growth Factor reporter gene expression and provide technology for establishing high-throughput zebrafish chemical screens.

Desarrollo de la imagen y el análisis automatizado de pantallas de química de pez cebra.

We demonstrate the application of image-based high-content screening (HCS) methodology to identify small molecules that can modulate the FGF/RAS/MAPK ...

Investigación

Biología

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Recruitment of transcriptional and epigenetic factors to their targets is a key step in their regulation. Prominently featured in recruitment are the protein domains that bind to specific histone modifications. One such domain is the plant homeodomain (PHD), found in several chromatin-binding proteins. The epigenetic factor RBP2 has multiple PHD domains, however, they have different functions (Figure 4). In particular, the C-terminal PHD domain, found in a RBP2 oncogenic fusion in human leukemia, binds to trimethylated lysine 4 in histone H3 (H3K4me3)1. The transcript corresponding to the RBP2 isoform containing the C-terminal PHD accumulates during differentiation of promonocytic, lymphoma-derived, U937 cells into monocytes2. Consistent with both sets of data, genome-wide analysis showed that in differentiated U937 cells, the RBP2 protein gets localized to genomic regions highly enriched for H3K4me33. Localization of RBP2 to its targets correlates with a decrease in H3K4me3 due to RBP2 histone demethylase activity and a decrease in transcriptional activity. In contrast, two other PHDs of RBP2 are unable to bind H3K4me3. Notably, the C-terminal domain PHD of RBP2 is absent in the smaller RBP2 isoform4. It is conceivable that the small isoform of RBP2, which lacks interaction with H3K4me3, differs from the larger isoform in genomic location. The difference in genomic location of RBP2 isoforms may account for the observed diversity in RBP2 function. Specifically, RBP2 is a critical player in cellular differentiation mediated by the retinoblastoma protein (pRB). Consistent with these data, previous genome-wide analysis, without distinction between isoforms, identified two distinct groups of RBP2 target genes: 1) genes bound by RBP2 in a manner that is independent of differentiation; 2) genes bound by RBP2 in a differentiation-dependent manner.
To identify differences in localization between the isoforms we performed genome-wide location analysis by ChIP-Seq. Using antibodies that detect both RBP2 isoforms we have located all RBP2 targets. Additionally we have antibodies that only bind large, and not small RBP2 isoform (Figure 4). After identifying the large isoform targets, one can then subtract them from all RBP2 targets to reveal the targets of small isoform. These data show the contribution of chromatin-interacting domain in protein recruitment to its binding sites in the genome.

Here we are presenting a chromatin immunoprecipitation (ChIP) procedure for genome-wide location analysis of protein isoforms that differ in a histone-binding domain. We are applying it to ChIP-Seq analysis to identify the targets of the KDM5A/JARID1A/RBP2 histone demethylase.

Análisis de todo el genoma con chip para identificar objetivos específicos para cada isoforma Gene

Recruitment of transcriptional and epigenetic factors to their targets is a key step in their regulation. Prominently featured in recruitment are the ...

High-throughput Screening and Biosensing with Fluorescent C. elegans Strains

High-throughput screening (HTS) is a powerful approach for identifying chemical modulators of biological processes. However, many compounds identified in screens using cell culture models are often found to be toxic or pharmacologically inactive in vivo1-2. Screening in whole animal models can help avoid these pitfalls and streamline the path to drug development.
C. elegans is a multicellular model organism well suited for HTS. It is small (&lt;1 mm) and can be economically cultured and dispensed in liquids. C. elegans is also one of the most experimentally tractable animal models permitting rapid and detailed identification of drug mode-of-action3.
We describe a protocol for culturing and dispensing fluorescent strains of C. elegans for high-throughput screening of chemical libraries or detection of environmental contaminants that alter the expression of a specific gene. Large numbers of developmentally synchronized worms are grown in liquid culture, harvested, washed, and suspended at a defined density. Worms are then added to black, flat-bottomed 384-well plates using a peristaltic liquid dispenser. Small molecules from a chemical library or test samples (e.g., water, food, or soil) can be added to wells with worms. In vivo, real-time fluorescence intensity is measured with a fluorescence microplate reader. This method can be adapted to any inducible gene in C. elegans for which a suitable reporter is available. Many inducible stress and developmental transcriptional pathways are well defined in C. elegans and GFP transgenic reporter strains already exist for many of them4. When combined with the appropriate transgenic reporters, our method can be used to screen for pathway modulators or to develop robust biosensor assays for environmental contaminants. 
We demonstrate our C. elegans culture and dispensing protocol with an HTS assay we developed to monitor the C. elegans cap &#x2018;n&#x2019; collar transcription factor SKN-1. SKN-1 and its mammalian homologue Nrf2 activate cytoprotective genes during oxidative and xenobiotic stress5-10. Nrf2 protects mammals from numerous age-related disorders such as cancer, neurodegeneration, and chronic inflammation and has become a major chemotherapeutic target11-13.Our assay is based on a GFP transgenic reporter for the SKN-1 target gene gst-414, which encodes a glutathione-s transferase6. The gst-4 reporter is also a biosensor for xenobiotic and oxidative chemicals that activate SKN-1 and can be used to detect low levels of contaminants such as acrylamide and methyl-mercury15-16.

High-throughput Screening and Biosensing with Fluorescent C. elegans Strains

A procedure for liquid-based culturing and dispensing of C. elegans strains expressing fluorescent reporter proteins is described that does not require expensive sorting equipment. This approach can be applied to numerous inducible C. elegans genes for drug discovery or biosensing of contaminants.

Selección de alto rendimiento y biosensores fluorescentes con C. elegans Las cepas

High-throughput screening (HTS) is a powerful approach for identifying chemical modulators of biological processes.  However, many compounds identified in ...

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated tools and resources for studies in this system are facilitating continued discovery of genes with more subtle phenotypes or roles. 
Here we present a generalized protocol we adapted for identifying C. elegans genes with postembryonic phenotypes of interest using RNAi2. This procedure is easily modified to assay the phenotype of choice, whether by light or fluorescence optics on a dissecting or compound microscope. This screening protocol capitalizes on the physical assets of the organism and molecular tools the C. elegans research community has produced. As an example, we demonstrate the use of an integrated transgene that expresses a fluorescent product in an RNAi screen to identify genes required for the normal localization of this product in late stage larvae and adults. First, we used a commercially available genomic RNAi library with full-length cDNA inserts. This library facilitates the rapid identification of multiple candidates by RNAi reduction of the candidate gene product. Second, we generated an integrated transgene that expresses our fluorecently tagged protein of interest in an RNAi-sensitive background. Third, by exposing hatched animals to RNAi, this screen permits identification of gene products that have a vital embryonic role that would otherwise mask a post-embryonic role in regulating the protein of interest. Lastly, this screen uses a compound microscope equipped for single cell resolution.

RNAi Screening to Identify Postembryonic Phenotypes in C. elegans

We describe a sensitized method to identify postembryonic regulators of protein expression and localization in C. elegans using an RNAi-based genomic screen and an integrated transgene that expresses a functional, fluorescently tagged protein.

RNAi de detección para identificar fenotipos postembrionarios en C. elegans</em

C. elegans has proven to be a valuable model system for the discovery and functional characterization of many genes and gene pathways1. More sophisticated ...

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Projects to obtain whole-genome sequences for 10,000 vertebrate species1 and for 5,000 insect and related arthropod species2 are expected to take place over the next 5 years. For example, the sequencing of the genomes for 15 malaria mosquitospecies is currently being done using an Illumina platform3,4. This Anopheles species cluster includes both vectors and non-vectors of malaria. When the genome assemblies become available, researchers will have the unique opportunity to perform comparative analysis for inferring evolutionary changes relevant to vector ability. However, it has proven difficult to use next-generation sequencing reads to generate high-quality de novo genome assemblies5. Moreover, the existing genome assemblies for Anopheles gambiae, although obtained using the Sanger method, are gapped or fragmented4,6.
Success of comparative genomic analyses will be limited if researchers deal with numerous sequencing contigs, rather than with chromosome-based genome assemblies. Fragmented, unmapped sequences create problems for genomic analyses because: (i) unidentified gaps cause incorrect or incomplete annotation of genomic sequences; (ii) unmapped sequences lead to confusion between paralogous genes and genes from different haplotypes; and (iii) the lack of chromosome assignment and orientation of the sequencing contigs does not allow for reconstructing rearrangement phylogeny and studying chromosome evolution. Developing high-resolution physical maps for species with newly sequenced genomes is a timely and cost-effective investment that will facilitate genome annotation, evolutionary analysis, and re-sequencing of individual genomes from natural populations7,8.
Here, we present innovative approaches to chromosome preparation, fluorescent in situ hybridization (FISH), and imaging that facilitate rapid development of physical maps. Using An. gambiae as an example, we demonstrate that the development of physical chromosome maps can potentially improve genome assemblies and, thus, the quality of genomic analyses. First, we use a high-pressure method to prepare polytene chromosome spreads. This method, originally developed for Drosophila9, allows the user to visualize more details on chromosomes than the regular squashing technique10. Second, a fully automated, front-end system for FISH is used for high-throughput physical genome mapping. The automated slide staining system runs multiple assays simultaneously and dramatically reduces hands-on time11. Third, an automatic fluorescent imaging system, which includes a motorized slide stage, automatically scans and photographs labeled chromosomes after FISH12. This system is especially useful for identifying and visualizing multiple chromosomal plates on the same slide. In addition, the scanning process captures a more uniform FISH result. Overall, the automated high-throughput physical mapping protocol is more efficient than a standard manual protocol.

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Genome assemblies based on massively parallel DNA sequencing technologies are usually highly fragmented. The development of physical chromosome maps can potentially improve genome assemblies. Here, we demonstrate innovative approaches to chromosome preparation, fluorescent in situ hybridization, and imaging that significantly increase throughput of the physical map development.

De alto rendimiento mapeo físico de cromosomas utilizando automatizado<em&gt; In situ</em&gt; La hibridación

Projects to obtain whole-genome sequences for 10,000 vertebrate species1 and for 5,000 insect and related arthropod species2 are expected to take place ...

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

Transposon mutagenesis and single-gene deletion are two methods applied in genome-wide gene knockout in bacteria 1,2. Although transposon mutagenesis is less time consuming, less costly, and does not require completed genome information, there are two weaknesses in this method: (1) the possibility of a disparate mutants in the mixed mutant library that counter-selects mutants with decreased competition; and (2) the possibility of partial gene inactivation whereby genes do not entirely lose their function following the insertion of a transposon. Single-gene deletion analysis may compensate for the drawbacks associated with transposon mutagenesis. To improve the efficiency of genome-wide single gene deletion, we attempt to establish a high-throughput technique for genome-wide single gene deletion using Streptococcus sanguinis as a model organism. Each gene deletion construct in S. sanguinis genome is designed to comprise 1-kb upstream of the targeted gene, the aphA-3 gene, encoding kanamycin resistance protein, and 1-kb downstream of the targeted gene. Three sets of primers F1/R1, F2/R2, and F3/R3, respectively, are designed and synthesized in a 96-well plate format for PCR-amplifications of those three components of each deletion construct. Primers R1 and F3 contain 25-bp sequences that are complementary to regions of the aphA-3 gene at their 5' end. A large scale PCR amplification of the aphA-3 gene is performed once for creating all single-gene deletion constructs. The promoter of aphA-3 gene is initially excluded to minimize the potential polar effect of kanamycin cassette. To create the gene deletion constructs, high-throughput PCR amplification and purification are performed in a 96-well plate format. A linear recombinant PCR amplicon for each gene deletion will be made up through four PCR reactions using high-fidelity DNA polymerase. The initial exponential growth phase of S. sanguinis cultured in Todd Hewitt broth supplemented with 2.5% inactivated horse serum is used to increase competence for the transformation of PCR-recombinant constructs. Under this condition, up to 20% of S. sanguinis cells can be transformed using ~50 ng of DNA. Based on this approach, 2,048 mutants with single-gene deletion were ultimately obtained from the 2,270 genes in S. sanguinis excluding four gene ORFs contained entirely within other ORFs in S. sanguinis SK36 and 218 potential essential genes. The technique on creating gene deletion constructs is high throughput and could be easy to use in genome-wide single gene deletions for any transformable bacteria.

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

An efficient genome-wide single gene mutation method has been established using Streptococcus sanguinis as a model organism. This method has achieved via high throughput recombinant PCRs and transformations.

Genoma escala supresiones de genes en<em&gt; Streptococcus sanguinis</em&gt; Por PCR de alto rendimiento

Transposon  mutagenesis and single-gene deletion are two methods applied in genome-wide  gene knockout in bacteria 1,2. Although transposon mutagenesis is ...

C. elegans Chemotaxis Assay

Many organisms use chemotaxis to seek out food sources, avoid noxious substances, and find mates. Caenorhabditis elegans has impressive chemotaxis behavior.
 The premise behind testing the response of the worms to an odorant is to place them in an area and observe the movement evoked in response to an odorant. Even with the many available assays, optimizing worm starting location relative to both the control and test areas, while minimizing the interaction of worms with each other, while maintaining a significant sample size remains a work in progress 1-10. The method described here aims to address these issues by modifying the assay developed by Bargmann et al.1. A Petri dish is divided into four quadrants, two opposite quadrants marked "Test" and two are designated "Control". Anesthetic is placed in all test and control sites. The worms are placed in the center of the plate with a circle marked around the origin to ensure that non-motile worms will be ignored. Utilizing a four-quadrant system rather than one 2 or two 1 eliminates bias in the movement of the worms, as they are equidistant from test and control samples, regardless of which side of the origin they began. This circumvents the problem of worms being forced to travel through a cluster of other worms to respond to an odorant, which can delay worms or force them to take a more circuitous route, yielding an incorrect interpretation of their intended path. This method also shows practical advantages by having a larger sample size and allowing the researcher to run the assay unattended and score the worms once the allotted time has expired.

C. elegans Chemotaxis Assay

A method of quantitatively evaluating the chemotactic response of Caenorhabditis elegans is described. A chemotactic index (CI) was employed as a way to precisely evaluate the response of worms to certain targets, and serve as a platform of comparison between strains and compounds of interest.

C. elegans Ensayo de quimiotaxis

Many organisms use chemotaxis to seek out food sources, avoid noxious substances, and find mates.  Caenorhabditis elegans has impressive chemotaxis ...

Biochemical and High Throughput Microscopic Assessment of Fat Mass in Caenorhabditis Elegans

The nematode C. elegans has emerged as an important model for the study of conserved genetic pathways regulating fat metabolism as it relates to human obesity and its associated pathologies. Several previous methodologies developed for the visualization of C. elegans triglyceride-rich fat stores have proven to be erroneous, highlighting cellular compartments other than lipid droplets. Other methods require specialized equipment, are time-consuming, or yield inconsistent results. We introduce a rapid, reproducible, fixative-based Nile red staining method for the accurate and rapid detection of neutral lipid droplets in C. elegans. A short fixation step in 40% isopropanol makes animals completely permeable to Nile red, which is then used to stain animals. Spectral properties of this lipophilic dye allow it to strongly and selectively fluoresce in the yellow-green spectrum only when in a lipid-rich environment, but not in more polar environments. Thus, lipid droplets can be visualized on a fluorescent microscope equipped with simple GFP imaging capability after only a brief Nile red staining step in isopropanol. The speed, affordability, and reproducibility of this protocol make it ideally suited for high throughput screens. We also demonstrate a paired method for the biochemical determination of triglycerides and phospholipids using gas chromatography mass-spectrometry. This more rigorous protocol should be used as confirmation of results obtained from the Nile red microscopic lipid determination. We anticipate that these techniques will become new standards in the field of C. elegans metabolic research.

Biochemical and High Throughput Microscopic Assessment of Fat Mass in Caenorhabditis Elegans

We present robust biochemical and microscopic methods for studying Caenorhabditis elegans lipid stores. A rapid, simple, fixing-staining procedure for fluorescent lipid droplet imaging leverages the spectral properties of the lipophilic dye Nile red. We then present biochemical measurement of triglycerides and phospholipids using solid phase extraction and gas chromatography-mass spectrometry.

Bioquímica y de Evaluación de Rendimiento microscópica de masa grasa en<em&gt; Caenorhabditis elegans</em

The nematode C. elegans has emerged as an important  model for the study of conserved genetic pathways regulating fat metabolism as  it relates to human ...

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.

Selección de alto rendimiento para moduladores químicos de genes post-transcripcionalmente regulados

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

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

The DNA adenine methyltransferase identification (DamID) assay is a powerful method to detect protein-DNA interactions both locally and genome-wide. It is an alternative approach to chromatin immunoprecipitation (ChIP). An expressed fusion protein consisting of the protein of interest and the E. coli DNA adenine methyltransferase can methylate the adenine base in GATC motifs near the sites of protein-DNA interactions. Adenine-methylated DNA fragments can then be specifically amplified and detected. The original DamID assay detects the genomic locations of methylated DNA fragments by hybridization to DNA microarrays, which is limited by the availability of microarrays and the density of predetermined probes. In this paper, we report the detailed protocol of integrating high throughput DNA sequencing into DamID (DamID-seq). The large number of short reads generated from DamID-seq enables detecting and localizing protein-DNA interactions genome-wide with high precision and sensitivity. We have used the DamID-seq assay to study genome-nuclear lamina (NL) interactions in mammalian cells, and have noticed that DamID-seq provides a high resolution and a wide dynamic range in detecting genome-NL interactions. The DamID-seq approach enables probing NL associations within gene structures and allows comparing genome-NL interaction maps with other functional genomic data, such as ChIP-seq and RNA-seq.

We describe herein an assay by coupling DNA adenine methyltransferase identification (DamID) to high throughput sequencing (DamID-seq). This improved method provides a higher resolution and a wider dynamic range, and allows analyzing DamID-seq data in conjunction with other high throughput sequencing data such as ChIP-seq, RNA-seq, etc.

-DamID siguientes: Genoma de toda la cartografía de la proteína-ADN Interacciones de alto rendimiento de secuenciación de fragmentos de ADN adenina-metilado

The DNA adenine methyltransferase identification (DamID) assay is a powerful method to detect protein-DNA interactions both locally and genome-wide. It is ...