Este trabajo es apoyado por la Universidad de Virginia, la Universidad de Virginia y el Centro de Cáncer F. Thomas y Kate Miller Jeffress Memorial Trust. Damos las gracias al James E. Darnell Lab (Rockefeller University) Robert Ross Lab (Fordham University) para las líneas celulares.

PLANIFICACIÓN El día antes de un experimento de chip está previsto, las células deben ser cultivadas de manera que un número suficiente esté disponible. Supongamos que cada chip de ensayo requerirá ~ 1-1,5 x 10 7 células. Siempre el plan de hacer las dos cosas los controles negativos (IgG) y positivo (anticuerpos histona pan) y los experimentos duplicados. Sugerencia - Para obtener las células 2FTGH, cada chip de ensayo requiere alrededor de un 15 cm placa de cultivo de tejidos en la confluencia del 80%. PARTE 1: Preparar la cromatina y REALIZAR chip <ol><li> Eliminar los medios de cultivo e inducir las células de los tiempos requeridos con 20 ml de 10% de suero de ternera cósmica (CCS) / MEDM con IFN-gamma a 5 ng / mL. Vuelva a colocar los medios de comunicación en las placas no inducido con 20 ml de 10% de CCS / DMEM así. </li><li> En una campana de extracción, añadir 540 l de formaldehído 37% a 20 ml de los medios de comunicación (1% concentración final) en el plato de 15 cm. Consejo - placa de inclinación y añadir el formaldehído para el grupo de medios - entonces la placa de roca para repartirla uniformemente. </li><li> Permitir la reticulación de proceder durante 10 minutos a temperatura ambiente. </li><li> Añadir a la glicina 0,125 M de concentración final para dejar de reticulación. </li><li> Vacío aspirar los medios de comunicación y lavar las células una vez con 10 ml de fosfato de hielo frío (PBS). </li><li> Muestras de células con un rascador de células en PBS ~ 7 ml y se combinan las células (de 6 placas) que fueron tratados de manera idéntica en 50 ml tubo cónico en el hielo. </li><li> Centrífuga (Beckman Coutler Allegra 12-R centrífuga) a 1800 rpm a 4 ° C durante 5 minutos y aspire el PBS. Consejo - Snap congelar el sedimento celular si parar aquí y almacenar a -80 ° C. </li><li> Resuspender el botón celular en tampón de 4 ml Inflamación (25 mM HEPES pH 7,8, 1,5 mM de MgCl2, 10 mM KCl, 0,1% de NP40. Añadir 1 mM DTT, los inhibidores de la proteasa completa y enfriar en hielo antes de su uso) y la transferencia a un 15 mL cónica del tubo. Consejo - El volumen del tampón inflamación es apropiado para una agrupación de 6 placas (~ 6.9 x 10 7 células). Tampón más o menos podría cambiar la eficiencia douncing. </li><li> Incubar la suspensión de células en hielo durante 10 minutos. </li><li> La transferencia de la suspensión a un pre-enfriado douncer 15 ml (Wheaton) y Dounce 20 golpes con su correspondiente mano A. </li><li> Transferencia dounced células a un tubo cónico de 15 ml en hielo. </li><li> Centrifugar a 2500 rpm durante 5 minutos a 4 ° C y descartar el sobrenadante. </li><li> Resuspender el pellet nuclear (~ 200 l de 6 platos) en 3 ml (15 volúmenes de pellets) de tampón de sonicación (50 mM HEPES pH 7,9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, desoxicolato de sodio al 0,1%, 0,1% SDS. Añadir inhibidores de la proteasa completa y enfriar en hielo antes de su uso). Consejo - El volumen del tampón de sonicación es apropiado para una agrupación de 6 placas (~ 9.6 x 10 7 células). Tampón más o menos podría cambiar la eficiencia de ultrasonidos. </li><li> Sonicar suspensión de núcleos de hielo durante 10 ciclos (20 segundos on/40 segundos / ajuste de amplitud de 8) con un Sonicator Misonix 3000 equipado con la micropunta. Esto generalmente resulta en un promedio de fragmentos de cromatina 200-1000 bps en tamaño. Consejo - Porque sonicadores variará, la eficiencia de ultrasonidos debe ser determinada empíricamente. Para ello, tomar alícuotas de 20 l antes de ultrasonidos y después de cada ciclo de tratamiento con ultrasonidos. El calor de estas muestras a 65 ° C durante 4 horas. Añadir buffer de ADN de carga y ejecuta un estándar de 1% de agarosa / TBE gel para visualizar fragmentos de ADN.) </li><li> Transferencia de material sonicado a un tubo de centrífuga y centrifugar SS34 durante 20 minutos a 4 ° C a 13000 rpm en un rotor SS34 (Sorvall RC6 Además centrífuga) para precipitar lo que es normalmente una pequeña cantidad de restos celulares. </li><li> Transferir cuidadosamente el sobrenadante a un tubo cónico de 15 ml en hielo. </li><li> Pre-claro añadiendo 360 l de esperma de salmón ADN / proteína A o G agarosa suspensión y balanceo a 4 ° C durante al menos 30 minutos. Sugerencia - Este paso se reduce el ruido en el ensayo que surge de la no-eventos específicos de carácter vinculante. </li><li> Centrifugar a 1000 rpm a 4 ° C durante 5 minutos para que sedimenten las perlas de agarosa. </li><li> Transferencia de pre-aprobados sobrenadante a otro tubo cónico de 15 ml en hielo. </li><li> Medir la A260 unidades de la cromatina pre-aprobados y ajustar el volumen con el tampón de sonicación cuatro (4) unidades de A260 (0,2 mg / mL asumiendo una unidad A260 = 0,050 mg / ml) Sugerencia - Para medir la A260 unidades, diluir 10 l de pre-aprobados de la cromatina en 190 l DDW, blanco del espectrofotómetro con 10 l de tampón de sonicación DDW l 190. </li><li> Ahorre un 75 l de la cromatina (a 4 unidades de A260) como la muestra de entrada y almacenar a 20 ° C hasta que esté listo para invertir enlaces cruzados. Sugerencia - Este paso es crucial para el análisis de datos. No se olviden de tomar la alícuota de entrada. </li><li> Alícuota de la cromatina dispuesta a 1.7 mL tubos de microcentrífuga de ice como alícuotas de 1 ml. Sugerencia - Si se detiene aquí, complemento congelar la cromatina preparados en hielo seco y almacenar a -80 ° C. NB: la cromatina almacenados pueden degradar, producir resultados menos que óptimos, así que evite en lo posible. </li><li> Añadir los anticuerpos chip de calidad a las muestras de inducido y no inducido establece por duplicado. Añadir IgG (2 mg) y de anticuerpos pan Histona H3 (15 l) como controles positivos y negativos de inducido y no inducido conjuntos de muestras. Sugerencia - La cantidad de anticuerpo a utilizar debe ser determinada empíricamente, o consulte la hoja del proveedor de productos para cantidades sugeridas. Típicamente 1-2 mg de un anticuerpo chip-grado funciona bien. El volumen apropiado debe ser determinada empíricamente para los anticuerpos que se suministran como suero. </li><li> Todos los tubos de rock la noche a 4 ° C. </li></ol> PARTE 2: Recopilación de inmunocomplejos <ol><li> Añadir 60 l de ADN de esperma de salmón / proteína A o proteína G agarosa suspensión de todos los tubos. Sugerencia Utilice una proteína de anticuerpos policlonales de conejo y la proteína G de anticuerpos monoclonales de ratón. </li><li> Rock en 4 ° C durante al menos 60 minutos. </li><li> Se precipitan los inmunocomplejos (perlas de agarosa) por microfuging suavemente a 2000 rpm a 4 ° C durante 3 minutos. </li><li> Aspirar el sobrenadante. </li><li> Lavado de los inmunocomplejos con 1 ml de cada uno de los tampones de lavado después de 10 minutos con la oscilación a 4 ° C. Microfuga durante 3 minutos a 2000 rpm a 4 ° C entre cada lavado y aspirado de sobrenadante. Mantener las muestras enfriadas en hielo. Añadir PMSF justo antes del uso. <ul><li> Lavar bajo contenido de sal - 0,1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl, pH 8,0, 150 mM NaCl, 1 mM PMSF </li><li> Lave Salinidad - 0,1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl, pH 8,0, 500 mM NaCl, 1 mM PMSF </li><li> LiCl Wash - 0,25 M LiCl, 1% NP-40, 1% de desoxicolato de sodio, 1 mM EDTA, 10 mM Tris-Cl, pH 8,0, 1 mM PMSF </li><li> TE Wash - dos lavados con buffer TE -10 mM Tris-Cl, pH 8,0, 1 mM EDTA, 1 mM PMSF </li></ul></li><li> Quitar el último lavado de buffer TE y de las cuentas, añadir 500 l Tampón de Elución (50 mM Tris-Cl, pH 8,0, 10 mM EDTA, 1% SDS). Consejo - el tampón de elución debe estar recién preparadas. </li><li> Vortex para mezclar bolas de agarosa en tampón de elución y el calor durante 30 minutos a 65 ° C. Consejo - cada tubo de vórtice por lo menos cada 10 minutos durante estos 30 minutos. </li><li> Microcentrífuga durante 30 segundos a 2000 rpm y transferir el eluyente a un tubo de microcentrífuga nuevo. Consejo - Durante la elución, descongelar las muestras de entrada y añadir 500 l Tampón de Elución a cada uno. Incluir estas muestras en todos los pasos en el futuro. </li><li> Añadir 5 M NaCl hasta una concentración final de 200 mM a todas las muestras y agitar. </li><li> Se incuba a 65 ° C durante la noche (o por lo menos 4 horas). </li></ol> PARTE 3: ChIP&#39;d purificar y entrada de ADN <ol><li> Microfuga todas las muestras durante 30 segundos para recoger la condensación en las tapas. </li><li> Añadir 1μL de RNasa A (10 U / l) a cada tubo y se incuban a temperatura ambiente durante 15 minutos. </li><li> Añadir 10 l de EDTA 0,5 M, 40 ml 0,5 M Tris-Cl pH 6,5, 2 l de proteinasa K (10 mg / ml) y se incuba a 45 ° C durante 60 minutos. Consejo Prepare una mezcla maestra de estos reactivos y añadir 52 l de cada tubo. </li><li> Fenol / cloroformo / isoamílico extracto de alcohol y cloroformo / alcohol isoamílico extraer las muestras. </li><li> Añadir 2 glucógeno l (25 mg / l) y 0,1 volúmenes de acetato de sodio 3M pH 5,2 y mezclar. </li><li> Añadir 2.5 volúmenes de etanol al 100% y agitar. </li><li> Se incuba a 20 ° C durante la noche. </li></ol> PARTE 4: ChIP&#39;d purificar y continuo aporte de ADN <ol><li> Muestras de microcentrífuga durante un mínimo de 20 minutos a 13000 rpm a 4 ° C para precipitar el ADN / pellets de glucógeno. </li><li> Lavar con sedimentos de ADN / glucógeno con 1 ml de etanol al 70%. </li><li> Seque al aire los pellets o se secan rápidamente en el ADN de centrífuga de vacío Savant velocidad. Sugerencia - No más seco del ADN. </li><li> Resuspender el ADN / pellets de glucógeno en 200 l de buffer TE. </li><li> ADN (1 l) está listo para la cuantificación mediante PCR en tiempo real. Tienda resto de ADN a 20 ° C. Consejo - El uso de más de 1 l de ADN puede inhibir las reacciones de PCR en tiempo real, por lo que ampliar con precaución. </li></ol> Parte 5: RESULTADOS DEL REPRESENTANTE: Muestras de chips de ADN y de entrada se han cuantificado con el Real-Time PCR 7,8 (Applied Biosystems 7500 Rápido PCR en tiempo real del sistema) con iniciadores específicos para el locus del gen de interés. Cebadores que la secuencia genómica conocida objetivo de ser enriquecido en o falta en la modificaciones de las histonas que se analizaron se pueden utilizar como controles positivos y negativos. Los datos se presentan como porcentaje de la entrada. El procedimiento de chip debe ser totalmente repeated con tres repeticiones biológica para asegurar los cambios reportados en modificaciones de las histonas son estadísticamente significativas. Hay varios aspectos importantes a considerar cuando se utiliza PCR en tiempo real para cuantificar el ADN, incluyendo el primer diseño, eficiencia de la PCR, y la forma apropiada de calcular el porcentaje de procedimientos de entrada y la normalización. Cuando el perfil de ocupación de modificación de las histonas a través de un gen, la eficiencia de la PCR debe ser consistente entre todos los pares de cebadores. El fabricante de PCR en tiempo real del sistema puede proporcionar la información necesaria y la capacitación. La figura 1 muestra los resultados representativos de la cromatina immunoprecipitated STAT1 en la activación del gen IRF1 9, provocada por el IFN-γ. <img src="/files/ftp_upload/2053/2053fig1.jpg" alt="Figura 1" /> Figura 1. Ocupación de STAT1, la RNA polimerasa II y H3K36me3 es dinámica durante STAT1 la activación del gen IRF1. (A, B, C) ​​con chip α-H3K36me3, STAT1 α y α-Pol II de la cromatina de las células recogidas 2FTGH inducidos con IFN-γ durante 30 minutos (cuadrados rojos), 1,5 horas (círculos azules), 5 horas ( triángulos verdes) o inducidas (diamante negro). IgG es el control negativo (gris cruces). (D) Pan H3 es el control positivo y muestra la ocupación de las histonas en el lugar en el inducido (círculos azules) y las condiciones no inducidas (diamante negro). La inmersión alrededor de -5 pb se debe a la disminución de nucleosomas que se encuentra en los sitios de inicio de la transcripción.

<ol>
	<li>Levy, D., Darnell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signalling:+Stats:+transcriptional+control+and+biological+impact.">Signalling: Stats: transcriptional control and biological impact.</a> Nature Reviews Molecular Cell Biology. 3, 651-662 (2002).</li><li>Bromberg, J., Darnell, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+STATs+in+transcriptional+control+and+their+impact+on+cellular+function.">The role of STATs in transcriptional control and their impact on cellular function.</a> Oncogene. 19, 2468-2473 (2000).</li><li>Hu, X., Ivashkiv, L. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cross-regulation+of+signaling+pathways+by+interferon-gamma:+implications+for+immune+responses+and+autoimmune+diseases.">Cross-regulation of signaling pathways by interferon-gamma: implications for immune responses and autoimmune diseases.</a> Immunity. 31, 539-550 (2009).</li><li>Campos, E. I., Reinberg, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histones:+annotating+chromatin.">Histones: annotating chromatin.</a> Annu Rev Genet. 43, 559-599 (2009).</li><li>Kouzarides, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+Modifications+and+Their+Function.">Chromatin Modifications and Their Function.</a> Cell. 128, 693-705 (2007).</li><li>Jenuwein, T., Allis, C. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Translating+the+histone+code.">Translating the histone code.</a> Science. 293, 1074-1080 (2001).</li><li>Wittwer, C. T., Herrmann, M. G., Moss, A. A., Rasmussen, R. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Continuous+fluorescence+monitoring+of+rapid+cycle+DNA+amplification.">Continuous fluorescence monitoring of rapid cycle DNA amplification.</a> Biotechniques. 22 (130-131), 134-138 (1997).</li><li>Higuchi, R., Dollinger, G., Walsh, P. S., Griffith, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simultaneous+amplification+and+detection+of+specific+DNA+sequences.">Simultaneous amplification and detection of specific DNA sequences.</a> Biotechnology (N Y). 10, 413-417 (1992).</li><li>Kroger, A., Koster, M., Schroeder, K., Hauser, H., Mueller, P. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activities+of+IRF-1.">Activities of IRF-1.</a> J Interferon Cytokine Res. 22, 5-14 (2002).</li><li>Ross, R. A., Spengler, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+neuroblastoma+stem+cells.">Human neuroblastoma stem cells.</a> Seminars in cancer biology. 17, 241-247 (2007).</li></ol>

El protocolo indica chip se ha utilizado con éxito en el laboratorio de ensayo de más de veinte diferentes modificaciones de las histonas. Además, se han caracterizado los cambios en la ocupación de los factores de transcripción, histonas modificación de enzimas, proteínas que reconocen modificaciones de las histonas y el ARN polimerasa II maquinaria de transcripción, en varios de IFN-γ inducida por los genes. También hemos utilizado el procedimiento para caracterizar los cambios en las modificaciones de las histonas durante la diferenciación de una célula madre del cáncer 10. La calidad de los datos del chip en última instancia depende de la eficacia de los anticuerpos utilizados y hay una considerable variabilidad entre los anticuerpos. La falta de un chip de modificación, por lo tanto, no puede interpretarse en el sentido de que dicha modificación no está presente. Además, los cambios en una determinada modificación observada en un experimento de chip puede simplemente reflejar un cambio en el reconocimiento del epítopo por el anticuerpo adicional causado por modificaciones de las histonas en los residuos cercanos. Por lo tanto, los resultados de chip debe ser validado con los enfoques que se relacionan con los cambios observados en una modificación de las histonas a un resultado biológico. Cuando se hace esto, chip es una forma poderosa para el estudio de la cromatina basada en mecanismos que contribuyen a la regulación de la expresión génica.

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		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>37% Formaldehyde</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP531-500</td>
<td>&nbsp;</td>
<tr>
<td>Chloroform/Isoamyl alcohol</td>
<td>&nbsp;</td>
<td>Acros</td>
<td>AC32715-5000</td>
<td>&nbsp;</td>
<tr>
<td>Complete Mini Protease Inhibitors</td>
<td>&nbsp;</td>
<td>Roche</td>
<td>1836153</td>
<td>&nbsp;</td>
<tr>
<td>Cosmic Calf Serum</td>
<td>&nbsp;</td>
<td>Hyclone</td>
<td>SH30087.04N</td>
<td>&nbsp;</td>
<tr>
<td>DMEM</td>
<td>&nbsp;</td>
<td>Hyclone</td>
<td>SH30243</td>
<td>&nbsp;</td>
<tr>
<td>DTT</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>D0632</td>
<td>&nbsp;</td>
<tr>
<td>EDTA</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP118-500</td>
<td>&nbsp;</td>
<tr>
<td>Ethanol</td>
<td>&nbsp;</td>
<td>Pharmco</td>
<td>zp1110EP</td>
<td>&nbsp;</td>
<tr>
<td>Glycine</td>
<td>&nbsp;</td>
<td>Roche</td>
<td>100149</td>
<td>&nbsp;</td>
<tr>
<td>Glycogen</td>
<td>&nbsp;</td>
<td>Roche</td>
<td>901393</td>
<td>&nbsp;</td>
<tr>
<td>HEPES</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>H3784</td>
<td>&nbsp;</td>
<tr>
<td>IFN-gamma</td>
<td>&nbsp;</td>
<td>R&amp;D Systems</td>
<td>285-IF-100</td>
<td>&nbsp;</td>
<tr>
<td>IgG</td>
<td>&nbsp;</td>
<td>Jackson Immunoresearch</td>
<td> 109-005-003</td>
<td>&nbsp;</td>
<tr>
<td>KCl</td>
<td>&nbsp;</td>
<td>MP Biologicals</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>LiCl</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>L4408</td>
<td>&nbsp;</td>
<tr>
<td>MgCl2</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>M8266</td>
<td>&nbsp;</td>
<tr>
<td>Sodium Acetate</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP333-500</td>
<td>&nbsp;</td>
<tr>
<td>Deoxycholic Acid Sodium Salt</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP349-100</td>
<td>&nbsp;</td>
<tr>
<td>NaCl</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>7647-14-5</td>
<td>&nbsp;</td>
<tr>
<td>NP40</td>
<td>&nbsp;</td>
<td>US Biological</td>
<td>N3500</td>
<td>&nbsp;</td>
<tr>
<td>Anti-Histone H3, CT, pan</td>
<td>&nbsp;</td>
<td>Millipore</td>
<td>07-690</td>
<td>&nbsp;</td>
<tr>
<td>Phenol/chloroform/isoamyl</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>108-95-2</td>
<td>&nbsp;</td>
<tr>
<td>Phosphate Buffered Saline</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>7647-14-5</td>
<td>&nbsp;</td>
<tr>
<td>PMSF</td>
<td>&nbsp;</td>
<td>EMD</td>
<td>50-230-0316</td>
<td>&nbsp;</td>
<tr>
<td>Proteinase K</td>
<td>&nbsp;</td>
<td>5-Prime</td>
<td>2500140</td>
<td>&nbsp;</td>
<tr>
<td>RNAse A</td>
<td>&nbsp;</td>
<td>5-Prime</td>
<td>2500130</td>
<td>&nbsp;</td>
<tr>
<td>Salmon Sperm DNA/Protein A Agarose</td>
<td>&nbsp;</td>
<td>Millipore</td>
<td>16-157</td>
<td>&nbsp;</td>
<tr>
<td>Salmon Sperm DNA/Protein G Agaorse</td>
<td>&nbsp;</td>
<td>Millipore</td>
<td>16-201</td>
<td>&nbsp;</td>
<tr>
<td>SDS</td>
<td>&nbsp;</td>
<td>Fisher</td>
<td>BP166-500</td>
<td>&nbsp;</td>
<tr>
<td>Tris-Cl</td>
<td>&nbsp;</td>
<td>Sigma</td>
<td>T5941</td>
<td>&nbsp;</td>
<tr>
<td>Triton X-100</td>
<td>&nbsp;</td>
<td>Acros</td>
<td>327372500</td>
<td>&nbsp;</td>
<tr>
<td>Anti-K36me3</td>
<td>&nbsp;</td>
<td>Abcam</td>
<td>ab9050</td>
<td>&nbsp;</td>
<tr>
<td>Anti-STAT1</td>
<td>&nbsp;</td>
<td>Santa Cruz</td>
<td>sc-345X</td>
<td>&nbsp;</td>
<tr>
<td>Anti-RNA Polymerase II</td>
<td>&nbsp;</td>
<td>Santa Cruz</td>
<td>sc-899</td>
<td>&nbsp;</td>		</tbody>
		</table>
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chromatin immunoprecipitation (chip) to assay dynamic histone modification in activated gene expression in human cells

En respuesta a una variedad de ligandos extracelulares, el STAT (transductor de señal y activador de la transcripción) factores de transcripción son rápidamente contratados en su estado latente en el citoplasma a los receptores de superficie celular en el que se activan por fosforilación en un único residuo de tirosina 1. A continuación, dímeros y trasladar al núcleo para conducir la transcripción de genes diana, lo que afecta el crecimiento, la diferenciación, la homeostasis y la respuesta inmune. No es de extrañar, dada su amplia participación en los procesos celulares normales, la desregulación de la función STAT contribuye a la enfermedad humana, en particular con el cáncer y enfermedades autoinmunes 2 3. Está bien establecido que la transcripción está regulada por la alteración de la plantilla de 4,5 cromatina. Estas alteraciones incluyen las actividades de la ATP-dependientes de los complejos, así como covalentes modificaciones de las histonas y la metilación del ADN 6. Debido a la activación de STAT de la expresión génica es a la vez rápido y transitorio, se requiere de mecanismos específicos para la modulación de la plantilla de la cromatina en los loci de genes dependientes de STAT. Para definir estos mecanismos, que caracterizan a la modificaciones de las histonas y la actividad enzimática que los generan en los loci de genes que responden a STAT de señalización. Este protocolo describe inmunoprecipitación de cromatina, un método que es valioso para el estudio de STAT de señalización de la cromatina en la expresión de genes activados.

Watch this Scientific Journal Video about Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells at JoVE.com

Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells

Este protocolo describe cómo inmunoprecipitación de cromatina (CHIP) se utiliza para estudiar las alteraciones dinámicas de la plantilla de la cromatina que regulan la transcripción inducida por una vía de transducción de señal.

Inmunoprecipitación de cromatina (CHIP) para el ensayo dinámico de modificación de las histonas en la expresión génica activado en las células humanas

In response to a variety of extracellular ligands, the STAT (signal transducer and activator of transcription) transcription factors are rapidly recruited ...

chromatin-immunoprecipitation-chip-to-assay-dynamic-histone

Nanyang Technological University

Research

JoVE Journal

Biology

Chromatin Immunoprecipitation (ChIP) to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells

28.6K vistas.  University of Virginia. Este protocolo describe cómo inmunoprecipitación de cromatina (CHIP) se utiliza para estudiar las alteraciones dinámicas de la plantilla de la cromatina que regulan la transcripción inducida por una vía de transducción de señal.

Video: Chromatin Immunoprecipitation ChIP to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells

Chromatin Immunoprecipitation from Human Embryonic Stem Cells

The functional and structural complexity of the myriad of cells in metazoan organisms arises from a small number of stem cells. Stem cells are characterized by two fundamental properties: self-renewal and multipotency that allows a stem cell to differentiate into virtually any cell type 1. The progression stem cell to differentiated cell is characterized by loss of multipotency, structural and morphological changes and the hierarchic activity of transcription factors and signaling molecules, whose activities establish and maintain cell-type specific gene expression patterns. At the molecular level, cell differentiation involves dynamic changes of the structure and composition of chromatin and the detection of those dynamic changes can provide valuable insights into the functional features of stem cells and the cell differentiation process 2,3. Chromatin is a highly compacted DNA-protein complex that forms when cells package chromosomal DNA with proteins, mainly histones 4. Stemcellness and cell differentiation has been correlated with the presence of specific arrays of regulatory proteins such as epigenetic factors, histone variants, and transcription factors 2,3,5.
 Chromatin immunoprecipitation (ChIP) provides a valuable method to monitor the presence of RNA, proteins, and protein modifications in chromatin 6,7. The comparison of chromatin from different cell types can elucidate dynamic changes in protein-chromatin associations that occur during cell differentiation.
Chromatin immunoprecipitation involves the purification of in vivo cross-linked chromatin. The isolated chromatin is reduced to smaller fragments by enzymatic digestion or mechanical force. Chromatin fragments are precipitated using specific antibodies to target proteins or protein and DNA modifications. The precipitated DNA or RNA is purified and used as a template for PCR or DNA microarray based assays. Prerequisites for a successful ChIP are high quality antibodies to the desired antigen and the availability of chromatin from control cells that do not express the target molecule. ChIP can correlate the presence of proteins, protein and RNA modifications, and RNA with specific target DNA, and depending on the choice of outread tool, detects the association of target molecules at specific target genes or in the context of an entire genome. The comparison of the distribution of proteins in the chromatin of differentiating cells can elucidate the dynamic changes of chromatin composition that coincide with the progression of cells along a cell lineage.

The differentiation of ESC coincides with cell-type specific changes in the structure and composition of chromatin. The detection of those changes provides valuable insights into the mechanisms that define stemcellness and cell differentiation. Chromatin immunoprecipitation (ChIP) represents a valuable method to dissect the molecular mechanisms underlying stem cell differentiation.

Inmunoprecipitación de la cromatina de células estaminales embrionarias humanas

The functional and structural complexity of the myriad of cells in metazoan organisms arises from a small number of stem cells. Stem cells are ...

Investigación

Biología

Using the Gene Pulser MXcell Electroporation System to Transfect Primary Cells with High Efficiency

It is becoming increasingly apparent that electroporation is the most effective way to introduce plasmid DNA or siRNA into primary cells. The Gene Pulser MXcell electroporation system and Gene Pulser electroporation buffer (Bio-Rad) were specifically developed to easily transfect nucleic acids into mammalian cells and difficult-to-transfect cells, such as primary and stem cells. We will demonstrate how to perform a simple experiment to quickly identify the best electroporation conditions. We will demonstrate how to run several samples through a range of electroporation conditions so that an experiment can be conducted at the same time as optimization is performed. We will also show how optimal conditions identified using 96-well electroporation plates can be used with standard electroporation cuvettes, facilitating the switch from electroporation plates to electroporation cuvettes while maintaining the same electroporation efficiency. In the video, we will also discuss some of the key factors that can lead to the success or failure of electroporation experiments.

This procedure shows how to use the Gene Pulser MXcell electroporation system to rapidly and easily identify the best electroporation conditions for mouse embryonic fibroblasts (MEFs) or other primary cells. Considerations for troubleshooting are also discussed in the associated video.

Utilizando el sistema de electroporación Gene Emisores MXcell para transfectar células primarias con alta eficiencia

It is becoming increasingly apparent that electroporation is the most effective way to introduce plasmid DNA or siRNA into primary cells. The Gene Pulser ...

Robotics and Dynamic Image Analysis for Studies of Gene Expression in Plant Tissues

Gene expression in plant tissues is typically studied by destructive extraction of compounds from plant tissues for in vitro analyses. The methods presented here utilize the green fluorescent protein (gfp) gene for continual monitoring of gene expression in the same pieces of tissues, over time. The gfp gene was placed under regulatory control of different promoters and introduced into lima bean cotyledonary tissues via particle bombardment. Cotyledons were then placed on a robotic image collection system, which consisted of a fluorescence dissecting microscope with a digital camera and a 2-dimensional robotics platform custom-designed to allow secure attachment of culture dishes. Images were collected from cotyledonary tissues every hour for 100 hours to generate expression profiles for each promoter. Each collected series of 100 images was first subjected to manual image alignment using ImageReady to make certain that GFP-expressing foci were consistently retained within selected fields of analysis. Specific regions of the series measuring 300 x 400 pixels, were then selected for further analysis to provide GFP Intensity measurements using ImageJ software. Batch images were separated into the red, green and blue channels and GFP-expressing areas were identified using the threshold feature of ImageJ. After subtracting the background fluorescence (subtraction of gray values of non-expressing pixels from every pixel) in the respective red and green channels, GFP intensity was calculated by multiplying the mean grayscale value per pixel by the total number of GFP-expressing pixels in each channel, and then adding those values for both the red and green channels. GFP Intensity values were collected for all 100 time points to yield expression profiles. Variations in GFP expression profiles resulted from differences in factors such as promoter strength, presence of a silencing suppressor, or nature of the promoter. In addition to quantification of GFP intensity, the image series were also used to generate time-lapse animations using ImageReady. Time-lapse animations revealed that the clear majority of cells displayed a relatively rapid increase in GFP expression, followed by a slow decline. Some cells occasionally displayed a sudden loss of fluorescence, which may be associated with rapid cell death. Apparent transport of GFP across the membrane and cell wall to adjacent cells was also observed. Time lapse animations provided additional information that could not otherwise be obtained using GFP Intensity profiles or single time point image collections.

We report a method for introduction, tracking and quantitative analysis of GFP expression in plant cells. This method utilizes a custom-designed robotics system for semi-continuous image collection from large numbers of samples, over time. We also demonstrate the use of ImageJ and ImageReady for analysis of image series.

Robótica y Análisis de Imagen Dinámica de Estudios de la expresión génica en los tejidos vegetales

Gene expression in plant tissues is typically studied by destructive extraction of compounds from plant tissues for in vitro analyses. The methods ...

Using an Automated Cell Counter to Simplify Gene Expression Studies: siRNA Knockdown of IL-4 Dependent Gene Expression in Namalwa Cells

The use of siRNA mediated gene knockdown is continuing to be an important tool in studies of gene expression.  siRNA studies are being conducted not only to study the effects of downregulating single genes, but also to interrogate signaling pathways and other complex interaction networks.  These pathway analyses require both the use of relevant cellular models and methods that cause less perturbation to the cellular physiology.  Electroporation is increasingly being used as an effective way to introduce siRNA and other nucleic acids into difficult to transfect cell lines and primary cells without altering the signaling pathway under investigation. There are multiple critical steps to a successful siRNA experiment, and there are ways to simplify the work while improving the data quality at several experimental stages.  To help you get started with your siRNA mediated gene knockdown project, we will demonstrate how to perform a pathway study complete from collecting and counting the cells prior to electroporation through post transfection real-time PCR gene expression analysis.  The following study investigates the role of the transcriptional activator STAT6 in IL-4 dependent gene expression of CCL17 in a Burkitt lymphoma cell line (Namalwa).  The techniques demonstrated are useful for a wide range of siRNA-based experiments on both adherent and suspension cells.  We will also show how to streamline cell counting with the TC10 automated cell counter, how to electroporate multiple samples simultaneously using the MXcell electroporation system, and how to simultaneously assess RNA quality and quantity with the Experion automated electrophoresis system.

This procedure describes a quick and easy workflow to introduce siRNA into difficult to transfect cell lines and follow gene expression by real-time PCR. Use of an automated cell counter, multi-well electroporation plate, and automated electrophoresis station provide quick and reliable results without the need for expensive robotic handling.

El uso de un contador de células automatizado para simplificar estudios de expresión génica: siRNA Derribo de IL-4 la expresión génica en células dependientes Namalwa

The use of siRNA mediated gene knockdown is continuing to be an important tool in studies of gene expression.  siRNA studies are being conducted not only ...

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

The number of significant genetic associations with common complex traits is constantly increasing. However, most of these associations have not been understood at molecular level. One of the mechanisms mediating the effect of DNA variants on phenotypes is gene expression, which has been shown to be particularly relevant for complex traits1.
This method tests in a cellular context the effect of specific DNA sequences on gene expression. The principle is to measure the relative abundance of transcripts arising from the two alleles of a gene, analysing cells which carry one copy of the DNA sequences associated with disease (the risk variants)2,3. Therefore, the cells used for this method should meet two fundamental genotypic requirements: they have to be heterozygous both for DNA risk variants and for DNA markers, typically coding polymorphisms, which can distinguish transcripts based on their chromosomal origin (Figure 1). DNA risk variants and DNA markers do not need to have the same allele frequency but the phase (haplotypic) relationship of the genetic markers needs to be understood. It is also important to choose cell types which express the gene of interest. This protocol refers specifically to the procedure adopted to extract nucleic acids from fibroblasts but the method is equally applicable to other cells types including primary cells.
DNA and RNA are extracted from the selected cell lines and cDNA is generated. DNA and cDNA are analysed with a primer extension assay, designed to target the coding DNA markers4. The primer extension assay is carried out using the MassARRAY (Sequenom)5 platform according to the manufacturer's specifications. Primer extension products are then analysed by matrix-assisted laser desorption/ionization time of-flight mass spectrometry (MALDI-TOF/MS). Because the selected markers are heterozygous they will generate two peaks on the MS profiles. The area of each peak is proportional to the transcript abundance and can be measured with a function of the MassARRAY Typer software to generate an allelic ratio (allele 1: allele 2) calculation. The allelic ratio obtained for cDNA is normalized using that measured from genomic DNA, where the allelic ratio is expected to be 1:1 to correct for technical artifacts. Markers with a normalised allelic ratio significantly different to 1 indicate that the amount of transcript generated from the two chromosomes in the same cell is different, suggesting that the DNA variants associated with the phenotype have an effect on gene expression. Experimental controls should be used to confirm the results.

Genetic associations often remain unexplained at a functional level. This method aims to assess the effect of phenotype-associated genetic markers on gene expression by analyzing cells heterozygous for transcribed SNPs. The technology allows accurate measurement by MALDI-TOF mass spectrometry to quantify allele-specific primer extension products.

Un alelo-específicas Gene ensayo de expresión para probar la base funcional de las asociaciones genéticas

The number of significant genetic associations with common complex traits is constantly increasing. However, most of these associations have not been ...

Clonogenic Assay: Adherent Cells

The clonogenic (or colony forming) assay has been established for more than 50 years; the original paper describing the technique was published in 19561. Apart from documenting the method, the initial landmark study generated the first radiation-dose response curve for X-ray irradiated mammalian (HeLa) cells in culture1. Basically, the clonogenic assay enables an assessment of the differences in reproductive viability (capacity of cells to produce progeny; i.e. a single cell to form a colony of 50 or more cells) between control untreated cells and cells that have undergone various treatments such as exposure to ionising radiation, various chemical compounds (e.g. cytotoxic agents) or in other cases genetic manipulation. The assay has become the most widely accepted technique in radiation biology and has been widely used for evaluating the radiation sensitivity of different cell lines. Further, the clonogenic assay is commonly used for monitoring the efficacy of radiation modifying compounds and for determining the effects of cytotoxic agents and other anti-cancer therapeutics on colony forming ability, in different cell lines. A typical clonogenic survival experiment using adherent cells lines involves three distinct components, 1) treatment of the cell monolayer in tissue culture flasks, 2) preparation of single cell suspensions and plating an appropriate number of cells in petri dishes and 3) fixing and staining colonies following a relevant incubation period, which could range from 1-3 weeks, depending on the cell line. Here we demonstrate the general procedure for performing the clonogenic assay with adherent cell lines with the use of an immortalized human keratinocyte cell line (FEP-1811)2. Also, our aims are to describe common features of clonogenic assays including calculation of the plating efficiency and survival fractions after exposure of cells to radiation, and to exemplify modification of radiation-response with the use of a natural antioxidant formulation.

The applicability of the clonogenic assay for evaluating reproductive viability has been established for more than 50 years. Here we demonstrate the general procedure for performing the clonogenic assay with adherent cells.

Ensayo clonigénicas: las células adherentes

The clonogenic (or colony forming) assay has been established for more than 50 years; the original paper describing the technique was published in 19561. ...

In vitro Reconstitution of the Active T. castaneum Telomerase

Efforts to isolate the catalytic subunit of telomerase, TERT, in sufficient quantities for structural studies, have been met with limited success for more than a decade. Here, we present methods for the isolation of the recombinant Tribolium castaneum TERT (TcTERT) and the reconstitution of the active T. castaneum telomerase ribonucleoprotein (RNP) complex in vitro.
Telomerase is a specialized reverse transcriptase1 that adds short DNA repeats, called telomeres, to the 3' end of linear chromosomes2 that serve to protect them from end-to-end fusion and degradation. Following DNA replication, a short segment is lost at the end of the chromosome3 and without telomerase, cells continue dividing until eventually reaching their Hayflick Limit4. Additionally, telomerase is dormant in most somatic cells5 in adults, but is active in cancer cells6 where it promotes cell immortality7.
The minimal telomerase enzyme consists of two core components: the protein subunit (TERT), which comprises the catalytic subunit of the enzyme and an integral RNA component (TER), which contains the template TERT uses to synthesize telomeres8,9. Prior to 2008, only structures for individual telomerase domains had been solved10,11. A major breakthrough in this field came from the determination of the crystal structure of the active12, catalytic subunit of T. castaneum telomerase, TcTERT1.
Here, we present methods for producing large quantities of the active, soluble TcTERT for structural and biochemical studies, and the reconstitution of the telomerase RNP complex in vitro for telomerase activity assays. An overview of the experimental methods used is shown in Figure 1.

In vitro Reconstitution of the Active T. castaneum Telomerase

Efforts to isolate the catalytic subunit of telomerase, TERT, in sufficient quantities for structural studies, have been met with limited success for more than a decade. Here, we present methods for the isolation of the recombinant Tribolium castaneum TERT (TcTERT) and the reconstitution of the active T. castaneum telomerase ribonucleoprotein (RNP) complex in vitro.

En la reconstitución in vitro de los activos T. castaneum telomerasa

Efforts to isolate the catalytic subunit of telomerase, TERT, in sufficient quantities for structural studies, have been met with limited success for more ...

Chromatin Immunoprecipitation (ChIP) using Drosophila tissue

Epigenetics remains a rapidly developing field that studies how the chromatin state contributes to differential gene expression in distinct cell types at different developmental stages. Epigenetic regulation contributes to a broad spectrum of biological processes, including cellular differentiation during embryonic development and homeostasis in adulthood. A critical strategy in epigenetic studies is to examine how various histone modifications and chromatin factors regulate gene expression. To address this, Chromatin Immunoprecipitation (ChIP) is used widely to obtain a snapshot of the association of particular factors with DNA in the cells of interest.
ChIP technique commonly uses cultured cells as starting material, which can be obtained in abundance and homogeneity to generate reproducible data. However, there are several caveats: First, the environment to grow cells in Petri dish is different from that in vivo, thus may not reflect the endogenous chromatin state of cells in a living organism. Second, not all types of cells can be cultured ex vivo. There are only a limited number of cell lines, from which people can obtain enough material for ChIP assay.
Here we describe a method to do ChIP experiment using Drosophila tissues. The starting material is dissected tissue from a living animal, thus can accurately reflect the endogenous chromatin state. The adaptability of this method with many different types of tissue will allow researchers to address a lot more biologically relevant questions regarding epigenetic regulation in vivo1, 2. Combining this method with high-throughput sequencing (ChIP-seq) will further allow researchers to obtain an epigenomic landscape.

Chromatin Immunoprecipitation ChIP using Drosophila tissue

Recently high-throughput sequencing technology has greatly increased sensitivity of Chromatin Immunoprecipitation (ChIP) experiment and prompted its application using purified cells or dissected tissue. Here we delineate a method to use ChIP technique with Drosophila tissue, which can address the endogenous chromatin state in a well-characterized biological system.

Inmunoprecipitación de cromatina (CHIP), utilizando Drosophila Tejido

Epigenetics remains a rapidly developing field that studies how the chromatin state contributes to differential gene expression in distinct cell types at ...

Chromatin Isolation by RNA Purification (ChIRP)

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression 1,2,3,4,5,6,7. The recent discovery of thousands of lncRNAs in association with specific chromatin modification complexes, such as Polycomb Repressive Complex 2 (PRC2) that mediates histone H3 lysine 27 trimethylation (H3K27me3), suggests broad roles for numerous lncRNAs in managing chromatin states in a gene-specific fashion 8,9. While some lncRNAs are thought to work in cis on neighboring genes, other lncRNAs work in trans to regulate distantly located genes. For instance, Drosophila lncRNAs roX1 and roX2 bind numerous regions on the X chromosome of male cells, and are critical for dosage compensation 10,11. However, the exact locations of their binding sites are not known at high resolution. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide 3,12,13, but how specificity is achieved is unclear. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. The classic trans-acting RNA scaffold is the TERC RNA that serves as the template and scaffold for the telomerase complex 14; HOTAIR can also serve as a scaffold for PRC2 and a H3K4 demethylase complex 13.
Prior studies mapping RNA occupancy at chromatin have revealed substantial insights 15,16, but only at a single gene locus at a time. The occupancy sites of most lncRNAs are not known, and the roles of lncRNAs in chromatin regulation have been mostly inferred from the indirect effects of lncRNA perturbation. Just as chromatin immunoprecipitation followed by microarray or deep sequencing (ChIP-chip or ChIP-seq, respectively) has greatly improved our understanding of protein-DNA interactions on a genomic scale, here we illustrate a recently published strategy to map long RNA occupancy genome-wide at high resolution 17. This method, Chromatin Isolation by RNA Purification (ChIRP) (Figure 1), is based on affinity capture of target lncRNA:chromatin complex by tiling antisense-oligos, which then generates a map of genomic binding sites at a resolution of several hundred bases with high sensitivity and low background. ChIRP is applicable to many lncRNAs because the design of affinity-probes is straightforward given the RNA sequence and requires no knowledge of the RNA's structure or functional domains.

Chromatin Isolation by RNA Purification ChIRP

ChIRP is a novel and rapid technique to map genomic binding sites of long noncoding RNAs (lncRNAs). The method takes advantage of the specificity of anti-sense tiling oligonucleotides to allow the enumeration of lncRNA-bound genomic sites.

Aislamiento de la cromatina mediante la purificación de ARN (chirp)

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental ...

Using SecM Arrest Sequence as a Tool to Isolate Ribosome Bound Polypeptides

Extensive research has provided ample evidences suggesting that protein folding in the cell is a co-translational process1-5. However, the exact pathway that polypeptide chain follows during co-translational folding to achieve its functional form is still an enigma. In order to understand this process and to determine the exact conformation of the co-translational folding intermediates, it is essential to develop techniques that allow the isolation of RNCs carrying nascent chains of predetermined sizes to allow their further structural analysis.
SecM (secretion monitor) is a 170 amino acid E. coli protein that regulates expression of the downstream SecA (secretion driving) ATPase in the secM-secA operon6. Nakatogawa and Ito originally found that a 17 amino acid long sequence (150-FSTPVWISQAQGIRAGP-166) in the C-terminal region of the SecM protein is sufficient and necessary to cause stalling of SecM elongation at Gly165, thereby producing peptidyl-glycyl-tRNA stably bound to the ribosomal P-site7-9. More importantly, it was found that this 17 amino acid long sequence can be fused to the C-terminus of virtually any full-length and/or truncated protein thus allowing the production of RNCs carrying nascent chains of predetermined sizes7. Thus, when fused or inserted into the target protein, SecM stalling sequence produces arrest of the polypeptide chain elongation and generates stable RNCs both in vivo in E. coli cells and in vitro in a cell-free system. Sucrose gradient centrifugation is further utilized to isolate RNCs.
The isolated RNCs can be used to analyze structural and functional features of the co-translational folding intermediates. Recently, this technique has been successfully used to gain insights into the structure of several ribosome bound nascent chains10,11. Here we describe the isolation of bovine Gamma-B Crystallin RNCs fused to SecM and generated in an in vitro translation system.

We describe here a technique that is now routinely used to isolate stably bound ribosome nascent chain complexes (RNCs). This technique takes advantage of the discovery that a 17 amino acid long SecM "arrest sequence" can halt translation elongation in a prokaryotic (E. coli) system, when inserted into (or fused to the C-terminus) of virtually any protein.

Usar secuencias de detención SecM como una herramienta para aislar Ribosome polipéptidos enlazados

Extensive research has provided ample evidences suggesting that protein folding in the cell is a co-translational process1-5. However, the exact pathway ...