Name: adapting 3' rapid amplification of cdna ends to map transcripts in cancer
Uploaded: 2018-03-28T15:00:00
Description: Watch this Scientific Journal Video about Adapting 3' Rapid Amplification of CDNA Ends to Map Transcripts in Cancer at JoVE.com

Nos gustaría reconocer a Bettine Gibbs por su ayuda técnica.

Usar una bata de laboratorio, guantes y gafas de seguridad en todo momento mientras se realizan todos los procedimientos en el presente Protocolo. Asegúrese de que envases y tubos que contienen el reactivo de fenol y guanidina isotiocianato sólo se abren en una capilla certificada y disponer de los residuos de fenol en un contenedor designado. Utilizar reactivos, puntas y tubos estériles libre de DNasa/Rnasa.
1. cultivo celular
<ol><li>Crecer la línea celular HeLa y dos suspensión manto...

<ol>
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W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+amplification+of+3&#8242;+cDNA+ends+(3&#8242;-RACE).">Rapid amplification of 3&#8242; cDNA ends (3&#8242;-RACE).</a> Cold Spring Harb Protoc. 2006 (1), (2006).</li><li>Masamha, C. 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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+amplification+of+cDNA+ends.">Rapid amplification of cDNA ends.</a> PCR Cloning Protocols: Methods in Molecular Biology. 67, 233-238 (1997).</li><li>Freeman, L. A., Freeman, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cloning+full-length+transcripts+and+transcript+variants+using+5'+and+3'+RACE.">Cloning full-length transcripts and transcript variants using 5' and 3' RACE.</a> Lipoproteins and Cardiovascular Disease: Methods in Molecular Biology (Methods and Protocols). 1027, 3-17 (2013).</li><li>Masamha, C. P., Albrecht, T. R., Wagner, E. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Discovery+and+characterization+of+a+novel+CCND1/MRCK+gene+fusion+in+mantle+cell+lymphoma.">Discovery and characterization of a novel CCND1/MRCK gene fusion in mantle cell lymphoma.</a> J Hematol Oncol. 9 (1), 1-5 (2016).</li><li>Parker, B. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+tumorigenic+FGFR3-TACC3+gene+fusion+escapes+miR-99a+regulation+in+glioblastoma.">The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma.</a> J Clin Investig. 123 (2), 855-865 (2013).</li><li>Prakash, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+of+conjoined+genes:+Another+mechanism+for+gene+regulation+in+eukaryotes.">Expression of conjoined genes: Another mechanism for gene regulation in eukaryotes.</a> PLOS ONE. 5 (10), e13284 (2010).</li><li>Mertens, F., Johansson, B., Fioretos, T., Mitelman, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+emerging+complexity+of+gene+fusions+in+cancer.">The emerging complexity of gene fusions in cancer.</a> Nat Rev Cancer. 15 (6), 371-381 (2015).</li><li>Mayr, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolution+and+biological+roles+of+alternative+3'UTRs.">Evolution and biological roles of alternative 3'UTRs.</a> Trends Cell Biol. 26 (3), 227-237 (2016).</li><li>International Committee For Standardization In, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protocol+for+evaluation+of+automated+blood+cell+counters.">Protocol for evaluation of automated blood cell counters.</a> Clin Lab Haematol. 6 (1), 69-84 (1984).</li><li>Desjardins, P., Conklin, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NanoDrop+microvolume+quantitation+of+nucleic+acids.">NanoDrop microvolume quantitation of nucleic acids.</a> J Vis Exp. (45), e2565 (2010).</li><li>Lorenz, T. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polymerase+chain+reaction:+Basic+protocol+plus+troubleshooting+and+optimization+strategies.">Polymerase chain reaction: Basic protocol plus troubleshooting and optimization strategies.</a> J Vis Exp. (63), e3998 (2012).</li><li>Lee, P. Y., Costumbrado, J., Hsu, C. -. Y., Kim, Y. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Agarose+gel+electrophoresis+for+the+separation+of+DNA+fragments.">Agarose gel electrophoresis for the separation of DNA fragments.</a> J Vis Exp. (62), e3923 (2012).</li><li>Curtis, P. C., Thomas, J. L., Phillips, N. R., Roby, R. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+of+primer+specific+filter+metrics+for+the+assessment+of+mitochondrial+DNA+sequence+data.">Optimization of primer specific filter metrics for the assessment of mitochondrial DNA sequence data.</a> Mitochondrial DNA. 21 (6), 191-197 (2010).</li><li>Letowski, J., Brousseau, R., Masson, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Designing+better+probes:+Effect+of+probe+size,+mismatch+position+and+number+on+hybridization+in+DNA+oligonucleotide+microarrays.">Designing better probes: Effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays.</a> J Microbiol Methods. 57 (2), 269-278 (2004).</li><li>Lefever, S., Pattyn, F., Hellemans, J., Vandesompele, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-nucleotide+polymorphisms+and+other+mismatches+reduce+performance+of+quantitative+PCR+assays.">Single-nucleotide polymorphisms and other mismatches reduce performance of quantitative PCR assays.</a> Clin Chem. 59 (10), 1470-1480 (2013).</li><li>Singh, V. K., Govindarajan, R., Naik, S., Kumar, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+effect+of+hairpin+structure+on+PCR+amplification+efficiency.">The effect of hairpin structure on PCR amplification efficiency.</a> Mol Biol Today. 1, 67-69 (2000).</li><li>Kalle, E., Kubista, M., Rensing, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multi-template+polymerase+chain+reaction.">Multi-template polymerase chain reaction.</a> Biomol Detect Quant. 2, 11-29 (2014).</li><li>Stransky, N., Cerami, E., Schalm, S., Kim, J. L., Lengauer, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+landscape+of+kinase+fusions+in+cancer.">The landscape of kinase fusions in cancer.</a> Nat Commun. 5, 4846 (2014).</li></ol>

A pesar del advenimiento de las tecnologías de secuenciación masiva en paralelo, sobre una base de gen por gen, 3' carrera sigue siendo el método más fácil y más económico para identificar la PAS y nucleótidos adyacentes a la cola de poly(A). La adaptación descrita aquí expande utilizando 3' carrera a amplificar tanto mapa secuencias que incluyen una porción del ORF, el codón de parada y el entero 3' UTR de la transcripción del mRNA de ANKHD1 . Una ventaja de 3' RACE es que con algunas adaptaciones ...

La formación del extremo 3' es un paso crítico en la maduración del ARNm que comprende el clivaje del pre-mRNA aguas abajo de un paso seguido por la adición de 250 untemplated adenines, que forman parte de la cola de poly(A)1,2. La proteína poly(A) (PABP) se une a la cola de poly(A), y este protege la transcripción del mRNA de la degradación y facilita la traducción1.
Las estimaciones actuales sugieren que el 70% de genes humanos tiene PASs múltiples y así experimentar la poliadenilación alternativa, resultando en múltiples 3' extremos3. Por lo tanto, es importante identificar donde la cola de poly(A) se fija al resto de los 3' UTR, así como identificar el PAS utilizado por cualquier transcripción dada. El advenimiento de la secuenciación de próxima generación ha dado como resultado la identificación simultánea de 3' UTRs y el paso de miles de genes. Este aumento en la capacidad de secuenciación ha requerido el desarrollo de algoritmos bioinformáticos para analizar los datos que implica alternativa poliadenilación del extremo 3'. Para la detección de novo o validación del PAS y por lo tanto, mapeo del extremo 3' de los genes individuales de datos de secuenciación a gran escala, 3' carrera sigue siendo el método de elección4,5. Las secuencias incluidas en productos de cDNA de 3' raza normalmente incluyen sólo una parte de los 3' UTR que contiene la cola de poly(A), el sitio de la hendidura, el PAS y las secuencias aguas arriba del PAS. A diferencia de la polimerización en cadena, que requiere el diseño y uso de iniciadores específicos de avance y retroceso de gen, 3' RACE sólo requiere iniciadores adelante anidados específicos de dos genes. Por lo tanto, la PCR requiere un conocimiento más detallado de la secuencia de nucleótidos de una región grande del gen está amplificado4,6. 3' carrera utiliza el mismo invertir cartilla que metas la poly(A) de la cola para todos contra RNA transcripciones, sólo los iniciadores hacia adelantados tienen que ser gene específico, así, que solo requieren conocimiento de una región significativamente menor del mRNA. Esto permite la amplificación de regiones cuyas secuencias no están completamente caracterizadas4,7. Esto ha permitido 3' carrera a utilizarse no sólo para determinar el extremo 3' de un gen, sino para también determinar y caracterizar grandes regiones corriente arriba del PAS que forman una parte importante de los 3' UTR. Al combinar la carrera con el modificado 3' carrera que incluye grandes porciones de 3' UTR y regiones flanqueantes 5', es posible totalmente la secuencia o clonar una toda transcripción de mRNA del extremo 5' a sus 3' extremo8.
Un ejemplo de esta aplicación del modificado 3' RACE es la reciente identificación de una novela CCND1 MRCK transcripción del gene de fusión de líneas de células del manto linfoma y pacientes con cáncer. El 3' UTR consistió en secuencias de genes CCND1 y de MRCK y era recalcitrante a miRNA Reglamento9. Los dos anidados CCND1 específicos hacia adelante fueron complementarias a la región inmediatamente adyacente y aguas abajo del codón de parada CCND1 . Aunque transcriptoma toda la secuencia junto con herramientas bioinformáticas específico se puede utilizar para detectar fusiones de genes dentro de los 3' UTR10, muchos laboratorios pueden carecer los recursos financieros o conocimientos de bioinformática para hacer uso de esta tecnología. Por lo tanto, 3' RACE es una alternativa para novo de identificación y validación de genes de fusión novedosa que implica el 3' UTR. Teniendo en cuenta el drástico aumento del número de genes de fusión reportado como Lee las transcripciones, 3' RACE se ha convertido en una poderosa herramienta en la caracterización de secuencias de genes11,12. Además, estudios recientes han demostrado que diferentes secuencias dentro de los 3' UTR como la longitud de los 3' UTR puede afectar estabilidad transcripción ARNm, localización, traducción y función13. Debido en parte a un creciente interés en la cartografía el transcriptoma, ha habido un aumento en el número de diferentes polimerasas de la DNA ser desarrollado para su uso en el laboratorio. Es importante determinar qué tipos de modificaciones pueden hacerse a los 3' protocolo de la raza en el fin de utilizar el repertorio disponible de polimerasas de la DNA.
Este trabajo informes de adaptación de raza para asignar los enteros 3' UTR 3', el PAS y el 3' final sitio de la hendidura de la transcripción de ANKHD1 utilizando anidados primers dentro de la sección ANKHD1 de la transcripción y dos diferentes polimerasas de la DNA.

<table>
	<tbody>
		<tr>
			<td>HeLa cells</td>
			<td>ATCC</td>
			<td>CCL-2</td>
			<td>Cervical cancer cell line.</td>
		</tr>
		<tr>
			<td>Jeko-1 cells</td>
			<td>ATCC</td>
			<td>CRL-3006</td>
			<td>Mantle cell lymphoma cell line.</td>
		</tr>
		<tr>
			<td>Granta-519 cells</td>
			<td>DSMZ</td>
			<td>ACC-342</td>
			<td>Mantle cell lymphoma cell line.</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Sigma Aldrich</td>
			<td>F6178</td>
			<td>Fetal bovine serum for cell culture.</td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin</td>
			<td>ThermoFisherScientific</td>
			<td>15140122</td>
			<td>Antibiotic and antimycotic.</td>
		</tr>
		<tr>
			<td>GlycoBlue</td>
			<td>Ambion</td>
			<td>AM9545</td>
			<td>Coprecipitant.</td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>ThermoFisherScientific</td>
			<td>10569044</td>
			<td>Gibco brand cell culture media with GlutaMAX.</td>
		</tr>
		<tr>
			<td>Nuclease Free-Water</td>
			<td>ThermoFisherScientific</td>
			<td>AM9938</td>
			<td>Ambion DNase and RNAse free water(non DEPC treated).</td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s Phosphate-Buffered Solution</td>
			<td>Corning</td>
			<td>21-030</td>
			<td>1X PBS.</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Sigma&#160; Aldrich</td>
			<td>C7559-5VL</td>
			<td></td>
		</tr>
		<tr>
			<td>2-propanol</td>
			<td>Sigma Aldrich</td>
			<td>I9516</td>
			<td></td>
		</tr>
		<tr>
			<td>Reagent Alcohol</td>
			<td>Sigma Aldrich</td>
			<td>793175</td>
			<td>Ethanol</td>
		</tr>
		<tr>
			<td>Ethidium Bromide solution</td>
			<td>Sigma Aldrich</td>
			<td>E1510</td>
			<td></td>
		</tr>
		<tr>
			<td>TRIzol Reagent</td>
			<td>ThermoFisherScientific</td>
			<td>15596026</td>
			<td>Monophasic phenol and guanidine isothiocyanate reagent.</td>
		</tr>
		<tr>
			<td>2X Extender PCR-to-Gel Master Mix</td>
			<td>Amresco</td>
			<td>N867</td>
			<td>2X PCR-to-Gel Master Mix&#160; containing loading dye used in routine quick PCR assays and primer search.</td>
		</tr>
		<tr>
			<td>10mM dNTP</td>
			<td>Amresco</td>
			<td>N557</td>
			<td></td>
		</tr>
		<tr>
			<td>RQ1 RNase-Free DNase</td>
			<td>Promega</td>
			<td>M6101</td>
			<td>Dnase treatment kit.</td>
		</tr>
		<tr>
			<td>Gel Loading Dye Orange (6X)</td>
			<td>New England BioLabs</td>
			<td>B7022S</td>
			<td></td>
		</tr>
		<tr>
			<td>2X Phusion High-Fidelity PCR Master Mix with HF buffer</td>
			<td>ThermoFisherScientific</td>
			<td>F531S</td>
			<td>2X PCR MasterMix containing a chimeric DNA polymerase consisting of a DNA binding domain fused to a Pyrococcus-like proofreading polymerase and other reagents.</td>
		</tr>
		<tr>
			<td>PfuUltra II Fusion HS DNA polymerase</td>
			<td>Agilent Technologies</td>
			<td>600670</td>
			<td>Modified DNA Polymerase from Pyrococcus furiosus (Pfu).</td>
		</tr>
		<tr>
			<td>RevertAid RT Reverse Transcription Kit</td>
			<td>Thermo Fischer</td>
			<td>K1691</td>
			<td>Used for&#160; reverse transcription of mRNA into&#160; cDNA synthesis. Kit includes&#160; Ribolock RNAse inhibitor, RevertAid M-MuLV reverse transcriptase and other reagents listed in manuscript.</td>
		</tr>
		<tr>
			<td>Pefect size 1Kb ladder</td>
			<td>5 Prime</td>
			<td>2500360</td>
			<td>Molecular weight DNA ladder.</td>
		</tr>
		<tr>
			<td>Alpha Innotech FluorChem Q MultiImage III</td>
			<td>Alpha Innotech</td>
			<td></td>
			<td>Used to visualise ethidium bromide stained agarose gel.</td>
		</tr>
		<tr>
			<td>Low Molecular Weight Ladder</td>
			<td>New England BioLabs</td>
			<td>N3233L</td>
			<td>Molecular weight DNA ladder.</td>
		</tr>
		<tr>
			<td>Vortex Mixer</td>
			<td>MidSci</td>
			<td>VM-3200</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini Centrifuge</td>
			<td>MidSci</td>
			<td>C1008-R</td>
			<td></td>
		</tr>
		<tr>
			<td>Dry Bath</td>
			<td>MidSci</td>
			<td>DB-D1</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoDrop 2000C</td>
			<td>ThermoFisherScientific</td>
			<td>ND-2000C</td>
			<td>Spectrophotometer.</td>
		</tr>
		<tr>
			<td>Wide Mini-Sub&#160;Cell GT Horizontal Electrophoresis System</td>
			<td>BioRad</td>
			<td>1704469</td>
			<td>Electrophoresis equipment-apparatus to set up gel</td>
		</tr>
		<tr>
			<td>PowerPac Basic Power Supply</td>
			<td>BioRad</td>
			<td>1645050</td>
			<td>Power supply for gel electrophoresis.</td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Dot Scientific</td>
			<td>AGLE-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Mastercycler Gradient</td>
			<td>Eppendorf</td>
			<td>950000015</td>
			<td>PCR thermocycler.</td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Eppendorf</td>
			<td>5810 R</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Eppendorf</td>
			<td>5430R</td>
			<td></td>
		</tr>
		<tr>
			<td>Wizard SV Gel and PCR Fragment DNA Clean-Up System</td>
			<td>Promega</td>
			<td>A9281</td>
			<td></td>
		</tr>
		<tr>
			<td>Zero Blunt TOPO PCR Cloning Kit, with One Shot&#160; TOP10 Chemically Competent E. coli cells</td>
			<td>ThermoFisherScientific</td>
			<td>K280020</td>
			<td></td>
		</tr>
		<tr>
			<td>MyPCR Preparation Station Mystaire</td>
			<td>MidSci</td>
			<td>MY-PCR24</td>
			<td>Hood dedicated to PCR work.</td>
		</tr>
		<tr>
			<td>Hamilton SafeAire II fume hood</td>
			<td>ThermoFisherScientific</td>
			<td></td>
			<td>Fume hood.</td>
		</tr>
		<tr>
			<td>Beckman Coulter Z1&#160;Particle&#160;Counter</td>
			<td>Beckman Coulter</td>
			<td>6605698</td>
			<td>Particle counter. For counting cells before plating&#160; for RNA extraction.</td>
		</tr>
		<tr>
			<td>Applied Biosystems Sequence Scanner Software v2.0</td>
			<td>Applied Biosystems (through ThermoFisherScientific)</td>
			<td></td>
			<td>Software to analyze Sanger sequencing data.</td>
		</tr>
	</tbody>
</table>

adapting 3' rapid amplification of cdna ends to map transcripts in cancer

Maduración de los mRNAs eucarióticos consiste en 3' final de formación, que consiste en la adición de una cola de poly(A). Para asignar el extremo 3' de un gen, el método tradicional de elección es 3' amplificación rápida del cDNA extremos (3' RACE). Protocolos para 3' raza requieren el cuidado diseño y selección de primers anidados dentro de la región 3' no traducida (3' UTR) del gen Diana de interés. Sin embargo, con algunas modificaciones, el protocolo puede utilizarse para incluir el entero 3' UTR y secuencias dentro del marco de lectura abierto (ORF), proporcionando una visión más comprensiva de la relación entre el ORF y el 3' UTR. Se trata además de identificación de la señal de poliadenilación (PAS), así como el escote y poliadenilación sitio provisto por convencional 3' RACE. Ampliado 3' RACE puede detectar inusual 3' UTRs, incluyendo fusiones de genes dentro de los 3' UTR, y la información de secuencia puede utilizarse para predecir potenciales sitios de unión de miRNA como AU rica desestabilizar elementos que puedan afectar la estabilidad de la transcripción.

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El gel de agarosa de La figura 1 muestra dos distintas gel productos de la PCR (carriles 1 y 2) que utilizan la misma adelante cartilla pero diferentes primers inversas. Carril 3 tiene un producto PCR distinto y distinto primer avance y retroceso. Los iniciadores ideal a utilizar para la reacción de PCR basado en son los que dan un producto PCR diferen...

Watch this Scientific Journal Video about Adapting 3' Rapid Amplification of CDNA Ends to Map Transcripts in Cancer at JoVE.com

Adapting 3' Rapid Amplification of CDNA Ends to Map Transcripts in Cancer

Adaptación de 3' amplificación rápida del CDNA termina para asignar las transcripciones en el cáncer

La dos diferentes 3' amplificación rápida del cDNA extremos (3' RACE) protocolos descrito aquí hacen uso de dos diferentes polimerasas de la DNA para asignar las secuencias que incluyen un segmento del marco de lectura abierto (ORF), el codón de parada y el entero 3' UTR de una transcripción utilizando RNA obtenidos de líneas celulares de cáncer diferentes.

Maturation of eukaryotic mRNAs involves 3&#39; end formation, which involves the addition of a poly(A) tail. In order to map the 3&#39; end of a gene, the ...

The overall goal of this procedure is to determine the sequences of mRNA transcripts from the three-prime end to regions within the protein coding region by using transcript-specific nested primers in two subsequent PCRs and sequencing the purified PCR products. This method can help answer key questions in the genetic field, such as determining the polyadenylation signal, the stop codon, and the sequence of the three-prime untranslated region of the transcript. The main advantage of this technique is that it can be applied to any transcript if the sequence of the small region of the open reading frame is The implication of this technique extend toward cancer diagnosis, because it can detect tumor specific fusion genes and splice variants.We first had the idea for this method when we identified novel transcripts with previously uncharacterized, three-primed untranslated regions. To begin the protocol, thaw the phenol and guanidine isothiocyanate cell mixture on ice. Once thawed, add 100 microliters of chloroform to the microcentrifuge tube in a PCR hood.Vortex the sample for 10 to 15 seconds until the mixture is pink and opaque. Next, incubate the sample on ice for 15 minutes. After incubation, centrifuge the sample for 15 minutes at 20, 800 g and four degrees Celsius.Carefully remove the upper colorless aqueous phase and transfer it to a new 1.5 milliliter microcentrifuge tube. Then, move on to precipitation and add an equal volume of isopropanol to the sample. Add one microliter of co-precipitant to the sample to act as a carrier for the RNA and to help visualize the RNA in subsequent steps.Incubate the samples at 80 degrees Celsius for at least four hours. After incubation, transfer the sample to a cooled centrifuge and spin for 35 minutes at 20, 800 g and four degrees Celsius. After the spin, the RNA will appear as a blue spec on the bottom of the tube.Carefully remove the isopropanol from the sample. Add 500 microliters of 80%ethanol and resuspend the pellet by briefly vortexing for three seconds. Centrifuge the sample again.Remove all the ethanol from the sample and let the sample air dry for about 10 minutes. Once the sample is dry, resuspend it in 35 microliters of RNase-free water. Then, place the sample on a heat block.Set at 65 degrees Celsius for five minutes to ensure that the RNA is fully in solution. After heating, immediately place the tube on ice. For a final reaction volume of 50 microliters, add four micrograms of total RNA with added water to a total volume of 22 microliters to a new tube.Add two microliters of the Oligo dT 25 primer from the 10 micromolar primer solution. From the reverse transcription kit, add two microliters of the RNase inhibitor, eight microliters of the 5x reaction buffer, four microliters of 10 millimolar dNTPs, and two microliters of the reverse transcriptase. Set up a reaction without reverse transcriptase to act as a negative control.Incubate the tube at 42 degrees Celsius for one hour. After incubation, transfer the tube directly to ice before transporting it to the heating block. Then, heat the tube at 75 degrees Celsius for five minutes.After heating it 75 degrees Celsius, place the tube on ice. Transfer two microliters of the cDNA to a fresh 0.5 milliliter PCR tube. Add one microliter of the forward primer and one microliter of the reverse primer from a 10 millimolar primer solution.Make up to 12.5 microliters by adding 8.5 microliters of nuclease-free water and add 12.5 microliters of the 2x PCR to gel master mix. Then, enter the PCR thermal cycling conditions listed on the screen and run the PCR. After the PCR, prepare a 1%agarose gel stained with ethidium bromide.Dissolve one gram of agarose in 100 milliliters of triacetate or TAE buffer in a 250 milliliter flask. Boil the contents in a microwave. Allow the gel to cool for one minute, and add 7.5 microliters of ethidium bromide solution in a fume hood.Mix well by swirling the flask. Pour the contents into a horizontal gel apparatus and allow the gel to solidify at room temperature in the fume hood for at least 30 minutes. Cover the gel with 1x TAE buffer and load 10 microliters of the PCR product onto the agarose gel together with three to five microliters of the DNA molecular weight ladder.Run the gel at 175 volts for 10 minutes. For the first PCR, transfer one microliter of cDNA to a PCR tube and add five microliters of 10x Pfu reaction buffer. Add one microliter of the first nested forward primer, one microliter of the T7 Oligo dT 25 primer, and one microliter of dNTPs from a 10 millimolar solution.Make up to 49 microliters of total volume by adding 40 microliters of water. Add one microliter of Pfu DNA polymerase and mix well. Then, run the PCR.Next, prepare the second PCR. Transfer two microliters of the products from the first PCR to a new PCR tube and mix it with five microliters of 10x Pfu ultra two reaction buffer. Add one microliter of the second nested PCR primer, one microliter of the T7 primer and one microliter of dNTPs.Make up to 49 microliters total reaction volume by adding 39 microliters of water and add one microliter of Pfu DNA polymerase. Run the PCR using the same PCR profile as the first PCR set up. Alternatively, instead of using Pfu DNA polymerase, a chimeric DNA polymerase can be used in the two different PCRs.Take five to ten microliters of the second PCR product and run it on an agarose gel. Finally, visualize the result on an imager. This agarose gel shows two distinct PCR products which use the same forward primer but different reverse primers and a distinct PCR product that has a distinct forward and reverse primer.The ideal primers to use for the PCR based reaction are those that give one distinct PCR product. Products from the second PCR reaction with Pfu DNA polymerase and chimeric DNA polymerase produced the same sized PCR products despite having different PCR cycling conditions for the three-prime RACE. The reverse transcriptase negative controls showed no genomic contamination of the RNA used in cDNA synthesis as well as in subsequent downstream reactions.Gel-purified PCR products were sent for sequencing. A representative Sanger sequence from a sequence chromatogram identified the location of the stop codon, putative polyadenylation signal and the site as well as the poly A tail in the three-prime RACE product. While attempting this procedure, it's important to remember to wear protective gear and gloves at all time.In addition, use sterile DNase and RNase for your reagents tubes and other disposables. Don't forget that working with phenol and chloroform can be extremely hazardous. And precautions such as using the reagents in a hood and disposing material in a designated waste container should always be taken while performing this procedure.

Research

JoVE Journal

Genetics

Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts

La fusión absoluta y relativa de datos de PCR cuantitativa para cuantificar STAT3 variante de empalme transcripciones

Human signal transducer and activator of transcription 3 (STAT3) is one of many genes containing a tandem splicing site. Alternative donor splice sites 3 ...

Investigación

Genética

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

Alta resolución fluorescente In Situ hibridación en embriones de Drosophila y tejidos utilizando amplificación de la señal de Tyramide

In our efforts to determine the patterns of expression and subcellular localization of Drosophila RNAs on a genome-wide basis, and in a variety of ...

CRISPR-Mediated Reorganization of Chromatin Loop Structure

Mediada por CRISPR reorganización de la estructura de bucles de cromatina

Recent studies have clearly shown that long-range, three-dimensional chromatin looping interactions play a significant role in the regulation of gene ...

A Murine Cell Line Based Model of Chronic CDK9 Inhibition to Study Widespread Non-Genetic Transcriptional Elongation Defects (TEdeff) in Cancers

A Murine Cell Line Based Model of Chronic CDK9 Inhibition to Study Widespread Non-Genetic Transcriptional Elongation Defects TEdeff in Cancers

Un modelo basado en la línea celular murina de la inhibición crónica de CDK9 para estudiar defectos de alargamiento transcripcional no genéticos generalizados (TEdefinitivamente)en cánceres

We have previously reported that a subset of cancers is defined by global transcriptional deregulations with widespread deficiencies in mRNA transcription ...

Discrimintion and Mapping of the Primary and Processed Transcripts in Maize Mitochondrion Using a Circular RT-PCR-based Strategy

Discriminción y mapeo de las transcripciones primarias y procesadas en mitocondrion de maíz utilizando una estrategia circular basada en RT-PCR

In plant mitochondria, some steady-state transcripts have 5&#39; triphosphate derived from transcription initiation (primary transcripts), while the ...

Investigation of the Transcriptional Role of a RUNX1 Intronic Silencer by CRISPR/Cas9 Ribonucleoprotein in Acute Myeloid Leukemia Cells

Investigation of the Transcriptional Role of a RUNX1 Intronic Silencer by CRISPR/Cas9 Ribonucleoprotein in Acute Myeloid Leukemia Cells

Investigación del papel transcripcional de un silenciador intrónico RUNX1 por RIBonucleoprotein CRISPR/Cas9 en células de leucemia mieloide aguda

The bulk of the human genome (~98%) is comprised of non-coding sequences. Cis-regulatory elements (CREs) are non-coding DNA sequences that contain binding ...

Detection of Human Immunodeficiency Virus Type 1 (HIV-1) Antisense Protein (ASP) RNA Transcripts in Patients by Strand-Specific RT-PCR

Detection of Human Immunodeficiency Virus Type 1 HIV-1 Antisense Protein ASP RNA Transcripts in Patients by Strand-Specific RT-PCR

Detección de transcripciones de ARN de proteína antisentido (VIH-1) de proteína antisentido (VIH-1) en pacientes por RT-PCR específico de Hebra

In retroviruses, antisense transcription has been described in both human immunodeficiency virus type 1 (HIV-1) and human T-lymphotropic virus 1 (HTLV-1). ...

Efficient Transcriptionally Controlled Plasmid Expression System for Investigation of the Stability of mRNA Transcripts in Primary Alveolar Epithelial Cells

Sistema eficiente de expresión de plásmido controlado por transcripción para la investigación de la estabilidad de las transcripciones de ARNm en células epiteliales alveolares primarias

Studying posttranscriptional regulation is fundamental to understanding the modulation of a given messenger RNA (mRNA) and its impact on cell homeostasis ...

Screening Sperm for the Rapid Isolation of Germline Edits in Zebrafish

Detección de espermatozoides para el aislamiento rápido de ediciones de la línea germinal en el pez cebra

The advent of targeted CRISPR-Cas nuclease technologies has revolutionized the ability to perform precise genome editing in both established and emerging ...