Agradecemos a John Darga do MGH DNA do núcleo para a preparação da biblioteca triagem DNA. Christopher Chigas de Perkin Elmer forneceu apoio inestimável para o nosso Wallac 1420 luminometer. Steven Ciacco e Martin Thomae de Agilent forneceu apoio para o robô Bravo. Agradecemos a Ron Johnson e Steve Tito no NIH para generosamente fornecer seu protocolo de ensaio de luciferase dual-brilho.

Para uma visão geral experimental, ver Figura 1. 1. Prepare plasmídeos repórter contendo a alfa-sinucleína Promotor Os elementos reguladores do gene da alfa-sinucleína (Figura 2) abranger cerca de 10 kb, a montante do PNS (A-beta não componente de peptídeo amilóide) dinucleótido sequência de repetição de 1,2 através de intrão 2 3. Nós incluem uma porção dessa região nossa construção repórter. Descobrimos que plasmídeos contendo intron 2 necessários procedimentos especiais para o crescimento, como descrito abaixo. Os plasmídeos de luciferase, e pGL4.10 pGL4.75 (Figura 3), encontram-se comercialmente disponíveis a partir de Promega e podem ser propagadas por meio de protocolos de biologia molecular convencionais. <ol><li> Amplificar os dois componentes do promotor de alfa-sinucleína em PCR separadas utilizando a receita na Tabela 1 e os iniciadores na Tabela 2. </li><li> Verify produtos de PCR sobre um gel de agarose e limpos utilizando o kit de purificação PCR QIAquick (Qiagen), eluindo-se em 50 ul de TE (Tris-EDTA). Armazenar o eluído fragmento 0,9 kb a -20 ° C para uso futuro. </li><li> Digerir o volume total de 3,4 kb do fragmento de PCR, assim como 5 ug de pGL4.10, com Saci e Xhol. Tratar o vector com fosfatase alcalina de intestino de vitelo (Roche) e purificar em gel utilizando o kit de PureLink rápida Gel Extraction (Invitrogen). </li><li> Ligar o fragmento e o vector utilizando ADN-ligase de T4 (NEB). Limpar a reacção concluída, utilizando o kit de PCR PureLink Micro (Invitrogen), eluindo-se em 10 ul de tampão TE. </li><li> Transformar 2 ul do limpa, reacção de ligação em 20 ul de células competentes Electromax Stbl4 (Invitrogen) e electroporate acordo com as instruções do fabricante. Agitar em um de 30 ° C numa estufa a 225 rpm durante 90 min. Espalhe 2 volumes em placas de LB contendo 100 mg / ml de ampicilina e incubar a 30 ° C durante 2 dias. </li><li> Usando um palito, selecione 4-6 pequenas colônias para inoculação em 2 ml de TB (Terrific Broth). Crescer estas culturas miniprep num agitador de 30 ° C O / N. </li><li> Purifica-se o DNA de plasmídeo a partir de 1,5 ml de cada cultura utilizando o kit miniprep PureLink HiPure plasmídeo Miniprep (Invitrogen). </li><li> Digerir as minipreps com BamHI e electroforese em gel de agarose. O clone correta deve produzir fragmentos de 2,8 kb e 4,9 kb. </li><li> Restreak a cultura restante de miniprep a partir do clone correcto em LB (Luria Broth) placa fresca e crescer a 30 ° C durante 2 dias. </li><li> Selecione uma pequena colônia e inocular uma cultura inicial de 1,5 ml TB. Agite O / N a 30 ° C. Não deixe que a cultura inicial crescer a saturação. </li><li> Diluir toda a cultura de arranque em 150 ml de TB pré-aquecido e agitar a 30 ° C por 2 dias. Antes de prosseguir para o próximo passo, utilizar de 1,5 ml desta cultura para uma digestão adicional e miniprep para confirmar que o clone não se transformam durante replicati<html> na. </li><li> Purifica-se o DNA de plasmídeo a partir da cultura restante, utilizando o kit Plasmid Maxiprep PureLink HiPure (Invitrogen). Rendimentos esperados deste plasmídeo intermediário são 50-150 mg por 150 ml de cultura. </li><li> Descongelar o fragmento de 0,9 kb congeladas na etapa 1.2. Repetir Passos 1,3-1,12 para clonar o fragmento de 0,9 kb no plasmídeo intermediário, digerindo vez com Kpnl e Saci. Ligadura, transformar, selecionar e crescer para maxipreps como acima. A digestão com BamHI deve originar fragmentos de 5,8 kb e 2,8 kb. Este é o plasmídeo que será utilizado para a tela. </li></ol> 2. Prepare células 293T, Repórter Plasmids e DNA Biblioteca de Triagem As células 293T foram semeadas em primeiro lugar em placas de 96 cavidades e foram transfectadas no dia seguinte. Os plasmídeos repórteres e ADN de biblioteca são diluídos em placas de 96 poços. Obtivemos placas de biblioteca de DNA transfecção-grade a partir do DNA do núcleo no Massachusetts General Hospital (obter = &quot;_blank&quot;&gt; dnacore.mgh.harvard.edu). Este protocolo transfects uma única chapa de biblioteca em duas placas idênticas de células 293T (Figura 1), assim, duas placas de células deveriam ser semeadas por cada placa de biblioteca a ser rastreada. Nota: Cresça as células em meio sem vermelho de fenol ou antibióticos, uma vez que estes interferem com os ensaios de luciferase e aumentar a toxicidade durante a transfecção, respectivamente. <ol><li> Para cada placa de biblioteca a ser rastreada, ressuspender as células 293T com tripsina a uma concentração de 1,5 x 10 5 células / ml em DMEM contendo 14% de FBS. Despeje em um reservatório estéril (Axygen). </li><li> Coloque o reservatório, 2 de fundo claro, placas de 96 poços (Corning), e uma caixa de filtro de pontas de pipeta (Agilent) sobre o convés do robô. Pipetar 100 ul de células em cada poço de ambas as placas, para uma densidade de 1,5 x 10 4 culas por po. </li><li> Centrifugar as placas de celulares a 50 xg por 2 min, usando baixas velocidades de rampa para garantir a igualdadedensidade celular ao longo de cada poço. Incubar a 37 ° C e 10% de CO 2 S / N. </li><li> Diluir o pirilampo e Renilla plasmídeos repórter a 5 ng / mL em meio isento de soro. Combina-se as diluições em uma proporção de 05:03 de pirilampo para Renilla plasmídeo (em volume) em um tubo de 15 ml. </li><li> Pipeta os plasmídeos combinadas em cada poço de uma placa de 96 poços, a dosificação de 17 ul por placa biblioteca, mais excesso de 2-10 ul, a cada poço. </li><li> Obtenção de placas da biblioteca de ADN de transfecção grau como acima e diluir a 13,3 ng / mL com água isenta de endotoxina. O volume mínimo por poço deve ser de 28 mL. </li></ol> 3. Realizar transfecções No dia 2 da tela, plasmídeos repórter e ADN de biblioteca são transfectados para células 293T. <ol><li> Para cada placa de biblioteca, mistura de 107,5 ul de RT Optifect (Invitrogen) com 4,3 ml de meio isento de soro (diluição 1:40) em um tubo de poliestireno. Incubar durante 5 min à temperatura ambiente, e on dispensar 44 ul (por placa de biblioteca) para cada poço de uma placa de 96 poços, de fundo V de poliestireno (Greiner). </li><li> Coloque a placa de diluído Optifect, plasmídeos repórter (Passo 2.5), DNAs biblioteca (Passo 2.6), e uma caixa de pontas de pipeta na plataforma do robô. </li><li> Aspirar 17 l de plasmídeos repórter, 43 mL de diluído Optifect, e 26 mL de DNA biblioteca, inserindo um espaço de ar 5 jul entre cada aspiração. O ADN da biblioteca devem ser aspirados última para evitar a contaminação cruzada. Dispense o conteúdo das dicas para uma nova placa de poliestireno-V fundo, misture, tampe e reserve por 20 minutos para permitir que os complexos de lipídios / DNA para formar. Se transfecção de múltiplas placas de biblioteca, substituir as pontas de pipeta e placa de biblioteca, e repita. </li><li> Descubra a placa de mistura Optifect / DNA e colocá-lo na plataforma do robô com 2 placas de células 293T. Usando uma única caixa de pontas de pipeta, aspirado 80 ml da Optifect: mistura de DNA e, lentamente, dispensar 40 mL em cada placa de células. Se transfecting múltiplas placas de biblioteca, repita para todos Optifect: placas de DNA. Cubra células. </li><li> Centrifugar as placas da célula de 1.200 xg durante 30 min. Cobrir e retornar para a incubadora. </li><li> Incubar as células por 4-6 horas. Durante esta incubação, preparar por meio fresco por mistura de 12 ml de DMEM contendo 10% de FBS e 10 ng / ml de ciprofloxacina (Cellgro) para cada placa transfectada biblioteca. Despeje meio fresco em um reservatório estéril. </li><li> Coloque 2 caixas de dicas robô, uma única placa de células, o reservatório contendo meio fresco, e um reservatório de resíduos para o convés do robô. Aspirar 100 ul de meio a partir das células e dispensar para o reservatório de resíduos parcialmente preenchido com etanol a 70%. Utilizando pontas frescas, aspirado de 100 ul de meio fresco e dispensar lentamente sobre as células. Repita o procedimento para todas as placas de células. </li><li> Retornar placas na incubadora durante 48 h. </li></ol> 4. Realizar luciferase dupla Ensaios No dia 4 de tela, ovaga-lume e Renilla ensaios de luciferase são executadas. Nota: O ensaio de luciferase dupla requer a adição sequencial de dois tampões de ensaio, 3X tampão de ensaio de pirilampo e Renilla tampão de ensaio 3X, como descrito na Tabela 3 do vaga-lume e luciferase Renilla não são segregadas, assim, as células devem ser lisados ​​antes de se medir a actividade da luciferase. . Tampão de ensaio de pirilampo lisa as células e proporciona substrato para a luciferase do pirilampo; tampão de ensaio de Renilla extingue o sinal de pirilampo e proporciona substrato para a luciferase de Renilla. <ol><li> Para cada placa de biblioteca, preparar 8 ml de tampão 3X pirilampo ensaio a partir de soluções estoque como descrito na Tabela 3, e dispensar 82 mL em cada poço de uma placa de 96 poços de fundo em V. </li><li> Para cada placa de biblioteca, também preparar-se 12 ml de tampão de ensaio 3X Renilla e dispensar 122 mL em cada poço de uma placa de 96 poços de fundo em V. Ponha de lado tanto ovaga-lume e Renilla buffers ensaio. </li><li> Colocar uma caixa de pontas de pipeta, um reservatório de resíduos, e duas placas de células (transf a partir da mesma chapa de biblioteca) sobre o convés do robô. </li><li> Aspirar 60 ul de meio de cada placa e descartar no reservatório de resíduos parcialmente preenchido com etanol a 70%. Placas de cobertura e reserve. Se transfecção de múltiplas placas de biblioteca, repita para todos os conjuntos de placas. </li><li> Coloque 2 caixas de pontas de pipeta, a placa de 3X tampão vagalume ensaio, e um conjunto de placas de celulares na plataforma do robô. </li><li> Aspirar 40 ul de tampão 3X pirilampo ensaio e adicioná-lo à primeira placa de células, misturando cuidadosamente. Mudar para novas pontas de pipeta, repita o procedimento para a segunda placa celular. Colocar as células à temperatura ambiente durante 10 min para completar a lise. Se transfecção de múltiplas placas de biblioteca, substituir as caixas de sugestões e placas celulares, e repita. </li><li> Ficha de luminescência de cada poço da placa de células em cada um luminómetro, a gravação de um segundo por poço. Retornar placas ao robôdeck. </li><li> Colocar duas caixas de pontas de pipeta, a placa de tampão de ensaio 3X Renilla, e um conjunto de placas da célula no convés do robô. </li><li> Aspirar 60 ul de tampão de ensaio 3X Renilla, e adicioná-lo à primeira placa de células, misturando cuidadosamente. Mudar para uma nova caixa de pontas de pipeta, repita o procedimento para a segunda placa celular. Se transfecção de múltiplas placas de biblioteca, repita para todos os conjuntos de placas celulares. </li><li> Grave luminescência de todas as placas em um luminometer, registrando cada poço por 1 segundo acima. Descarte placas. </li></ol> 5. Análise de Dados <ol><li> Calcule o vaga-lume: relação Renilla luminescência (&quot;F: Relação R&quot;) para cada bem, dividindo as acusações de sinal de vaga-lume pelas acusações de sinal Renilla. </li><li> Calcular o valor de indução através da divisão do F: razão R de cada poço pela média F: relação R da placa, excluindo o mais alto e mais baixo de 25% dos poços. </li><li> Calcular a média dos valores de indução através de repetiçõespara uma única placa de biblioteca transfectadas. Genes induzindo ou reprimindo alfa-sinucleína mais de três dobras são considerados &quot;hits&quot; nesta tela e estão sujeitos a uma validação adicional e telas secundárias. </li></ol>

<ol>
	<li>Chiba-Falek, O., Nussbaum, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+allelic+variation+at+the+NACP-Rep1+repeat+upstream+of+the+&#945;-synuclein+gene+(SNCA)+on+transcription+in+a+cell+culture+luciferase+reporter+system.">Effect of allelic variation at the NACP-Rep1 repeat upstream of the &#945;-synuclein gene (SNCA) on transcription in a cell culture luciferase reporter system.</a> Hum. Mol. Genet. 10 (26), 3101-3109 (2001).</li><li>Chiba-Falek, O., Touchman, J. W., Nussbaum, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Functional+analysis+of+intra-allelic+variation+at+NACP-Rep1+in+the+alpha-synuclein+gene.">Functional analysis of intra-allelic variation at NACP-Rep1 in the alpha-synuclein gene.</a> 113 (5), 426-431 (2003).</li><li>Scherzer, C. R., 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=GATA+transcription+factors+directly+regulate+the+Parkinson's+disease-linked+gene+&#945;-synuclein.">GATA transcription factors directly regulate the Parkinson's disease-linked gene &#945;-synuclein.</a> Proc. Natl. Acad. Sci. USA. 105 (31), 10907-10912 (2008).</li><li>Spillantini, M. G., Schmidt, M. L., Lee, V. M. Y., Trojanowski, J. Q., Jakes, R., Goedert, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=&#945;-Synuclein+in+Lewy+Bodies.">&#945;-Synuclein in Lewy Bodies.</a> Nature. 388 (6645), 839-840 (1997).</li><li>Pankratz, N., 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=Meta-analysis+of+Parkinson's+disease:+identification+of+a+novel+locus,+RIT2.">Meta-analysis of Parkinson's disease: identification of a novel locus, RIT2.</a> Ann. Neurol. 71 (3), 370-384 (2012).</li><li>Satake, W., 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=Genome-wide+association+study+identifies+common+variants+at+four+loci+as+genetic+risk+factors+for+Parkinson's+disease.">Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease.</a> Nat. Genet. 41 (12), 1303-1307 (2009).</li><li>Sim&#243;n-S&#225;nchez, J., 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=Genome-wide+association+study+reveals+genetic+risk+underlying+Parkinson's+disease.">Genome-wide association study reveals genetic risk underlying Parkinson's disease.</a> Nat. Genet. 41 (12), 1308-1312 (2009).</li><li>Polymeropoulos, M. 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=Mutation+in+the+alpha-synuclein+gene+identified+in+families+with+Parkinson's+disease.">Mutation in the alpha-synuclein gene identified in families with Parkinson's disease.</a> Science. 276 (5321), 2045-2047 (1997).</li><li>Ib&#225;&#241;ez, P., 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=Causal+relationship+between+a-synuclein+gene+duplication+and+familial+Parkinson's+disease.">Causal relationship between a-synuclein gene duplication and familial Parkinson's disease.</a> Lancet. 364 (9440), 1169-1171 (2004).</li><li>Chartier-Harlin, M. -. 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=a-Synuclein+locus+duplication+as+a+cause+of+familial+Parkinson's+disease.">a-Synuclein locus duplication as a cause of familial Parkinson's disease.</a> Lancet. 364 (9440), 1167-1169 (2004).</li><li>Singleton, A. B., 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=a-Synuclein+locus+triplication+causes+Parkinson's+disease.">a-Synuclein locus triplication causes Parkinson's disease.</a> Science. 302 (5646), 841 (2003).</li><li>Ahn, T. -. B., 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=a-Synuclein+gene+duplication+is+present+in+sporadic+Parkinson+disease.">a-Synuclein gene duplication is present in sporadic Parkinson disease.</a> Neurology. 70 (1), 43-49 (2008).</li><li>Boyce, F. M., Bucher, N. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Baculovirus-mediated+gene+transfer+into+mammalian+cells.">Baculovirus-mediated gene transfer into mammalian cells.</a> Proc. Nat. Acad. USA. 93 (6), 2348-2352 (1996).</li><li>Montigny, W. J., 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=Parameters+influencing+high-efficiency+transfection+of+bacterial+artificial+chromosomes+into+cultured+mammalian+cells.">Parameters influencing high-efficiency transfection of bacterial artificial chromosomes into cultured mammalian cells.</a> Biotechniques. 35, 796-807 (2003).</li><li>Gorman, C. M., Moffat, L. F., Howard, B. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recombinant+genomes+which+express+chloramphenicol+acetyltransferase+in+mammalian+cells.">Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells.</a> Mol. Cell. Biol. 2 (9), 1044-1051 (1982).</li><li>Li, J. J., Herskowitz, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+ORC6,+a+Component+of+the+Yeast+Origin+Recognition+Complex+by+a+One-Hybrid+System.">Isolation of ORC6, a Component of the Yeast Origin Recognition Complex by a One-Hybrid System.</a> Science. 262, 1870-1874 (1993).</li><li>Dejardin, J., Kingston, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+of+Proteins+Associated+with+Specific+Genomic+Loci.">Purification of Proteins Associated with Specific Genomic Loci.</a> Cell. 136, 175-186 (2009).</li><li>Shen, Y., 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=A+map+of+the+cis-regulatory+sequences+in+the+mouseGenome.">A map of the cis-regulatory sequences in the mouseGenome.</a> Nature. 488, 116-120 (2012).</li><li>Fan, F., Wood, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bioluminescent+assays+for+high-throughput+screening.">Bioluminescent assays for high-throughput screening.</a> Assay Drug Dev. Technol. 5 (1), 127-136 (2007).</li><li>Hampf, M., Gossen, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+protocol+for+combined+Photinus+and+Renilla+luciferase+quantification+compatible+with+protein+assays.">A protocol for combined Photinus and Renilla luciferase quantification compatible with protein assays.</a> Anal. Biochem. 356 (1), 94-99 (2006).</li><li>Auld, D. S., Thorne, N., Maguire, W. F., Inglese, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanism+of+PTC124+activity+in+cell-based+luciferase+assays+of+nonsense+codon+suppression.">Mechanism of PTC124 activity in cell-based luciferase assays of nonsense codon suppression.</a> Proc. Natl. Acad. Sci. USA. 106 (9), 3585-3590 (2009).</li><li>Pearlberg, J., 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=Screens+using+RNAi+and+cDNA+expression+as+surrogates+for+genetics+in+mammalian+tissue+culture+cells.">Screens using RNAi and cDNA expression as surrogates for genetics in mammalian tissue culture cells.</a> Cold Spring Harb.Symp. Quant. Biol. 70, 449-459 (2005).</li></ol>

Este trabalho foi apoiado por royalties obtidos por BacMamreagents licenciamento (Patente dos EUA 5.731.182).

Alfa-sinucleína foi implicada na doença de Parkinson (PD), como um componente de corpos de Lewy, 4 inclusões intracelulares considerados patognomónico para a doença. Numerosos estudos de associação do genoma ligaram polimorfismos de nucleotídeo único em alfa-sinucleína com risco aumentado para esporádica PD 5,6,7. Embora menos comum do que a PD esporádica, PD familiar também pode ser causada por mutações em alfa-sinucleína 8, bem como a duplicação e triplicação do loc...

A capacidade de identificar elementos reguladores genéticos chave e os fatores que atuam sobre eles é fundamental para a exploração de numerosos processos biológicos. No entanto, a identificação de fatores que regulam a expressão de genes em tipos de células raras, como populações neuronais específicas, pode ser um desafio. Aqui, nós apresentamos um protocolo para a identificação de novos reguladores transcricionais de alfa-sinucleína (SNCA), um gene associado com a doença de Parkinson e expresso em neurónios dopaminérgicos na substantianigra região pars compacta do mesencéfalo. Nós conseguimos isso usando uma tela repórter de alto rendimento, dual-luciferase, in vitro para desconstruir expressão alfa-sinucleína em células 293T. O promotor de alfa-sinucleína é primeiro clonado num plasmídeo repórter contendo o gene da luciferase do pirilampo. Um plasmídeo disponível comercialmente contendo a luciferase de Renilla sob o controlo de um promotor constitutivamente activo serve como um controlo interno. Tsconstruções repórter e são co-transfectados para células 293T em microplacas com plasmídeos de uma biblioteca de expressão de ADN, de modo a que cada poço é transfectada com um único plasmídeo biblioteca. Após 48 horas, a atividade de luciferase para cada repórter é medido sequencialmente através de um ensaio duplo-brilho. A expressão relativa de alfa-sinucleína em resposta a cada gene biblioteca é inferida pela relação de pirilampo: a actividade da luciferase de Renilla em cada poço (F: razão R) após normalização com base em placa. Este protocolo prevê a possibilidade de um número elevado de genes (~ 2.500 por semana) por sua capacidade de transativar um gene repórter utilizando mão de obra mínima (1-2 pessoas) e um custo mínimo (cerca de US $ 3 Custo reagente por ensaio microplaca). Reguladores da transcrição de genes neuronais (por exemplo, alfa-sinucleína), que são difíceis de estudar em neurónios cultivados refractários a manipulação genética, podem ser comparados lado a lado no presente ensaio funcional directa. Nós incluímos em nossoprotocolo de um método detalhado para a clonagem e crescimento de plasmídeos contendo o promotor de alfa-sinucleína, uma vez que descobrimos que os plasmídeos contendo esta região são instáveis ​​quando cultivadas com procedimentos convencionais (ver discussão). Nós também incluímos uma alternativa barata para comercialmente disponíveis reagentes dual-luciferase para ensaios de alto rendimento. Este protocolo pode ser facilmente adaptado para atacar outros elementos reguladores de interesse, ou para qualquer processo que requer a high-throughput transfecções transientes.

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 <tr>
 <td>QIAQuick PCR Purification Kit</td>
 <td>Qiagen</td>
 <td>28106</td>
 <td></td>
 </tr>
 <tr>
 <td>PureLink Quick Gel Extraction Kit</td>
 <td>Invitrogen</td>
 <td>K2100-12</td>
 <td></td>
 </tr>
 <tr>
 <td>PureLink PCR Micro Kit</td>
 <td>Invitrogen</td>
 <td>K310250</td>
 <td></td>
 </tr>
 <tr>
 <td>PureLinkHiPure Plasmid Miniprep Kit</td>
 <td>Invitrogen</td>
 <td>K2100-03</td>
 <td></td>
 </tr>
 <tr>
 <td>PureLinkHiPure Plasmid Maxiprep Kit</td>
 <td>Invitrogen</td>
 <td>K2100-07</td>
 <td></td>
 </tr>
 <tr>
 <td>Bravo Robot</td>
 <td>Agilent</td>
 <td>-</td>
 <td></td>
 </tr>
 <tr>
 <td>Robot Pipet Tips with Filter</td>
 <td>Agilent</td>
 <td>19477-022</td>
 <td></td>
 </tr>
 <tr>
 <td>Robot Pipet Tips without Filter</td>
 <td>Agilent</td>
 <td>19477-002</td>
 <td></td>
 </tr>
 <tr>
 <td>Clear-bottomed 96-well Plates</td>
 <td>Corning</td>
 <td>3610</td>
 <td></td>
 </tr>
 <tr>
 <td>Reservoirs</td>
 <td>Axygen</td>
 <td>RES-SW96-HP-SI</td>
 <td></td>
 </tr>
 <tr>
 <td>Polystyrene V-bottomed 96-well Plate</td>
 <td>Greiner</td>
 <td>651101</td>
 <td></td>
 </tr>
 <tr>
 <td>Polypropylene V-bottomed 96-well Plate</td>
 <td>Greiner</td>
 <td>651201</td>
 <td></td>
 </tr>
 <tr>
 <td>Adhesive Plate Covers</td>
 <td>CryoStuff</td>
 <td>#FS100</td>
 <td></td>
 </tr>
 <tr>
 <td></td>
 <td></td>
 <td></td>
 <td>Reagent</td>
 </tr>
 <tr>
 <td>Phusion DNA Polymerase</td>
 <td>New England Biolabs</td>
 <td>M0530L</td>
 <td></td>
 </tr>
 <tr>
 <td>BAC 2002-D6</td>
 <td>Invitrogen</td>
 <td>2002-D6</td>
 <td></td>
 </tr>
 <tr>
 <td>Calf Intestine Alkaline Phosphatase</td>
 <td>Roche</td>
 <td>10713023001</td>
 <td></td>
 </tr>
 <tr>
 <td>T4 DNA Ligase</td>
 <td>New England Biolabs</td>
 <td>M0202L</td>
 <td></td>
 </tr>
 <tr>
 <td>pGL4.10</td>
 <td>Promega</td>
 <td>E6651</td>
 <td></td>
 </tr>
 <tr>
 <td>pGL4.74</td>
 <td>Promega</td>
 <td>E6931</td>
 <td></td>
 </tr>
 <tr>
 <td>ElectroMAX Stbl4 Competent Cells</td>
 <td>Invitrogen</td>
 <td>11635-018</td>
 <td></td>
 </tr>
 <tr>
 <td>Subcloning Efficiency DH5&alpha; Competent Cells</td>
 <td>Invitrogen</td>
 <td>18265-017</td>
 <td></td>
 </tr>
 <tr>
 <td>DMEM without Phenol Red</td>
 <td>Invitrogen</td>
 <td>31053-028</td>
 <td></td>
 </tr>
 <tr>
 <td>Optifect</td>
 <td>Invitrogen</td>
 <td>12579017</td>
 <td></td>
 </tr>
 <tr>
 <td>Ciprofloxacin</td>
 <td>CellGro</td>
 <td>61-277-RF</td>
 <td></td>
 </tr>
 <tr>
 <td>Tris-Hydrochloride Powder</td>
 <td>Sigma</td>
 <td>93287</td>
 <td></td>
 </tr>
 <tr>
 <td>Tris-Base Powder </td>
 <td>Sigma</td>
 <td>93286</td>
 <td></td>
 </tr>
 <tr>
 <td>Triton X-100 Pure Liquid</td>
 <td>Fisher</td>
 <td>BP151-100</td>
 <td></td>
 </tr>
 <tr>
 <td>DTT</td>
 <td>Invitrogen</td>
 <td>15508-013</td>
 <td></td>
 </tr>
 <tr>
 <td>Coenzyme A</td>
 <td>Nanolight</td>
 <td>309</td>
 <td></td>
 </tr>
 <tr>
 <td>ATP</td>
 <td>Sigma</td>
 <td>A6419</td>
 <td></td>
 </tr>
 <tr>
 <td>Luciferin</td>
 <td>Invitrogen</td>
 <td>L2912</td>
 <td></td>
 </tr>
 <tr>
 <td>h-CTZ</td>
 <td>Nanolight</td>
 <td>301</td>
 <td></td>
 </tr>
 <tr>
 <td>PTC124</td>
 <td>SelleckBiochemicals</td>
 <td>S6003</td>
 <td></td>
 </tr>
 </tbody>
</table>

high-throughput functional screening using a homemade dual-glow luciferase assay

Apresenta-se um protocolo rápido e barato de rastreio de alto rendimento para identificar reguladores transcricionais de alfa-sinucleína, um gene associado com a doença de Parkinson. As células 293T são transfectadas transitoriamente com os plasmídeos a partir de uma biblioteca de expressão de ORF formado, em conjunto com os plasmídeos repórter da luciferase, em um formato de um gene-por-microplaca. A actividade da luciferase do pirilampo é ensaiado após 48 horas para determinar os efeitos de cada biblioteca de genes mediante transcrição alfa-sinucleína, normalizadas para a expressão de uma construção de controlo interno (de um promotor de hCMV dirige a luciferase da Renilla). Este protocolo é facilitada por um robô de bancada fechado numa cabine de segurança biológica, que executa a manipulação asséptica líquido em formato de 96 poços. O protocolo de transfecção automatizado é facilmente adaptável para maior rendimento da produção de biblioteca lentiviral ou outros protocolos de rastreio funcionais que requerem triple-transfecções de um grande número de plasmídeos biblioteca original em conjunction com um conjunto comum de plasmídeos auxiliares. Apresentamos também uma alternativa barata e validado para comercialmente disponíveis, dupla reagentes luciferase que emprega PTC124, EDTA, e pirofosfato de suprimir a atividade da luciferase de vaga-lume antes da medição de Renilla luciferase. Usando esses métodos, nós analisamos 7.670 genes humanos e identificou 68 reguladores de alfa-sinucleína. Este protocolo é facilmente modificável para atingir outros genes de interesse.

Os valores típicos da luciferase, F: rácios R e os valores de indução para um único semi-placa são mostrados na Figura 4 Nota da batida no bem H2, um indutor de 32 vezes.. Genes que causam toxicidade excessiva (por exemplo, bem E3), ou poços que foram mal transfectadas, irá produzir valores baixos, tanto para vaga-lume e luciferases Renilla, mas um valor médio de indução. Os genes que causam indução não específica da actividade da luciferase, talvez através da interacç...

Watch this Scientific Journal Video about High-throughput Functional Screening using a Homemade Dual-glow Luciferase Assay at JoVE.com

High-throughput Functional Screening using a Homemade Dual-glow Luciferase Assay

Apresentamos um método de triagem rápida e de baixo custo para a identificação de reguladores de transcrição usando de alto rendimento transfections robóticos e um ensaio de luciferase dual-brilho caseiro. Este protocolo gera rapidamente dados funcionais diretos side-by-side para milhares de genes e é facilmente modificável para atingir qualquer gene de interesse.

De alta capacidade de Triagem funcional usando um caseiro Dual-brilho ensaio de luciferase

We present a rapid and inexpensive high-throughput screening protocol to identify transcriptional regulators of alpha-synuclein, a gene associated with ...

high-throughput-functional-screening-using-homemade-dual-glow

Research

JoVE Journal

Biology

23.3K visualizações.  Massachusetts General Hospital.  Apresentamos um método de triagem rápida e de baixo custo para a identificação de reguladores de transcrição usando de alto rendimento transfections robóticos e um ensaio de luciferase dual-brilho caseiro. Este protocolo gera rapidamente dados funcionais diretos side-by-side para milhares de genes e é facilmente modificável para atingir qualquer gene de interesse. 

Vídeo: High-throughput Functional Screening using a Homemade Dual-glow Luciferase Assay

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.

Alto rendimento Triagem e Biossensoriais com Fluorescente C. elegans Cepas

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

Biologia

High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli

Cellulase enzymes (endoglucanases, cellobiohydrolases, and &beta;-glucosidases) hydrolyze cellulose into component sugars, which in turn can be converted into fuel alcohols1. The potential for enzymatic hydrolysis of cellulosic biomass to provide renewable energy has intensified efforts to engineer cellulases for economical fuel production2. Of particular interest are fungal cellulases3-8, which are already being used industrially for foods and textiles processing.
Identifying active variants among a library of mutant cellulases is critical to the engineering process; active mutants can be further tested for improved properties and/or subjected to additional mutagenesis. Efficient engineering of fungal cellulases has been hampered by a lack of genetic tools for native organisms and by difficulties in expressing the enzymes in heterologous hosts. Recently, Morikawa and coworkers developed a method for expressing in E. coli the catalytic domains of endoglucanases from H. jecorina3,9, an important industrial fungus with the capacity to secrete cellulases in large quantities. Functional E. coli expression has also been reported for cellulases from other fungi, including Macrophomina phaseolina10 and Phanerochaete chrysosporium11-12. 
We present a method for high throughput screening of fungal endoglucanase activity in E. coli. (Fig 1) This method uses the common microbial dye Congo Red (CR) to visualize enzymatic degradation of carboxymethyl cellulose (CMC) by cells growing on solid medium. The activity assay requires inexpensive reagents, minimal manipulation, and gives unambiguous results as zones of degradation (&#x201C;halos&#x201D;) at the colony site. Although a quantitative measure of enzymatic activity cannot be determined by this method, we have found that halo size correlates with total enzymatic activity in the cell. Further characterization of individual positive clones will determine , relative protein fitness. 
Traditional bacterial whole cell CMC/CR activity assays13 involve pouring agar containing CMC onto colonies, which is subject to cross-contamination, or incubating cultures in CMC agar wells, which is less amenable to large-scale experimentation. Here we report an improved protocol that modifies existing wash methods14 for cellulase activity: cells grown on CMC agar plates are removed prior to CR staining. Our protocol significantly reduces cross-contamination and is highly scalable, allowing the rapid screening of thousands of clones. In addition to H. jecorina enzymes, we have expressed and screened endoglucanase variants from the Thermoascus aurantiacus and Penicillium decumbens (shown in Figure 2), suggesting that this protocol is applicable to enzymes from a range of organisms.

High Throughput Screening of Fungal Endoglucanase Activity in Escherichia coli

We describe a low cost, high throughput method to screen for fungal endoglucanase activity in E. coli. The method relies on a simple visual readout of substrate degradation, does not require enzyme purification, and is highly scalable. This allows for the rapid screening of large libraries of enzyme variants.

High Throughput Screening da atividade endoglucanase de fungos em Escherichia coli</em

Cellulase enzymes (endoglucanases, cellobiohydrolases, and &beta;-glucosidases) hydrolyze cellulose into component sugars, which in turn can be converted ...

High-throughput Saccharification Assay for Lignocellulosic Materials

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be 
used in establishing a biorefinery. These raw materials would constitute a new industrial platform, which is both sustainable and carbon neutral, to replace 
the current dependency on fossil fuel. The recalcitrance to deconstruction observed in lignocellulosic materials is produced by several intrinsic properties 
of plant cell walls. Crystalline cellulose is embedded in matrix polysaccharides such as xylans and arabinoxylans, and the whole structure is encased by the 
phenolic polymer lignin, that is also difficult to digest 1. In order to improve the digestibility of plant materials we need to discover the main bottlenecks 
for the saccharification of cell walls and also screen mutant and breeding populations to evaluate the variability in saccharification 2. These tasks require 
a high throughput approach and here we present an analytical platform that can perform saccharification analysis in a 96-well plate format. This platform has 
been developed to allow the screening of lignocellulose digestibility of large populations from varied plant species. We have scaled down the reaction volumes 
for gentle pretreatment, partial enzymatic hydrolysis and sugar determination, to allow large numbers to be assessed rapidly in an automated system.
This automated platform works with milligram amounts of biomass, performing ball milling under controlled conditions to reduce the plant 
materials to a standardised particle size in a reproducible manner. Once the samples are ground, the automated formatting robot dispenses specified and recorded 
amounts of material into the corresponding wells of 96 deep well plate (Figure 1). Normally, we dispense the same material into 4 wells to have 4 replicates for 
analysis. Once the plates are filled with the plant material in the desired layout, they are manually moved to a liquid handling station (Figure 2). In this 
station the samples are subjected to a mild pretreatment with either dilute acid or alkaline and incubated at temperatures of up to 90&deg;C. The pretreatment solution 
is subsequently removed and the samples are rinsed with buffer to return them to a suitable pH for hydrolysis. The samples are then incubated with an enzyme
mixture for a variable length of time at 50&deg;C. An aliquot is taken from the hydrolyzate and the reducing sugars are automatically determined by the MBTH 
colorimetric method.

A simple, rapid method for determining the saccharification potential of large numbers of plant biomass samples is described. The automated platform for this analysis involves the preparation of the plant biomass for analysis in 96 well plates and the subsequent performance of pretreatment, hydrolysis and quantification of the sugars released.

Alto rendimento Assay Sacarificação para materiais lignocelulósicos

Polysaccharides that make up plant lignocellulosic biomass can be broken down to produce a range of sugars that subsequently can be 
used in establishing ...

Use of a Robot for High-throughput Crystallization of Membrane Proteins in Lipidic Mesophases

Structure-function studies of membrane proteins greatly benefit from having available high-resolution 3-D structures of the type provided through macromolecular X-ray crystallography (MX). An essential ingredient of MX is a steady supply of ideally diffraction-quality crystals. The in meso or lipidic cubic phase (LCP) method for crystallizing membrane proteins is one of several methods available for crystallizing membrane proteins. It makes use of a bicontinuous mesophase in which to grow crystals. As a method, it has had some spectacular successes of late and has attracted much attention with many research groups now interested in using it. One of the challenges associated with the method is that the hosting mesophase is extremely viscous and sticky, reminiscent of a thick toothpaste. Thus, dispensing it manually in a reproducible manner in small volumes into crystallization wells requires skill, patience and a steady hand. A protocol for doing just that was developed in the Membrane Structural &amp; Functional Biology (MS&amp;FB) Group1-3. JoVE video articles describing the method are available1,4. 
The manual approach for setting up in meso trials has distinct advantages with specialty applications, such as crystal optimization and derivatization. It does however suffer from being a low throughput method. Here, we demonstrate a protocol for performing in meso crystallization trials robotically. A robot offers the advantages of speed, accuracy, precision, miniaturization and being able to work continuously for extended periods under what could be regarded as hostile conditions such as in the dark, in a reducing atmosphere or at low or high temperatures. An in meso robot, when used properly, can greatly improve the productivity of membrane protein structure and function research by facilitating crystallization which is one of the slow steps in the overall structure determination pipeline. 
In this video article, we demonstrate the use of three commercially available robots that can dispense the viscous and sticky mesophase integral to in meso crystallogenesis. The first robot was developed in the MS&amp;FB Group5,6. The other two have recently become available and are included here for completeness.	
An overview of the protocol covered in this article is presented in Figure 1. All manipulations were performed at room temperature (~20 &deg;C) under ambient conditions.

Herein is described a robotic approach to high-throughput crystallization of membrane proteins in lipidic mesophases for use in structure determination using macromolecular X-ray crystallography. Three robots capable of handling the viscous and sticky protein-laden mesophase integral to the method are introduced.

A utilização de um robô para alta capacidade de cristalização de proteínas de membrana em mesofases lipídicas

Structure-function studies of membrane proteins greatly benefit from having available high-resolution 3-D structures of the type provided through ...

High-throughput Titration of Luciferase-expressing Recombinant Viruses

Standard plaque assays to determine infectious viral titers can be time consuming, are not amenable to a high volume of samples, and cannot be done with viruses that do not form plaques. As an alternative to plaque assays, we have developed a high-throughput titration method that allows for the simultaneous titration of a high volume of samples in a single day. This approach involves infection of the samples with a Firefly luciferase tagged virus, transfer of the infected samples onto an appropriate permissive cell line, subsequent addition of luciferin, reading of plates in order to obtain luminescence readings, and finally the conversion from luminescence to viral titers. The assessment of cytotoxicity using a metabolic viability dye can be easily incorporated in the workflow in parallel and provide valuable information in the context of a drug screen. This technique provides a reliable, high-throughput method to determine viral titers as an alternative to a standard plaque assay.

This article presents a high-throughput luciferase expression-based method of titrating various RNA and DNA viruses using automated and manual liquid handlers.

De alta capacidade de Titulação de luciferase expressando recombinantes Vírus

Standard plaque assays to determine infectious viral titers can be time consuming, are not amenable to a high volume of samples, and cannot be done with ...

A Manual Small Molecule Screen Approaching High-throughput Using Zebrafish Embryos

Zebrafish have become a widely used model organism to investigate the mechanisms that underlie developmental biology and to study human disease pathology due to their considerable degree of genetic conservation with humans. Chemical genetics entails testing the effect that small molecules have on a biological process and is becoming a popular translational research method to identify therapeutic compounds. Zebrafish are specifically appealing to use for chemical genetics because of their ability to produce large clutches of transparent embryos, which are externally fertilized. Furthermore, zebrafish embryos can be easily drug treated by the simple addition of a compound to the embryo media. Using whole-mount in situ hybridization (WISH), mRNA expression can be clearly visualized within zebrafish embryos. Together, using chemical genetics and WISH, the zebrafish becomes a potent whole organism context in which to determine the cellular and physiological effects of small molecules. Innovative advances have been made in technologies that utilize machine-based screening procedures, however for many labs such options are not accessible or remain cost-prohibitive. The protocol described here explains how to execute a manual high-throughput chemical genetic screen that requires basic resources and can be accomplished by a single individual or small team in an efficient period of time. Thus, this protocol provides a feasible strategy that can be implemented by research groups to perform chemical genetics in zebrafish, which can be useful for gaining fundamental insights into developmental processes, disease mechanisms, and to identify novel compounds and signaling pathways that have medically relevant applications.

The zebrafish is an excellent experimental organism to study vertebrate developmental processes and model human disease. Here, we describe a protocol on how to perform a manual high-throughput chemical screen in zebrafish embryos with a whole-mount in situ hybridization (WISH) read-out.

Um manual de tela pequena molécula Aproximando de alta capacidade Usando embriões Zebrafish

Zebrafish have become a widely used model organism to investigate the mechanisms that underlie developmental biology and to study human disease pathology ...

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.

Rastreio de alto rendimento para moduladores químicos de Genes Post-transcriptionally Regulamentados

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

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Luminescent Identification of Functional Elements in 3&#8217;UTRs (3&#8217;LIFE) allows the rapid identification of targets of specific miRNAs within an array of hundreds of queried 3&#8217;UTRs. Target identification is based on the dual-luciferase assay, which detects binding at the mRNA level by measuring translational output, giving a functional readout of miRNA targeting. 3&#8217;LIFE uses non-proprietary buffers and reagents, and publically available reporter libraries, making genome-wide screens feasible and cost-effective. 3&#8217;LIFE can be performed either in a standard lab setting or scaled up using liquid handling robots and other high-throughput instrumentation. We illustrate the approach using a dataset of human 3&#8217;UTRs cloned in 96-well plates, and two test miRNAs, let-7c and miR-10b. We demonstrate how to perform DNA preparation, transfection, cell culture and luciferase assays in 96-well format, and provide tools for data analysis. In conclusion 3&#39;LIFE is highly reproducible, rapid, systematic, and identifies high confidence targets.

Detection of miRNA Targets in High-throughput Using the 3&#039;LIFE Assay

Luminescent identification of functional elements in 3&#8217; untranslated regions (3&#8217;UTRs) (3&#8217;LIFE) is a technique to identify functional regulation in 3&#8217;UTRs by miRNAs or other regulatory factors. This protocol utilizes high-throughput methodology such as 96-well transfection and luciferase assays to screen hundreds of putative interactions for functional repression.

Detecção de alvos miRNA em métodos de alta capacidade utilizando o ensaio 3&#39;LIFE

Luminescent Identification of Functional Elements in 3&#8217;UTRs (3&#8217;LIFE) allows the rapid identification of targets of specific miRNAs within an ...

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic chromosome, synIII1, and one synthetic chromosome arm, synIXR2, have been constructed and their in vivo function validated in the absence of the corresponding wild type chromosomes. An important design feature of Sc2.0 chromosomes is the introduction of PCRTags, which are short, re-coded sequences within open reading frames (ORFs) that enable differentiation of synthetic chromosomes from their wild type counterparts. PCRTag primers anneal selectively to either synthetic or wild type chromosomes and the presence/absence of each type of DNA can be tested using a simple PCR assay. The standard readout of the PCRTag assay is to assess presence/absence of amplicons by agarose gel electrophoresis. However, with an average PCRTag amplicon density of one per 1.5 kb and a genome size of ~12 Mb, the completed Sc2.0 genome will encode roughly 8,000 PCRTags. To improve throughput, we have developed a real time PCR-based detection assay for PCRTag genotyping that we call qPCRTag analysis. The workflow specifies 500 nl reactions in a 1,536 multiwell plate, allowing us to test up to 768 PCRTags with both synthetic and wild type primer pairs in a single experiment.

Designer chromosomes of the Synthetic Yeast Genome project, Sc2.0, can be distinguished from their native counterparts using a PCR-based genotyping assay called PCRTagging, which has a presence/absence endpoint. Here we describe a high-throughput real time PCR detection method for PCRTag genotyping.

Análise qPCRTag - A High Throughput, PCR em Tempo Real Ensaio para Sc2.0 Genotipagem

The Synthetic Yeast Genome Project (Sc2.0) aims to build 16 designer yeast chromosomes and combine them into a single yeast cell. To date one synthetic ...

Identification of Kinase-substrate Pairs Using High Throughput Screening

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

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

Identificação de pares Kinase-substrato utilizando High Throughput Screening


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