Name: an allele-specific gene expression assay to test the functional basis of genetic associations
Uploaded: 2010-11-03T16:00:00
Duration: 10 min 17 s
Description: Watch this Scientific Journal Video about An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations at JoVE.com

के लिए अनुदान के माध्यम से इस काम के लिए वेलकम ट्रस्ट द्वारा वित्त पोषित किया गया था एपीएम [076566/Z/05/Z], JCK [074318] और ह्यूमन जेनेटिक्स के लिए एक कोर वेलकम ट्रस्ट सेंटर पुरस्कार [075491/Z/04].

<ol>
	<li>Cookson, W., Liang, L., Abecasis, G., Moffatt, M., Lathrop, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+complex+disease+traits+with+global+gene+expression.">Mapping complex disease traits with global gene expression.</a> Nat Rev Genet. 10, 184-194 (2009).</li><li>Singer-Sam, J., LeBon, J. M., Dai, A., Riggs, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+sensitive,+quantitative+assay+for+measurement+of+allele-specific+transcripts+differing+by+a+single+nucleotide.">A sensitive, quantitative assay for measurement of allele-specific transcripts differing by a single nucleotide.</a> PCR Methods Appl. 1, 160-163 (1992).</li><li>Yan, H., Yuan, W., Velculescu, V. E., Vogelstein, B., Kinzler, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Allelic+variation+in+human+gene+expression.">Allelic variation in human gene expression.</a> Science. 297, 1143-11 (2002).</li><li>Ding, C., Cantor, C. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+high-throughput+gene+expression+analysis+technique+using+competitive+PCR+and+matrix-assisted+laser+desorption+ionization+time-of-flight+MS.">A high-throughput gene expression analysis technique using competitive PCR and matrix-assisted laser desorption ionization time-of-flight MS.</a> Proc Natl Acad Sci U S A. 100, 3059-3064 (2003).</li><li>Gabriel, S., Ziaugra, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SNP+genotyping+using+Sequenom+MassARRAY+7K+platform.">SNP genotyping using Sequenom MassARRAY 7K platform.</a> Curr Protoc Hum Genet Chapter. Chapter 2 (Unit 2), 12-12 (2004).</li><li>Lo, H. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Allelic+variation+in+gene+expression+is+common+in+the+human+genome.">Allelic variation in gene expression is common in the human genome.</a> Genome Res. 13 (8), 1855-1862 (2003).</li><li>Liu, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression-based+discovery+of+variation+in+the+human+glutathione+S-transferase+M3+promoter+and+functional+analysis+in+a+glioma+cell+line+using+allele-specific+chromatin+immunoprecipitation.">Expression-based discovery of variation in the human glutathione S-transferase M3 promoter and functional analysis in a glioma cell line using allele-specific chromatin immunoprecipitation.</a> Cancer Res. 65, 99-104 (2005).</li><li>Knight, J. C., Keating, B. J., Rockett, K. A., Kwiatkowski, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+characterization+of+regulatory+polymorphisms+by+allele-specific+quantification+of+RNA+polymerase+loading.">In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading.</a> Nat Genet. 33 (4), 469-475 (2003).</li><li>Pastinen, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+survey+of+genetic+and+epigenetic+variation+affecting+human+gene+expression.">A survey of genetic and epigenetic variation affecting human gene expression.</a> Physiol Genomics. 16 (2), 184-193 (2004).</li><li>Francks, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+77-kilobase+region+of+chromosome+6p22.2+is+associated+with+dyslexia+in+families+from+the+United+Kingdom+and+from+the+United+States.">A 77-kilobase region of chromosome 6p22.2 is associated with dyslexia in families from the United Kingdom and from the United States.</a> Am J Hum Genet. 75 (6), 1046-1058 (2004).</li><li>Paracchini, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+chromosome+6p22+haplotype+associated+with+dyslexia+reduces+the+expression+of+KIAA0319,+a+novel+gene+involved+in+neuronal+migration.">The chromosome 6p22 haplotype associated with dyslexia reduces the expression of KIAA0319, a novel gene involved in neuronal migration.</a> Hum Mol Genet. 15 (10), 1659-1666 (2006).</li></ol>

ब्याज की कोई संघर्ष की घोषणा की.

इस विधि प्रतिलेख स्तर में vivo एलील विशेष अंतर का आकलन करके रोग से जुड़े जीन की अभिव्यक्ति पर डीएनए वेरिएंट के प्रभाव के मूल्यांकन के लिए सक्षम बनाता है. इस प्रोटोकॉल में रिश्तेदार प्रतिलेख बहुतायत MALDI-TOF लेकिन अन्य एलील विशिष्ट ऐसे 6,7 TaqMan के रूप में मात्रा का ठहराव, की अनुमति प्रौद्योगिकियों के द्वारा मापा जाता है, इस्तेमाल किया जा सकता है. इस दृष्टिकोण के प्रमुख सीमा कोडन लिखित मार्करों की उपलब्धता है. सिद्धांत पर आधारित तरीके यहाँ वर्णित है, लेकिन बहुरूपताओं के विभिन्न वर्गों के लाभ लेने, वर्णित किया गया है. haploChip परख एलील विशेष transcriptional शुरू करने या एक जीन जो chromatin immunoprecipitated द्वितीय 8 पोलीमरेज़ आरएनए विशिष्ट एंटीबॉडी के साथ अलग सामग्री में मौजूद होगा के अंत साइट के 1 केबी के भीतर स्थित मार्कर का उपयोग कर अभिव्यक्ति के उपाय. वैकल्पिक रूप से, intronic SNPs जब टेम्पलेट heteronuclear 9 शाही सेना इस्तेमाल किया जा सकता है . विशिष्ट प्रोटोकॉल यहाँ वर्णित है, haploChip परख के साथ संयोजन में सफलतापूर्वक इस्तेमाल किया गया है डिस्लेक्सिया (या पढ़ने विकलांगता) के लिए एक उम्मीदवार जीन की पहचान. शुरू में एक आनुवंशिक संघ अध्ययन एक डीएनए डिस्लेक्सिया और जो तीन 10 जीनों फैले था के साथ जुड़े अनुक्रम की पहचान की . एलील विशिष्ट जीन की अभिव्यक्ति परख से पता चला है कि डिस्लेक्सिया जुड़े डीएनए वेरिएंट अभिव्यक्ति भिन्नता की उपस्थिति में केवल तीन जीनों के एक लिए मनाया था, लेकिन दो अन्य नहीं 11.

<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>PBS</td>
			<td>&nbsp;</td>
			<td>Sigma</td>
			<td>P-4417-100TAB</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>SDS</td>
			<td>&nbsp;</td>
			<td>Biorad</td>
			<td>161-0416</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>&nbsp;</td>
			<td>VWR</td>
			<td>27788.366</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>&nbsp;</td>
			<td>Sigma</td>
			<td>T1503-1KG</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>&nbsp;</td>
			<td>Sigma</td>
			<td>E5134-500G</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>RNase A</td>
			<td>&nbsp;</td>
			<td>Qiagen</td>
			<td>19101</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>&nbsp;</td>
			<td>Sigma</td>
			<td>P2308-500MG</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Phenol: chloroform</td>
			<td>&nbsp;</td>
			<td>Sigma</td>
			<td>77617</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>&nbsp;</td>
			<td>VWR</td>
			<td>100777C</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>&nbsp;</td>
			<td>Sigma</td>
			<td>32221-2.5L</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Trizol</td>
			<td>&nbsp;</td>
			<td>Invitrogen</td>
			<td>15596-018</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>RNeasy kit</td>
			<td>&nbsp;</td>
			<td>Qiagen</td>
			<td>74104</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>SuperScript III Reverse Transcriptase</td>
			<td>&nbsp;</td>
			<td>Invitrogen</td>
			<td>18080-044</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Immolase Taq</td>
			<td>&nbsp;</td>
			<td>Bioline</td>
			<td>BIO-21048</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>dNTP</td>
			<td>&nbsp;</td>
			<td>Sigma</td>
			<td>DNTP100A</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Exonuclease 1</td>
			<td>&nbsp;</td>
			<td>NEB</td>
			<td>M0293S</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Shrimp Alkaline Phosphatase</td>
			<td>&nbsp;</td>
			<td>GE Healthcare</td>
			<td>E70092Z</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>SpectroCLEAN resin</td>
			<td>&nbsp;</td>
			<td>Sequenom</td>
			<td>10053</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>MassEXTEND ddNTP/dNTP mix </td>
			<td>&nbsp;</td>
			<td>Sequenom</td>
			<td>&nbsp;</td>
			<td>Varies according to assay design</td>
		</tr>
		<tr>
			<td>MassEXTEND thermosequenase </td>
			<td>&nbsp;</td>
			<td>Sequenom</td>
			<td>10052</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Chilled microcentrifuge</td>
			<td>&nbsp;</td>
			<td>Eppendorf</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>NanoDrop Spectrophotometer</td>
			<td>&nbsp;</td>
			<td>Thermo Scientific</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>SpectroPOINT nanolitre dispenser</td>
			<td>&nbsp;</td>
			<td>Sequenom</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>SpectroREADER mass spectrometer</td>
			<td>&nbsp;</td>
			<td>Sequenom</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
		</tr>
	</tbody>
</table>

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.

Watch this Scientific Journal Video about An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations at JoVE.com

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

आनुवंशिक संघों अक्सर एक कार्यात्मक स्तर पर अस्पष्टीकृत रहते हैं. इस विधि के लिए जीन अभिव्यक्ति पर लिखित SNPs के लिए विषमयुग्मजी कोशिकाओं का विश्लेषण करके phenotype - जुड़े आनुवंशिक मार्करों के प्रभाव का आकलन करना है. प्रौद्योगिकी MALDI-TOF मास स्पेक्ट्रोमेट्री द्वारा सटीक माप एलील विशिष्ट प्राइमर विस्तार उत्पादों यों की अनुमति देता है.

एक ऐल्लि विशिष्ट जीन एक्सप्रेशन आनुवंशिक संघों के कार्यात्मक आधार टेस्ट परख

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

Research

JoVE Journal

Biology

Light/dark Transition Test for Mice

/ प्रकाश अंधेरे चूहे के लिए संक्रमण टेस्ट

Although all of the mouse genome sequences have been determined, we do not yet know the functions of most of these genes. Gene-targeting techniques, ...

The Preparation of Primary Hematopoietic Cell Cultures From Murine Bone Marrow for Electroporation

प्राथमिक electroporation के लिए murine अस्थि मज्जा से hematopoietic सेल संस्कृतियों की तैयारी

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

Spinal Cord Electrophysiology

स्पाइनल कॉर्ड इलैक्ट्रोफिजियोलॉजी

The neonatal mouse spinal cord is a model for studying the development of neural circuitries and locomotor movement. We demonstrate the spinal cord ...

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

जीन Pulser MXcell electroporation प्रणाली का उपयोग करने के लिए उच्च क्षमता के साथ प्राथमिक कोशिकाओं transfect

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

एक स्वचालित सेल काउंटर का उपयोग करने के लिए जीन एक्सप्रेशन अध्ययन सरल: आईएल-4 निर्भर जीन एक्सप्रेशन के Namalwa कक्ष में siRNA नॉकडाउन

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 ...

A Reverse Genetic Approach to Test Functional Redundancy During Embryogenesis

एक रिवर्स जेनेटिक Embryogenesis दौरान दृष्टिकोण कार्यात्मक अतिरेक टेस्ट

Gene function during embryogenesis is typically defined by loss-of-function experiments, for example by targeted mutagenesis (knockout) in the mouse. In ...

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

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

Chromatin परख सक्रिय मानव कोशिकाओं में जीन एक्सप्रेशन में गतिशील histone संशोधन करने के लिए immunoprecipitation (चिप)

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

Paraffin-Embedded and Frozen Sections of Drosophila Adult Muscles

Paraffin-Embedded and Frozen Sections of Drosophila Adult Muscles

के आयल - एंबेडेड और जमे हुए वर्गों ड्रोसोफिला वयस्क स्नायु

The molecular characterization of muscular dystrophies and myopathies in humans has revealed the complexity of muscle disease and genetic analysis of ...

In vitro Reconstitution of the Active T. castaneum Telomerase

In vitro Reconstitution of the Active T. castaneum Telomerase

सक्रिय टी. के पुनर्गठन इन विट्रो में castaneum टेलोमिरेज

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

Pharmacological and Functional Genetic Assays to Manipulate Regeneration of the Planarian Dugesia japonica

Pharmacological and Functional Genetic Assays to Manipulate Regeneration of the Planarian Dugesia japonica

भेषज और कार्यात्मक जेनेटिक Assays Planarian की पुनर्जनन में हेरफेर करने के लिए बिही Dugesia</em

Free-living planarian flatworms have a long history of experimental usage owing to their remarkable regenerative abilities1. Small fragments excised from ...