Name: a reporter based cellular assay for monitoring splicing efficiency
Uploaded: 2021-09-15T14:00:00
Description: Watch this Scientific Journal Video about A Reporter Based Cellular Assay for Monitoring Splicing Efficiency at JoVE.com

这项工作得到了美国国立卫生研究院（R21CA170786和R01GM127464）和美国癌症协会（机构研究资助74-001-34-IRG）以及山谷研究合作计划（P1-4009和VRP77）向S.S.和W.M的资金支持。内容完全由作者负责，并不一定代表美国国立卫生研究院的官方观点。

1. 试剂和缓冲液
注意：所有使用真空过滤器的灭菌都应在生物安全柜中使用0.2μm聚醚砜（PES）膜进行。
<ol><li>将1.0 mL焦碳酸二乙酯（DEPC）加入1.0升去离子水中，在室温（RT）下混合至少1小时，高压灭菌两次，然后在使用前冷却至室温，以制备不含RNase的水。</li>
	<li>通过将一包DMEM粉末（13.4克），3.7克碳酸氢钠，100毫升胎牛血清（FBS），青霉素和链霉素与约800毫升无菌去离?...

<ol>
	<li>Zhuang, Y., Weiner, A. 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+compensatory+base+change+in+U1+snRNA+suppresses+a+5'+splice+site+mutation.">A compensatory base change in U1 snRNA suppresses a 5' splice site mutation.</a> Cell. 46 (6), 827-835 (1986).</li><li>Scotti, M. M., Swanson, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+mis-splicing+in+disease.">RNA mis-splicing in disease.</a> Nature Review Genetics. 17 (1), 19-32 (2016).</li><li>Ward, A. J., Cooper, T. 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+pathobiology+of+splicing.">The pathobiology of splicing.</a> Journal of Pathology. 220 (2), 152-163 (2010).</li><li>Scalet, D., 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=Disease-causing+variants+of+the+conserved++2T+of+5'+splice+sites+can+be+rescued+by+engineered+U1snRNAs.">Disease-causing variants of the conserved +2T of 5' splice sites can be rescued by engineered U1snRNAs.</a> Human Mutatation. 40 (1), 48-52 (2019).</li><li>Yamazaki, 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=Use+of+modified+U1+small+nuclear+RNA+for+rescue+from+exon+7+skipping+caused+by+5'-splice+site+mutation+of+human+cathepsin+A+gene.">Use of modified U1 small nuclear RNA for rescue from exon 7 skipping caused by 5'-splice site mutation of human cathepsin A gene.</a> Gene. 677, 41-48 (2018).</li><li>Yanaizu, M., Sakai, K., Tosaki, Y., Kino, Y., Satoh, J. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small+nuclear+RNA-mediated+modulation+of+splicing+reveals+a+therapeutic+strategy+for+a+TREM2+mutation+and+its+post-transcriptional+regulation.">Small nuclear RNA-mediated modulation of splicing reveals a therapeutic strategy for a TREM2 mutation and its post-transcriptional regulation.</a> Science Reports. 8 (1), 6937 (2018).</li><li>Balestra, D., 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=Splicing+mutations+impairing+CDKL5+expression+and+activity+can+be+efficiently+rescued+by+U1snRNA-based+therapy.">Splicing mutations impairing CDKL5 expression and activity can be efficiently rescued by U1snRNA-based therapy.</a> International Journal of Molecular Sciences. 20 (17), 20174130 (2019).</li><li>Donadon, I., 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=Exon-specific+U1+snRNAs+improve+ELP1+exon+20+definition+and+rescue+ELP1+protein+expression+in+a+familial+dysautonomia+mouse+model.">Exon-specific U1 snRNAs improve ELP1 exon 20 definition and rescue ELP1 protein expression in a familial dysautonomia mouse model.</a> Human Molecular Genetics. 27 (14), 2466-2476 (2018).</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> Journal of Visualized Experiments. (45), e2565 (2010).</li><li>Summer, H., Gramer, R., Droge, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Denaturing+urea+polyacrylamide+gel+electrophoresis+(Urea+PAGE).">Denaturing urea polyacrylamide gel electrophoresis (Urea PAGE).</a> Journal of Visualized Experiments. (32), e1485 (2009).</li><li>Dominski, Z., Kole, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selection+of+splice+sites+in+pre-mRNAs+with+short+internal+exons.">Selection of splice sites in pre-mRNAs with short internal exons.</a> Molecular Cell Biology. 11 (12), 6075-6083 (1991).</li><li>Amir-Ahmady, B., Boutz, P. L., Markovtsov, V., Phillips, M. L., Black, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exon+repression+by+polypyrimidine+tract+binding+protein.">Exon repression by polypyrimidine tract binding protein.</a> RNA. 11 (5), 699-716 (2005).</li><li>Le Guedard-Mereuze, S., 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=Sequence+contexts+that+determine+the+pathogenicity+of+base+substitutions+at+position++3+of+donor+splice-sites.">Sequence contexts that determine the pathogenicity of base substitutions at position +3 of donor splice-sites.</a> Human Mutation. 30 (9), 1329-1339 (2009).</li><li>Sharma, S., Wongpalee, S. P., Vashisht, A., Wohlschlegel, J. A., Black, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stem-loop+4+of+U1+snRNA+is+essential+for+splicing+and+interacts+with+the+U2+snRNP-specific+SF3A1+protein+during+spliceosome+assembly.">Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly.</a> Genes and Development. 28 (22), 2518-2531 (2014).</li><li>Steitz, J. A., 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> Functions of the abundant U-snRNPs. Structure and function of major and minor small nuclear ribonucleoprotein particles. , 115-154 (1988).</li><li>Fortes, 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=Inhibiting+expression+of+specific+genes+in+mammalian+cells+with+5'+end-mutated+U1+small+nuclear+RNAs+targeted+to+terminal+exons+of+pre-mRNA.">Inhibiting expression of specific genes in mammalian cells with 5' end-mutated U1 small nuclear RNAs targeted to terminal exons of pre-mRNA.</a> Proceedings of the National Academy of Sciences U.S.A. 100 (14), 8264-8269 (2003).</li><li>Roca, X., 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=Widespread+recognition+of+5'+splice+sites+by+noncanonical+base-pairing+to+U1+snRNA+involving+bulged+nucleotides.">Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides.</a> Genes and Development. 26 (10), 1098-1109 (2012).</li><li>Roca, X., Krainer, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recognition+of+atypical+5'+splice+sites+by+shifted+base-pairing+to+U1+snRNA.">Recognition of atypical 5' splice sites by shifted base-pairing to U1 snRNA.</a> Nature Structural Molecular Biology. 16 (2), 176-182 (2009).</li><li>Taladriz-Sender, A., Campbell, E., Burley, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Splice-switching+small+molecules:+A+new+therapeutic+approach+to+modulate+gene+expression.">Splice-switching small molecules: A new therapeutic approach to modulate gene expression.</a> Methods. 167, 134-142 (2019).</li><li>Hamid, F. M., Makeyev, E. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+mechanism+underlying+position-specific+regulation+of+alternative+splicing.">A mechanism underlying position-specific regulation of alternative splicing.</a> Nucleic Acids Research. 45 (21), 12455-12468 (2017).</li><li>Martelly, 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=Synergistic+roles+for+human+U1+snRNA+stem-loops+in+pre-mRNA+splicing.">Synergistic roles for human U1 snRNA stem-loops in pre-mRNA splicing.</a> RNA Biology. , 1-18 (2021).</li></ol>

该测定可以适用于HeLa以外的细胞系中的剪接分析，但是，可能需要优化影响转染效率的因素，例如细胞汇合度和DNA数量。报告者与U1构建比是另一个关键参数，可能需要根据在其他细胞类型中观察到的表达水平来确定。提取的RNA的质量对于剪接分析至关重要;因此，强烈建议使用不含RNase的水并用RNase灭活剂对表面进行去污。
通过引物延伸或荧光RT-PCR对报告转录本的分析产生类...

前mRNA剪接是一个重要的处理步骤，它去除非编码内含子并精确地标记编码外显子以形成成熟的mRNA。通过剪接机械的组件识别外显子-内含子交界处的共识序列，称为5'-拼接位点和3'-拼接位点，启动拼接过程。U1小核核糖核蛋白（snRNP）通过将U1 snRNA与前mRNA1的碱基配对来识别5'-剪接位点。改变5'-剪接位点序列的遗传突变与许多疾病有关2，3。据预测，U1 snRNA与突变5'-剪接位点的碱基配对的损失会导致异常剪接，这可能会损害受影响转录本的翻译。纠正剪接缺陷的潜在治疗方法包括通过修饰的U1 snRNA在其5'-区域携带代偿核苷酸变化来抑制突变，该区域与5'-剪接位点基本配对。这种修饰的U1 snRNA，也称为外显子特异性U1 snRNA，已被发现可有效逆转剪接缺陷，导致获救的mRNA4，5，6，7，8的蛋白质表达增加。
在这里，我们描述了U1 snRNP补集测定，这是一种基于报告的细胞剪接测定，可以评估5'-ss突变对外显子剪接的影响，也可用于开发修饰的U1 snRNA，以挽救外显子包涵体。我们还提供通过引物延伸和RT-PCR监测剪接报告转录本的方案，以及通过引物延伸和RT-qPCR确定修饰的U1 snRNA的表达的方案。

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Reagent Grade Deionized Water</td>
			<td>ThermoFisher Scientific</td>
			<td>23-751628</td>
			<td></td>
		</tr>
		<tr>
			<td>Diethyl pyrocarbonate (DEPC)</td>
			<td>Sigma-Aldrich</td>
			<td>D5758-25ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle Medium (DMEM) powder packet</td>
			<td>Gibco</td>
			<td>12100-046</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Bicarbonate</td>
			<td>ThermoFisher Scientific</td>
			<td>S233-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum (FBS), Australian Source, Heat Inactivated</td>
			<td>Omega Scientific</td>
			<td>FB-22</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin (P/S)</td>
			<td>Sigma-Aldrich</td>
			<td>P4458-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Hydroxide, Standard Solution 1.0N</td>
			<td>Sigma-Aldrich</td>
			<td>S2567-16A</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric Acid, Certified ACS Plus, 36.5 to 38.0%</td>
			<td>ThermoFisher Scientific</td>
			<td>A144-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Disposable PES Bottle Top Filters</td>
			<td>ThermoFisher Scientific</td>
			<td>FB12566510</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA Disodium Salt Dihydrate</td>
			<td>Amresco</td>
			<td>0105-2.5KG</td>
			<td></td>
		</tr>
		<tr>
			<td>2.5% Trypsin (10x), no phenol red</td>
			<td>ThermoFisher Scientific</td>
			<td>15090046</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>Fisher Bioreagent</td>
			<td>BP358-212</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Chloride</td>
			<td>Fisher Bioreagent</td>
			<td>BP366-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Disodium Hydrogen Phosphate Heptahydrate</td>
			<td>Fisher Bioreagent</td>
			<td>BP332-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Dihydrogen Phosphate</td>
			<td>Fisher Bioreagent</td>
			<td>BP362-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Transfection medium - Opti-MEM&#8482; I Reduced Serum Medium, no phenol red</td>
			<td>ThermoFisher Scientific</td>
			<td>11058021</td>
			<td></td>
		</tr>
		<tr>
			<td>Transfection Reagent - Lipofectamine&#8482; 2000</td>
			<td>ThermoFisher Scientific</td>
			<td>13778150</td>
			<td></td>
		</tr>
		<tr>
			<td>TRIzol&#8482; Reagent</td>
			<td>ThermoFisher Scientific</td>
			<td>15596018</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform (Approx. 0.75% Ethanol as Preservative/Molecular Biology)</td>
			<td>ThermoFisher Scientific</td>
			<td>BP1145-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol, Absolute (200 Proof), Molecular Biology Grade, Fisher BioReagents</td>
			<td>ThermoFisher Scientific</td>
			<td>BP2818-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Isopropanol, Molecular Biology Grade, Fisher BioReagents</td>
			<td>ThermoFisher Scientific</td>
			<td>BP2618-212</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycogen (5 mg/ml)</td>
			<td>ThermoFisher Scientific</td>
			<td>AM9510</td>
			<td></td>
		</tr>
		<tr>
			<td>Direct-zol RNA Miniprep Kit</td>
			<td>Zymo Research</td>
			<td>R2052</td>
			<td></td>
		</tr>
		<tr>
			<td>ATP, [&#947;-32P]- 6000Ci/mmol 150mCi/ml Lead, 1 mCi</td>
			<td>PerkinElmer</td>
			<td>NEG035C001MC</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 Polynucleotide Kinase</td>
			<td>New England Biolabs</td>
			<td>M0201L</td>
			<td></td>
		</tr>
		<tr>
			<td>Size exclusion beands - Sephadex&#174; G-25</td>
			<td>Sigma-Aldrich</td>
			<td>G2580-10G</td>
			<td></td>
		</tr>
		<tr>
			<td>Size exclusion mini columns</td>
			<td>USA Scientific</td>
			<td>1415-0600</td>
			<td></td>
		</tr>
		<tr>
			<td>pBR322 DNA-MspI Digest</td>
			<td>New England Biolabs</td>
			<td>N3032S</td>
			<td></td>
		</tr>
		<tr>
			<td>Low Molecular Weight Marker, 10-100 nt</td>
			<td>Affymetrix</td>
			<td>76410 100 UL</td>
			<td></td>
		</tr>
		<tr>
			<td>Rnase inactivating reagents - RNaseZAP&#8482;</td>
			<td>Sigma-Aldrich</td>
			<td>R2020-250ML</td>
			<td></td>
		</tr>
		<tr>
			<td>dNTP Mix (10 mM ea)</td>
			<td>ThermoFisher Scientific</td>
			<td>18427013</td>
			<td></td>
		</tr>
		<tr>
			<td>RNaseOUT&#8482; Recombinant Ribonuclease Inhibitor</td>
			<td>ThermoFisher Scientific</td>
			<td>10777019</td>
			<td></td>
		</tr>
		<tr>
			<td>Reverse Transcriptase - M-MLV Reverse Transcriptase</td>
			<td>ThermoFisher Scientific</td>
			<td>28025013</td>
			<td>used for primer extension</td>
		</tr>
		<tr>
			<td>Taq DNA Polymerase</td>
			<td>ThermoFisher Scientific</td>
			<td>10342020</td>
			<td></td>
		</tr>
		<tr>
			<td>Random Hexamers (50 &#181;M)</td>
			<td>ThermoFisher Scientific</td>
			<td>N8080127</td>
			<td></td>
		</tr>
		<tr>
			<td>Real time PCR mix - SYBR&#8482; Select Master Mix</td>
			<td>ThermoFisher Scientific</td>
			<td>4472903</td>
			<td></td>
		</tr>
		<tr>
			<td>SuperScript&#8482; III Reverse Transcriptase</td>
			<td>ThermoFisher Scientific</td>
			<td>18080093</td>
			<td>used for cDNA preparation</td>
		</tr>
		<tr>
			<td>Dithiothreitol (DTT)</td>
			<td>ThermoFisher Scientific</td>
			<td>18080093</td>
			<td></td>
		</tr>
		<tr>
			<td>5X First-Strand Buffer</td>
			<td>ThermoFisher Scientific</td>
			<td>18080093</td>
			<td></td>
		</tr>
		<tr>
			<td>Formamide (&#8805;99.5%)</td>
			<td>ThermoFisher Scientific</td>
			<td>BP228-100</td>
			<td>Review Material Safety Data Sheets</td>
		</tr>
		<tr>
			<td>Bromophenol Blue sodium salt</td>
			<td>Sigma-Aldrich</td>
			<td>114405-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene Cyanol FF</td>
			<td>Sigma-Aldrich</td>
			<td>2650-17-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris Base (White Crystals or Crystalline Powder/Molecular Biology)</td>
			<td>ThermoFisher Scientific</td>
			<td>BP152-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Boric Acid (Crystalline/Electrophoresis)</td>
			<td>ThermoFisher Scientific</td>
			<td>BP168-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Acrylamide: Bis-Acrylamide 19:1 (40% Solution/Electrophoresis)</td>
			<td>ThermoFisher Scientific</td>
			<td>BP1406-1</td>
			<td>Review Material Safety Data Sheets</td>
		</tr>
		<tr>
			<td>Urea (Colorless-to-White Crystals or Crystalline Powder/Mol. Biol.)</td>
			<td>ThermoFisher Scientific</td>
			<td>BP169-212</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium peroxodisulphate (APS) &#8805;98%, Pro-Pure, Proteomics Grade</td>
			<td>VWR</td>
			<td>M133-25G</td>
			<td></td>
		</tr>
		<tr>
			<td>Sigmacote</td>
			<td>Sigma-Aldrich</td>
			<td>SL2-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>N,N,N&#39;,N&#39;-Tetramethylethylenediamine (TEMED) &#8805;99%, Ultrapure</td>
			<td>VWR</td>
			<td>0761-25ML</td>
			<td>Review Material Safety Data Sheets</td>
		</tr>
		<tr>
			<td>Adjustable Slab Gel Systems, Expedeon</td>
			<td>VWR</td>
			<td>ASG-400</td>
			<td></td>
		</tr>
		<tr>
			<td>Vertical Gel Wrap&#8482; Glass Plate Sets, 16.5 x 14.5cm</td>
			<td>VWR</td>
			<td>NGP-125NR</td>
			<td></td>
		</tr>
		<tr>
			<td>Vertical Gel Wrap&#8482; Glass Plate Sets, 16.5 x 22.0cm</td>
			<td>VWR</td>
			<td>NGP-200NR</td>
			<td></td>
		</tr>
		<tr>
			<td>Vertical Gel Wrap&#8482; Glass Plate Sets, 16.5 x 38.7cm</td>
			<td>VWR</td>
			<td>NGP-400NR</td>
			<td></td>
		</tr>
		<tr>
			<td>GE Storage Phosphor Screens</td>
			<td>Sigma-Aldrich</td>
			<td>GE28-9564</td>
			<td></td>
		</tr>
		<tr>
			<td>Typhoon&#8482; FLA 7000 Biomolecular Imager</td>
			<td>GE Healthcare</td>
			<td>28-9610-73 AB</td>
			<td></td>
		</tr>
		<tr>
			<td>Beckman Coulter LS6500 Liquid Scintillation Counter</td>
			<td>GMI</td>
			<td>8043-30-1194</td>
			<td></td>
		</tr>
		<tr>
			<td>C1000 Touch Thermal Cycler</td>
			<td>ThermoFisher Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>QuantStudio 6 Flex Real-Time PCR Systems</td>
			<td>ThermoFisher Scientific</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

a reporter based cellular assay for monitoring splicing efficiency

在基因表达过程中，前mRNA剪接的关键步骤涉及精确识别剪接位点和高效组装剪接体复合物，以在成熟mRNA的细胞质输出之前加入外显子并去除内含子。剪接效率可以通过剪接位点突变的存在，反式剪接因子的影响或治疗活性来改变。在这里，我们描述了可用于监测任何给定外显子的剪接效率的细胞测定方案。该测定使用适应性强的质粒编码为3-外显子/2-内含子的微型基因报告基因，可通过瞬时转染在哺乳动物细胞中表达。转染后，分离总细胞RNA，并通过引物延伸或半定量逆转录酶 - 聚合酶链反应（RT-PCR）确定报告mRNA中外显子剪接的效率。我们描述了如何通过在报告中引入疾病相关的5′剪接位点突变来确定其影响;以及如何通过与U1小核RNA（snRNA）构建体共转染来实现这些突变的抑制，该构建体在其5'区域中携带代偿性突变，该区域与前mRNA中外显子 - 内含子连接处的5'-剪接位点基本配对。因此，报告基因可用于设计治疗性U1颗粒，以提高对突变体5′剪接位点的识别。将 顺式作用调节位点（例如剪接增强剂或消音器序列）插入报告程序中也可用于检查U1 snRNP在由特定替代剪接因子介导的调节中的作用。最后，将报告细胞与小分子孵育，以确定潜在疗法对组成前mRNA剪接或携带突变5′剪接位点的外显子的影响。总体而言，报告基因检测可用于监测各种条件下的剪接效率，以研究基本的剪接机制和剪接相关疾病。

剪接报告人Dup51是一种三外显子二内含子微型基因，来源于人类β珠蛋白基因，之前已有描述（图1A）11，12 。我们通过引入Usher综合征相关的5'剪接位点突变创建了一个突变报告者Dup51p，这些突变发生在原钙粘蛋白15（PCDH15）基因13的外显子3中。外显子2-内含子2结处的5'-接头位点序列从CAG/GUUGGUAUC改为AUG/GUGUGUA...

Watch this Scientific Journal Video about A Reporter Based Cellular Assay for Monitoring Splicing Efficiency at JoVE.com

A Reporter Based Cellular Assay for Monitoring Splicing Efficiency

该协议描述了一种微型基因报告基因检测，用于监测5'-剪接位点突变对剪接的影响，并开发抑制因子U1 snRNA以挽救突变诱导的剪接抑制。报告基因和抑制子U1 snRNA构建体在HeLa细胞中表达，并通过引物延伸或RT-PCR分析剪接。

一种基于报告基因的细胞检测，用于监测剪接效率

During gene expression, the vital step of pre-mRNA splicing involves accurate recognition of splice sites and efficient assembly of spliceosomal complexes ...

该协议描述了使用适应性强的管理报告程序进行监测剪接效率的细胞测定。该检测试剂盒可用于研究与疾病相关的突变在埃克森美孚或剪接位点中的作用，并设计用于治疗，特别是一个颗粒，以提高突变体对五点剪接位点的识别。Hela细胞中的传代吸吸用过的培养基，并在37摄氏度下以含有1毫摩尔EDTA的0.2 5%行程的三毫升孵育细胞三分钟。在7毫升新鲜DMEM下孵育后，将细胞悬浮液转移到10毫升管中。离心细胞。然后将细胞沉淀重悬于10毫升新鲜DMEM中，并将细胞以20%汇合度接种在新的组织培养皿上，以进行瞬时转染。用干净的血细胞计数器载玻片计数hela细胞，并制备密度为每毫升2.5倍10至第五个细胞的悬浮液，将一毫升细胞悬浮液接种到12孔板的每个孔中，并在37摄氏度下孵育过夜。第二天吸出用过的培养基，并将800微升新鲜DMEM与血清加入板中。准备转染混合物并涡旋15秒。然后离心混合物并在室温下孵育五分钟。孵育后，将所有200微升转染混合物加入12孔hela细胞板的一个孔中，以达到每孔1毫升的最终体积，并将板在37摄氏度下孵育48小时。制备的标记反应正在孵育。通过轻柔涡旋10秒钟重悬25千吨道尔顿分子量截止尺寸排除珠。接下来将600微升重悬的珠子转移到一次性迷你柱中，置于1.5毫升的收集管中，并将珠子库存返回到4摄氏度。离心柱并丢弃流经它们的流量。然后通过向色谱柱中加入300微升RNA游离水来洗涤珠子两次。第二次洗涤后，将迷你色谱柱转移到新的1.5毫升离心管中，并将激酶反应混合物加入色谱柱中。离心柱并收集通过含有P32标记的寡核苷酸的流动。将两微克从螺旋细胞中提取的RNA加入200微升微量离心管中，并加入RNA游离水以构成6.55微升的体积。接下来，向每个含有RNA样品的PCR管中加入0.9微升的预混液，并首先在65摄氏度下孵育管5分钟，然后在冰上孵育一分钟。接下来在2.55微升下，将两个预混液，到每个含有RNA的试管和预混料一个，并将试管在室温下孵育10分钟。孵育后，将管转移到热循环仪中，首先在50摄氏度下孵育60分钟，然后在70摄氏度下孵育15分钟。孵育后，向每个样品中加入10微升2X甲酰胺RNA上样染料，然后通过UIA页面分离片段。珀西DNA合成。将从转染的hela细胞中提取的2微克RNA加入200微升微米离心管中，并加入RNA游离水以构成低11微升的体积。接下来，加入两微升，每个样品一个预混液，首先在65摄氏度下孵育五分钟，然后在冰上孵育一分钟。接下来，向每个管中加入七微升，预混两个，并将管子在室温下孵育10分钟，然后在50摄氏度下孵育60分钟，在70摄氏度下孵育15分钟。接下来，对于PCR，稀释C DNA反应以产生每微升100纳克的浓度，并将每个CDNA样品的一微升转移到新的PCR管中。向每个含有CDNA的管中加入10.5微升的预混液，并进行PCR。PCR完成后使用热循环仪。向每个管中加入12.5微升2X甲酰胺DNA加载染料。将样品在95摄氏度下加热五分钟，然后继续执行UIA页面。将五微升稀释的CDNA移入96孔qpcr板的单个孔中，一式三份。接下来，向每个孔中加入10微升的实时PCR混合物，用光学膜密封板，然后离心以收集孔底部的反应，然后在收集目标扩增子的阈值定量循环值的同时进行qpcr。在加载标记物和样品之前，用TBE缓冲液冲洗孔以除去沉降的尿素。然后，每孔加载每个样品的10微升，并将凝胶以300至500伏特运行两到三个小时，或直到二甲苯到达底部。电泳后，从电泳装置中取出玻璃板，并小心地将两个板分开，使凝胶平放在任一玻璃表面上，然后将凝胶转移到滤纸上并用保鲜膜覆盖，使用凝胶干燥器在80摄氏度下真空干燥凝胶30分钟， 然后将干燥的凝胶置于荧光粉成像盒中，在室温下孵育过夜。当在hela细胞中表达时，切片报告程序dup 51 minnijean表达成熟的全长转录本，其中埃克森美孚二号被有效地拼接。五个主要剪接位点突变和dup 51 P将埃克森美孚的两个包涵体从95%降低到30%，导致形成较短的转录本。dup 51 P与U15A SNRNA的共表达挽救了埃克森美孚的两次剪接，并恢复了全长转录本的形成。相比之下，与野生型U1或U15G变体的共表达对dup 51P拼接没有类似的效果。通过原代扩展检测U15A变异转录本，使用U1 7至26寡核苷酸，其长度为20个核苷酸，碱基对靠近U1 SNRNA第五位置的腺嘌呤。在仅存在DATP的情况下，U1 7至26允许为内源性野生型U1 SNRNA掺入2至3个核苷酸，产生22或23个核苷酸长产物。对于U15A和U15G变体，在添加产生21核苷酸产物的单个腺苷酸后，延伸终止。在归一化为U2 SNRNA表达后，转染的U1野生型U1 5g和U15A变体在内源性SNRNA上以三到五倍的速度表达。提取的RNA的质量对于剪接分析至关重要。因此，强烈建议使用不含RNA的水，并用RNA灭活剂对服务进行去污。这里描述的报告系统可以应用于研究U1 SN RNAs在剪接调节中的作用，以使用修饰U1SN RNA进行基因沉默的闪速剪接突变的逆转效应。

a-reporter-based-cellular-assay-for-monitoring-splicing-efficiency

Research

Education

JoVE Journal

JoVE Core

Cell Biology

Biochemistry

Unit 1

Transcription: DNA to RNA

SCIENTISTS IN ACTION

A Fluorescence-based Assay of Phospholipid Scramblase Activity

Scramblases translocate phospholipids across the membrane bilayer bidirectionally in an ATP-independent manner. The first scramblase to be identified and biochemically verified was opsin, the apoprotein of the photoreceptor rhodopsin. Rhodopsin is a G protein-coupled receptor localized in rod photoreceptor disc membranes of the retina where it is responsible for the perception of light. Rhodopsin&#39;s scramblase activity does not depend on its ligand 11-cis-retinal, i.e., the apoprotein opsin is also active as a scramblase. Although constitutive and regulated phospholipid scrambling play an important role in cell physiology, only a few phospholipid scramblases have been identified so far besides opsin. Here we describe a fluorescence-based assay of opsin&#39;s scramblase activity. Opsin is reconstituted into large unilamellar liposomes composed of phosphatidylcholine, phosphatidylglycerol and a trace quantity of fluorescent NBD-labeled PC (1-palmitoyl-2-{6-[7-nitro-2-1,3-benzoxadiazole-4-yl)amino]hexanoyl}-sn-glycero-3-phosphocholine). Scramblase activity is determined by measuring the extent to which NBD-PC molecules located in the inner leaflet of the vesicle are able to access the outer leaflet where their fluorescence is chemically eliminated by a reducing agent that cannot cross the membrane. The methods we describe have general applicability and can be used to identify and characterize scramblase activities of other membrane proteins.

We describe a fluorescence-based assay to measure phospholipid scrambling in large unilamellar liposomes reconstituted with opsin.

磷脂Scramblase活动的基于荧光的测定法

Scramblases translocate phospholipids across the membrane bilayer bidirectionally in an ATP-independent manner. The first scramblase to be identified and ...

科研

生物化学

Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1

Direct electrochemical detection of c-type cytochrome complexes embedded in the bacterial outer membrane (outer membrane c-type cytochrome complexes; OM c-Cyts) has recently emerged as a novel whole-cell analytical method to characterize the bacterial electron transport from the respiratory chain to the cell exterior, referred to as the extracellular electron transport (EET). While the pathway and kinetics of the electron flow during the EET reaction have been investigated, a whole-cell electrochemical method to examine the impact of cation transport associated with EET has not yet been established. In the present study, an example of a biochemical technique to examine the deuterium kinetic isotope effect (KIE) on EET through OM c-Cyts using a model microbe, Shewanella oneidensis MR-1, is described. The KIE on the EET process can be obtained if the EET through OM c-Cyts acts as the rate-limiting step in the microbial current production. To that end, before the addition of D2O, the supernatant solution was replaced with fresh media containing a sufficient amount of the electron donor to support the rate of upstream metabolic reactions, and to remove the planktonic cells from a uniform monolayer biofilm on the working electrode. Alternative methods to confirm the rate-limiting step in microbial current production as EET through OM c-Cyts are also described. Our technique of a whole-cell electrochemical assay for investigating proton transport kinetics can be applied to other electroactive microbial strains.

Electrochemical Detection of Deuterium Kinetic Isotope Effect on Extracellular Electron Transport in Shewanella oneidensis MR-1

Here we present a protocol of whole-cell electrochemical experiments to study the contribution of proton transport to the rate of extracellular electron transport via the outer-membrane cytochromes complex in Shewanella oneidensis MR-1.

电化学检测氘动力学同位素对希瓦氏菌 oneidensis MR-1 细胞外电子传输的影响

Direct electrochemical detection of c-type cytochrome complexes embedded in the bacterial outer membrane (outer membrane c-type cytochrome complexes; OM ...

An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity

N6-isopentenyladenosine RNA modifications are functionally diverse and highly conserved among prokaryotes and eukaryotes. One of the most highly conserved N6-isopentenyladenosine modifications occurs at the A37 position in a subset of tRNAs. This modification improves translation efficiency and fidelity by increasing the affinity of the tRNA for the ribosome. Mutation of enzymes responsible for this modification in eukaryotes are associated with several disease states, including mitochondrial dysfunction and cancer. Therefore, understanding the substrate specificity and biochemical activities of these enzymes is important for understanding of normal and pathologic eukaryotic biology. A diverse array of methods has been employed to characterize i6A modifications. Herein is described a direct approach for the detection of isopentenylation by Mod5. This method utilizes incubation of RNAs with a recombinant isopentenyl transferase, followed by RNase T1 digestion, and 1-dimensional gel electrophoresis analysis to detect i6A modifications. In addition, the potential adaptability of this protocol to characterize other RNA-modifying enzymes is discussed.

An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity

Here, we describe a protocol for the biochemical characterization of the yeast RNA-modifying enzyme, Mod5, and discuss how this protocol could be applied to other RNA-modifying enzymes.

体外检测 tRNA-Isopentenyl 转移酶活性的实验研究

N6-isopentenyladenosine RNA modifications are functionally diverse and highly conserved among prokaryotes and eukaryotes. One of the most highly conserved ...

A High-Throughput Luciferase Assay to Evaluate Proteolysis of the Single-Turnover Protease PCSK9

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a single-turnover protease which regulates serum low-density lipoprotein (LDL) levels and, consequently, cardiovascular disease. Although PCSK9 proteolysis is required for its full hypercholesterolemic effect, the evaluation of its proteolytic function is challenging: PCSK9 is only known to cleave itself, undergoes only a single turnover, and after proteolysis, retains its substrate in its active site as an auto-inhibitor. The methods presented here describe an assay which overcomes these challenges. The assay focuses on intermolecular proteolysis in a cell-based context and links successful cleavage to the secreted luciferase activity, which can be easily read out in the conditioned medium. Via sequential steps of mutagenesis, transient transfection, and a luciferase readout, the assay can probe PCSK9 proteolysis under conditions of either genetic or molecular perturbation in a high-throughput manner. This system is well suited for both the biochemical evaluation of clinically discovered missense single-nucleotide polymorphisms (SNPs), as well as for the screening of small-molecule inhibitors of PCSK9 proteolysis.

This protocol presents a method to evaluate the proteolytic activity of an intrinsically low-activity, single turnover protease in a cellular context. Specifically, this method is applied to evaluate the proteolytic activity of PCSK9, a key driver of lipid metabolism whose proteolytic activity is required for its ultimate hypercholesterolemic function.

高通量荧光素酶法评价单周转蛋白酶 PCSK9 的蛋白质水解

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a single-turnover protease which regulates serum low-density lipoprotein (LDL) levels and, ...

Screening for Phytoestrogens using a Cell-based Estrogen Receptor  &#946; Reporter Assay

Plants are a source of food for many animals, and&#160;they can produce thousands of chemicals. Some of these compounds affect physiological processes in the vertebrates that consume them, such as endocrine function. Phytoestrogens, the most well studied endocrine-active phytochemicals, directly interact with the hypothalamo-pituitary gonadal axis of the vertebrate endocrine system. Here we present the novel use of a cell-based assay to screen plant extracts for the presence of compounds that have estrogenic biological activity. This assay uses mammalian cells engineered to highly express estrogen receptor beta (ER&#946;) and that have been transfected with a luciferase gene. Exposure to compounds with estrogenic activity results in the cells producing light. This assay is a reliable and simple way to test for biological estrogenic activity. It has several improvements over transient transfection assays, most notably, ease of use, the stability of the cells, and the sensitivity of the assay.

We have optimized a commercially available estrogen receptor &#946; reporter assay for screening human and nonhuman primate foods for estrogenic activity. We validated this assay by showing that the known estrogenic human food soy registers high, while other foods show no activity.

使用基于细胞的雌激素受体对植物雌激素进行筛查β记者分析

Plants are a source of food for many animals, and&#160;they can produce thousands of chemicals. Some of these compounds affect physiological processes in ...

An Electrochemiluminescence-Based Assay for MeCP2 Protein Variants

The ECLIA is a versatile method which is able to quantify endogenous and recombinant protein amounts in a 96-well format. To demonstrate ECLIA efficiency, this assay was used to analyze intrinsic levels of MeCP2 in mouse brain tissue and the uptake of TAT-MeCP2 in human dermal fibroblasts. The MeCP2-ECLIA produces highly accurate and reproducible measurements with low intra- and inter-assay error. In summary, we developed a quantitative method for the evaluation of MeCP2 protein variants that can be utilized in high-throughput screens.

The electrochemiluminescence immunoassay (ECLIA) is a novel approach for quantitative detection of endogenous and exogenously applied MeCP2 protein variants, which produces highly quantitative, accurate and reproducible measurements with low intra- and inter-assay error over a wide working range. Here, the protocol for the MeCP2-ECLIA in a 96-well format is described.

MeCP2蛋白质变异的电化学发光测定

The ECLIA is a versatile method which is able to quantify endogenous and recombinant protein amounts in a 96-well format. To demonstrate ECLIA efficiency, ...

Assessment of Cellular Oxidation using a Subcellular Compartment-Specific Redox-Sensitive Green Fluorescent Protein

Measuring the intracellular oxidation/reduction balance provides an overview of the physiological and/or pathophysiological redox status of an organism. Thiols are especially important for illuminating the redox status of cells via their reduced dithiol and oxidized disulfide ratios. Engineered cysteine-containing fluorescent proteins open a new era for redox-sensitive biosensors. One of them, redox-sensitive green fluorescent protein (roGFP), can easily be introduced into cells with adenoviral transduction, allowing the redox status of subcellular compartments to be evaluated without disrupting cellular processes. Reduced cysteines and oxidized cystines of roGFP have excitation maxima at 488 nm and 405 nm, respectively, with emission at 525 nm. Assessing the ratios of these reduced and oxidized forms allows the convenient calculation of redox balance within the cell. In this method article, immortalized human triple-negative breast cancer cells (MDA-MB-231) were used to assess redox status within the living cell. The protocol steps include MDA-MB-231 cell line transduction with adenovirus to express cytosolic roGFP, treatment with H2O2, and assessment of cysteine and cystine ratio with both flow cytometry and fluorescence microscopy.

This protocol describes the assessment of subcellular compartment-specific redox status within the cell. A redox-sensitive fluorescent probe allows convenient ratiometric analysis in intact cells.

使用亚细胞室特异性红氧敏感绿色荧光蛋白评估细胞氧化

Measuring the intracellular oxidation/reduction balance provides an overview of the physiological and/or pathophysiological redox status of an organism. ...

Complementation of Splicing Activity by a Galectin-3 - U1 snRNP Complex on Beads

Classic depletion-reconstitution experiments indicate that galectin-3 is a required splicing factor in nuclear extracts. The mechanism of incorporation of galectin-3 into the splicing pathway is addressed in this paper. Sedimentation of HeLa cell nuclear extracts on 12%-32% glycerol gradients yields fractions enriched in an endogenous ~10S particle that contains galectin-3 and U1 snRNP. We now describe a protocol to deplete nuclear extracts of U1 snRNP with concomitant loss of splicing activity. Splicing activity in the U1-depleted extract can be reconstituted by the galectin-3 - U1 snRNP particle trapped on agarose beads covalently coupled with anti-galectin-3 antibodies. The results indicate that the galectin-3 - U1 snRNP - pre-mRNA ternary complex is a functional E complex leading to intermediates and products of the splicing reaction and that galectin-3 enters the splicing pathway through its association with U1 snRNP. The scheme of using complexes affinity- or immuno-selected on beads to reconstitute splicing activity in extracts depleted of a specific splicing factor may be generally applicable to other systems.

This article describes the experimental procedures for (a) depletion of U1 snRNP from nuclear extracts, with concomitant loss of splicing activity; and (b) reconstitution of splicing activity in the U1-depleted extract by galectin-3 - U1 snRNP particles bound to beads covalently coupled with anti-galectin-3 antibodies.

半乳糖凝集素-3 - U1 snRNP复合物在珠子上的剪接活性的补充

Classic depletion-reconstitution experiments indicate that galectin-3 is a required splicing factor in nuclear extracts. The mechanism of incorporation of ...

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Fragment-based screening (FBS) is a well-validated and accepted concept within the drug discovery process both in academia and industry. The greatest advantage of NMR-based fragment screening is its ability not only to detect binders over 7-8 orders of magnitude of affinity but also to monitor purity and chemical quality of the fragments and thus to produce high quality hits and minimal false positives or false negatives. A prerequisite within the FBS is to perform initial and periodic quality control of the fragment library, determining solubility and chemical integrity of the fragments in relevant buffers, and establishing multiple libraries to cover diverse scaffolds to accommodate various macromolecule target classes (proteins/RNA/DNA). Further, an extensive NMR-based screening protocol optimization with respect to sample quantities, speed of acquisition and analysis at the level of biological construct/fragment-space, in condition-space (buffer, additives, ions, pH, and temperature) and in ligand-space (ligand analogues, ligand concentration) is required. At least in academia, these screening efforts have so far been undertaken manually in a very limited fashion, leading to limited availability of screening infrastructure not only in the drug development process but also in the context of chemical probe development. In order to meet the requirements economically, advanced workflows are presented. They take advantage of the latest state-of-the-art advanced hardware, with which the liquid sample collection can be filled in a temperature-controlled fashion into the NMR-tubes in an automated manner. 1H/19F NMR ligand-based spectra are then collected at a given temperature. High-throughput sample changer (HT sample changer) can handle more than 500 samples in temperature-controlled blocks. This together with advanced software tools speeds up data acquisition and analysis. Further, application of screening routines on protein and RNA samples are described to make aware of the established protocols for a broad user base in biomacromolecular research.

Fragment-based screening by NMR is a robust method to rapidly identify small molecule binders to biomacromolecules (DNA, RNA, or proteins). Protocols describing automation-based sample preparation, NMR experiments &#38; acquisition conditions, and analysis workflows are presented. The technique allows for optimal exploitation of both 1H and 19F NMR-active nuclei for detection.

基于核磁共振的片段筛选，样品最少，自动化程度最高

Fragment-based screening (FBS) is a well-validated and accepted concept within the drug discovery process both in academia and industry. The greatest ...

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

RNA adopts diverse structural folds, which are essential for its functions and thereby can impact diverse processes in the cell. In addition, the structure and function of an RNA can be modulated by various trans-acting factors, such as proteins, metabolites or other RNAs. Frameshifting RNA molecules, for instance, are regulatory RNAs located in coding regions, which direct translating ribosomes into an alternative open reading frame, and thereby act as gene switches. They may also adopt different folds after binding to proteins or other trans-factors. To dissect the role of RNA-binding proteins in translation and how they modulate RNA structure and stability, it is crucial to study the interplay and mechanical features of these RNA-protein complexes simultaneously.&#160;This work illustrates how to employ single-molecule-fluorescence-coupled optical tweezers to explore the conformational and thermodynamic landscape of RNA-protein complexes at a high resolution. As an example, the interaction of the SARS-CoV-2 programmed ribosomal frameshifting element with the trans-acting factor short isoform of zinc-finger antiviral protein is elaborated. In addition, fluorescence-labeled ribosomes were monitored using the confocal unit, which would ultimately enable the study of translation elongation. The fluorescence coupled OT assay can be widely applied to explore diverse RNA-protein complexes or trans-acting factors regulating translation and could facilitate studies of RNA-based gene regulation.

This protocol presents a complete experimental workflow for studying RNA-protein interactions using optical tweezers. Several possible experimental setups are outlined including the combination of optical tweezers with confocal microscopy.