Name: comprehensive workflow for the genome-wide identification and expression meta-analysis of the atl e3 ubiquitin ligase gene family in grapevine
Uploaded: 2017-12-22T12:30:00
Description: Watch this Scientific Journal Video about Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine at JoVE.com

这项工作得到了维罗纳大学在联合项目2014的框架内的支持 (在葡萄藤中的 ATL 基因家族的特性及其对霜霉病霜霉病的抗性)。

1. 确定假想的 ATL 基因家族成员 (s)
<ol>
	<li>爆炸网络版
	<ol>
		<li>打开爆炸网页13 , 然后单击 "蛋白质爆炸" 部分。</li>
		<li>在 "输入查询序列" 字段中, 输入蛋白质的氨基酸序列 (这里 VIT_05s0077g01970), 它将用作探针来识别其他家族成员。 注意: 应该使用一种很好的代表性蛋白质 (一种蛋白质, 显示家庭的所有重要特征)。</li>
		<li>在 "选择搜索集" 字段中, 选择 "参考蛋白...

<ol>
	<li>Jaillon, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+grapevine+genome+sequence+suggests+ancestral+hexaploidization+in+major+angiosperm+phyla.">The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.</a> Nature. 449 (7161), 463-467 (2007).</li><li>Adam-Blondon, A. -. F., 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> Genetics, Genomics, and Breeding of Grapes. , 211-234 (2011).</li><li>Chen, L., Hellmann, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plant+E3+Ligases:+Flexible+Enzymes+in+a+Sessile+World.">Plant E3 Ligases: Flexible Enzymes in a Sessile World.</a> Mol. Plant. 6 (5), 1388-1404 (2013).</li><li>Vierstra, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ubiquitin-26S+proteasome+system+at+the+nexus+of+plant+biology.">The ubiquitin-26S proteasome system at the nexus of plant biology.</a> Nat. Rev. Mol. Cell Biol. 10 (6), 385-397 (2009).</li><li>Serrano, M., Parra, S., Alcaraz, L. D., Guzm&#225;n, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ATL+Gene+Family+from+Arabidopsis+thaliana+and+Oryza+sativa+Comprises+a+Large+Number+of+Putative+Ubiquitin+Ligases+of+the+RING-H2+Type.">The ATL Gene Family from Arabidopsis thaliana and Oryza sativa Comprises a Large Number of Putative Ubiquitin Ligases of the RING-H2 Type.</a> J. Mol. Evol. 62 (4), 434-445 (2006).</li><li>Aguilar-Hern&#225;ndez, V., Aguilar-Henonin, L., Guzm&#225;n, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diversity+in+the+Architecture+of+ATLs,+a+Family+of+Plant+Ubiquitin-Ligases,+Leads+to+Recognition+and+Targeting+of+Substrates+in+Different+Cellular+Environments.">Diversity in the Architecture of ATLs, a Family of Plant Ubiquitin-Ligases, Leads to Recognition and Targeting of Substrates in Different Cellular Environments.</a> PLoS One. 6 (8), e23934 (2011).</li><li>Guzm&#225;n, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+prolific+ATL+family+of+RING-H2+ubiquitin+ligases.">The prolific ATL family of RING-H2 ubiquitin ligases.</a> Plant Signal Behav. 7 (8), 1014-1021 (2012).</li><li>Grimplet, 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=The+grapevine+gene+nomenclature+system.">The grapevine gene nomenclature system.</a> BMC Genomics. 15, 1077 (2014).</li><li>Prince, V. 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Gen. 92 (1), 155-161 (2013).</li><li>Wang, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Patterns+of+Gene+Duplication+and+Their+Contribution+to+Expansion+of+Gene+Families+in+Grapevine.">Patterns of Gene Duplication and Their Contribution to Expansion of Gene Families in Grapevine.</a> Plant Mol. Biol. Rep. 31 (4), 852-861 (2013).</li><li>Fasoli, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Grapevine+Expression+Atlas+Reveals+a+Deep+Transcriptome+Shift+Driving+the+Entire+Plant+into+a+Maturation+Program.">The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program.</a> Plant Cell. 24 (9), 3489-3505 (2012).</li><li>. BLAST2.6.0 Available from: <a target="_blank" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">https://blast.ncbi.nlm.nih.gov/Blast.cgi</a> (2016)</li><li>. Vitis vinifera cv. Corvina gene expression Atlas Available from: <a target="_blank" href="https://www.researchgate.net/publication/273383414_54sample_datamatrix_geneIDs_Fasoli2012">https://www.researchgate.net/publication/273383414_54sample_datamatrix_geneIDs_Fasoli2012</a> (2015)</li><li>. Sequence Read Archive (SRA) Available from: <a target="_blank" href="https://www.ncbi.nlm.nih.gov/sra">https://www.ncbi.nlm.nih.gov/sra</a> (2017)</li><li>Bolger, A. M., Lohse, M., Usadel, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trimmomatic:+a+flexible+trimmer+for+Illumina+sequence+data.">Trimmomatic: a flexible trimmer for Illumina sequence data.</a> Bioinformatics. 30 (15), 2114-2120 (2014).</li><li>Langmead, B., Salzberg, S. 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E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=limma+powers+differential+expression+analyses+for+RNA-sequencing+and+microarray+studies.">limma powers differential expression analyses for RNA-sequencing and microarray studies.</a> Nucleic Acids Res. 43 (7), e47 (2015).</li><li>Love, M. I., Huber, W., Anders, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Moderated+estimation+of+fold+change+and+dispersion+for+RNA-seq+data+with+DESeq2.">Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.</a> Genome Biology. 15 (12), 550 (2014).</li><li>Ariani, P. <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+characterisation+and+expression+profile+of+the+grapevine+ATL+ubiquitin+ligase+family+reveal+biotic+and+abiotic+stress-responsive+and+development-related+members.">Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members.</a> Sci. 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Biol. 314 (5), 1041-1052 (2001).</li><li>Kaduk, M., Sonnhammer, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+orthology+inference+with+Hieranoid+2.">Improved orthology inference with Hieranoid 2.</a> Bioinformatics. 33 (8), (2017).</li><li>Cramer, G. 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=Transcriptomic+analysis+of+the+late+stages+of+grapevine+(Vitis+vinifera+cv.+Cabernet+Sauvignon)+berry+ripening+reveals+significant+induction+of+ethylene+signaling+and+flavor+pathways+in+the+skin.">Transcriptomic analysis of the late stages of grapevine (Vitis vinifera cv. Cabernet Sauvignon) berry ripening reveals significant induction of ethylene signaling and flavor pathways in the skin.</a> BMC Plant Biol. 14, 370 (2014).</li><li>Juretic, N., Hoen, D. R., Huynh, M. L., Harrison, P. 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G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Autoregulation+of+FCA+pre-mRNA+processing+controls+Arabidopsis+flowering+time.">Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time.</a> EMBO J. 22 (12), 3142-3152 (2003).</li><li>Wong, D. C. J., Gutierrez, R. L., Gambetta, G. A., Castellarin, S. D. <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+analysis+of+cis-regulatory+element+structure+and+discovery+of+motif-driven+gene+co-expression+networks+in+grapevine.">Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine.</a> DNA Res. 24 (3), 311-326 (2017).</li><li>Wong, D. C. J., Matus, J. 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在基因组时代, 许多植物物种被深深地刻画了。这些信息是初步的功能研究, 并提供一个框架, 进一步调查不同成员在一个家庭中的作用。在这方面, 还需要一个命名系统, 允许唯一地识别家庭中的每个成员, 避免在不同的研究组独立于不同的基因分配姓名时可能出现的冗余和混乱。
经过深思熟虑的考虑, 葡萄科学界同意命名的葡萄基因在一个家庭的基础上与拟南芥基因的...

在过去的十年中, 对葡萄基因组学进行了大量的研究。葡萄是一种公认的经济相关作物, 它已成为研究果实发育和木本植物对生物和非生物学胁迫反应的模型。在此上下文中,葡萄亚种cv. PN40024 基因组在 2007年1及其更新版本2中的发布导致了 "学" 数据的快速积累和大量高通量的研究。根据所公布的序列数据, 对某一特定基因家族 (通常由分享保守主题的蛋白质、结构和/或功能相似性和进化关系) 的综合分析, 现在可以进行, 以揭示其分子功能, 进化和基因表达谱。这些分析有助于理解基因家族如何控制整个基因组的生理过程。
植物生命周期的许多方面是由泛素介导的关键蛋白降解, 这需要一个 fine-tuned 的营业额, 以确保正常的细胞过程。泛素介导的降解过程的重要组成部分是 E3 泛素酶, 这是负责系统的灵活性, 由于具体目标的招聘3。因此, 这些酶代表一个巨大的基因家族, 约 1400 E3 连接编码基因预测在拟南芥基因组4, 每 E3 泛素连接作用于特定靶蛋白泛。尽管基质特异泛在植物细胞调控中的重要性, 但很少有人知道如何调节泛通路和目标蛋白只在少数情况下被识别。对这种特异性和调节机制的破译首先依赖于系统的不同组成部分的识别和定性, 特别是 E3 酶。在泛素酶中, ATL 亚科的特征是: 在a. 南芥中, 显示一个 RING-H2 手指域5,6, 其中一些在防御和荷尔蒙应答中扮演了一个角色7。
定义新基因家族成员的第一个关键步骤是对家庭特征的精确定义, 如一致主题、关键域和蛋白质序列特征。事实上, 基于爆炸分析的所有基因家族成员的可靠检索需要一些强制性的序列特性, 特别是蛋白质的功能/活动, 作为蛋白质的签名。这可以通过先前对其他植物物种的同一基因家族的描述来促进, 或者通过分析不同植物物种中属于同一家族的不同基因认定来分离共同的序列。然后, 家庭成员可以根据国际财团为某种特定植物所定的共同规则, 单独命名。例如, 在小道消息, 这种程序受到了葡萄基因注释 (sNCGGa) 的超级命名委员会的建议, 建立了一个系统系统树的构建, 包括五亚种和a. 南芥基因家族成员允许基于核苷酸序列的基因注释8。
染色体定位的家庭成员和基因重复调查允许突出的存在, 全基因组或串联复制基因。这种信息似乎有助于解开假定的基因功能, 因为它可能显示功能冗余或揭示不同的情况,即, non-functionalization, 新官能化, 或 sub-functionalization9。新的和 sub-functionalization 都是重要的事件, 创造了基因的新奇, 为植物适应变化的环境提供了新型的细胞组件10。特别是, 在葡萄基因组的进化过程中, 祖先基因的重复和新基因的产生是非常频繁的, 而新形成的基因则是来自葡萄的近端和串联重叠, 更有可能产生新函数11。
破译基因家族功能的另一个关键因素是组剖面。因此, 可以利用公共数据库访问大量的组数据, 从而利用 large-scale在 "硅片" 表达式分析中为基因家族成员分配假定函数。的确, 特定植物器官中某些基因的奇特表达或对某些压力的反应, 可以给出一些关于在定义条件下相应蛋白质的假定作用的提示, 并支持关于可能的假设sub-functionalization 重复的基因来应对不同的挑战。为此, 重要的是要考虑几个数据集: 这些可以已经可用的基因表达矩阵, 如葡萄器官的全基因组组图谱和发育阶段12, 或者可以通过以下方式生成ad hoc检索特定植物物种的组数据集的定义应力。此外, 一个简单的方法使用两个矩阵, 一个具有成对相似性的数据和另一个具有两两表达系数, 可以用来评价序列相似性和表达模式之间的关系在一个基因家族。
这项工作的目的是提供一个全球性的方法, 定义基因结构, 保守的蛋白质主题, 染色体位置, 基因重复, 和表达模式, 以及预测蛋白质本地化和磷酸化的网站, 以达到植物基因家族的详尽描述。这种综合的方法在这里适用于描述的 ATL E3 泛素连接家族的葡萄。根据 ATL 亚科成员在调控关键细胞过程中的新作用7, 这项工作可以很好地帮助识别功能性研究的强候选者, 并最终解开控制这一重要作物对其环境的适应。

<table>
	<tbody>
		<tr>
			<td>Personal computer</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Basic Local Alignment Search Tool (BLAST)</td>
			<td></td>
			<td></td>
			<td>https://blast.ncbi.nlm.nih.gov/Blast.cgi</td>
		</tr>
		<tr>
			<td>Molecular Evolutionary Genetics Analysis (MEGA)</td>
			<td></td>
			<td></td>
			<td>http://www.megasoftware.net/</td>
		</tr>
		<tr>
			<td>Motif-based sequence analysis tools (MEME)</td>
			<td></td>
			<td></td>
			<td>http://meme-suite.org/</td>
		</tr>
		<tr>
			<td>Geneious</td>
			<td>Biomatters Limited</td>
			<td></td>
			<td>http://www.geneious.com/</td>
		</tr>
		<tr>
			<td>ProtParam Tool</td>
			<td></td>
			<td></td>
			<td>http://web.expasy.org/protparam/</td>
		</tr>
		<tr>
			<td>ngLOC</td>
			<td></td>
			<td></td>
			<td>http://genome.unmc.edu/ngLOC/index.html</td>
		</tr>
		<tr>
			<td>TargetP v1.1 Server</td>
			<td></td>
			<td></td>
			<td>http://www.cbs.dtu.dk/services/TargetP/</td>
		</tr>
		<tr>
			<td>Protein Prowler</td>
			<td></td>
			<td></td>
			<td>http://bioinf.scmb.uq.edu.au:8080/pprowler_webapp_1-2/</td>
		</tr>
		<tr>
			<td>MUsite</td>
			<td></td>
			<td></td>
			<td>http://musite.sourceforge.net/</td>
		</tr>
		<tr>
			<td>Pfam</td>
			<td></td>
			<td></td>
			<td>http://pfam.xfam.org/</td>
		</tr>
		<tr>
			<td>TMHMM Server v. 2.0</td>
			<td></td>
			<td></td>
			<td>http://www.cbs.dtu.dk/services/TMHMM/</td>
		</tr>
		<tr>
			<td>ProtScale</td>
			<td></td>
			<td></td>
			<td>http://web.expasy.org/protscale/</td>
		</tr>
		<tr>
			<td>Grape Genome Database (CRIBI)</td>
			<td></td>
			<td></td>
			<td>http://genomes.cribi.unipd.it/grape/</td>
		</tr>
		<tr>
			<td>PhenoGram</td>
			<td></td>
			<td></td>
			<td>http://visualization.ritchielab.psu.edu/phenograms/plot</td>
		</tr>
		<tr>
			<td>MCScanX</td>
			<td></td>
			<td></td>
			<td>http://chibba.pgml.uga.edu/mcscan2/</td>
		</tr>
		<tr>
			<td>Interactive Tree Of Life (iTOL)</td>
			<td></td>
			<td></td>
			<td>http://itol.embl.de/</td>
		</tr>
		<tr>
			<td>UniProt</td>
			<td></td>
			<td></td>
			<td>http://www.uniprot.org/</td>
		</tr>
		<tr>
			<td>Phylogeny.fr</td>
			<td></td>
			<td></td>
			<td>http://www.phylogeny.fr/index.cgi</td>
		</tr>
		<tr>
			<td>MUSCLE</td>
			<td></td>
			<td></td>
			<td>http://www.ebi.ac.uk/Tools/msa/muscle/</td>
		</tr>
		<tr>
			<td>Gblocks Server</td>
			<td></td>
			<td></td>
			<td>http://molevol.cmima.csic.es/castresana/Gblocks_server.html</td>
		</tr>
		<tr>
			<td>Vitis vinifera cv. Corvina gene expression Atlas datamatrix</td>
			<td></td>
			<td></td>
			<td>https://www.researchgate.net/publication/273383414_54sample_datamatrix_geneIDs_Fasoli2012</td>
		</tr>
		<tr>
			<td>Multi Experiment Viewer (MeV)</td>
			<td></td>
			<td></td>
			<td>http://mev.tm4.org/#/welcome</td>
		</tr>
		<tr>
			<td>Sequence Read Archive (SRA)</td>
			<td></td>
			<td></td>
			<td>https://www.ncbi.nlm.nih.gov/sra</td>
		</tr>
		<tr>
			<td>R</td>
			<td></td>
			<td></td>
			<td>https://www.r-project.org/</td>
		</tr>
		<tr>
			<td>EMBOSS Needle (EMBL-EBI)</td>
			<td></td>
			<td></td>
			<td>http://www.ebi.ac.uk/Tools/psa/emboss_needle/</td>
		</tr>
	</tbody>
</table>

comprehensive workflow for the genome-wide identification and expression meta-analysis of the atl e3 ubiquitin ligase gene family in grapevine

家庭中基因的分类和命名可以显著地有助于描述编码蛋白质的多样性, 以及基于几个特征的家庭功能的预测, 如序列主题的存在或特定修饰修改的网站和家庭成员在不同条件下的表达谱。这项工作描述了一个关于基因家族特性的详细的协议。在这里, 这个过程被应用到在 Levadura 中的拟南芥 Tóxicos的描述 (ATL) E3 泛素连接家族的葡萄。这些方法包括家庭成员的全基因组鉴定、基因定位、结构和复制的特征、保守蛋白的分析、蛋白质定位和磷酸化的预测以及基因表达谱在不同的数据集的整个家族。这种程序可以扩展到根据实验目的进一步分析, 可适用于任何基因组的任何植物物种, 为其提供基因数据, 并提供有价值的信息, 以确定感兴趣的候选人为功能性研究, 提供对植物适应环境的分子机制的洞察。

VIT_05s0077g01970 基因, 被确定为最相似的a. 南芥 ATL2 (At3g16720) 通过 BLASTp 搜索, 被用作探针, 以调查的 ATL 家族成员在葡萄基因组 (五亚种cv 皮诺 PN40024)。PSI-爆炸分析在几个周期之后汇合, 揭示了属于葡萄树 ATL 基因家族 (图 1A) 的假定基因列表。在分析中确定的所有条目的肌肉对齐方式的视觉检查 (图 1B) 中, 对每个候选?...

Watch this Scientific Journal Video about Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine at JoVE.com

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

本文介绍了一个基因家族的鉴定和描述的程序, 适用于在 Levadura 的家庭的葡萄Tóxicos 的拟南芥(ATL) E3 泛素酶。

葡萄全基因组鉴定与表达的综合工作流 E3 泛素连接基因家族的 Meta 分析

Classification and nomenclature of genes in a family can significantly contribute to the description of the diversity of encoded proteins and to the ...

Research

JoVE Journal

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

主电穿孔的小鼠骨髓造血细胞培养制备

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

科研

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Spinal Cord Electrophysiology

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

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使用基因脉冲MXcell电穿孔系统主细胞的转染效率高

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

机器人技术和植物组织的基因表达研究的动态图像分析

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

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

使用自动细胞计数器简化基因表达研究：在Namalwa细胞的IL - 4依赖的基因表达的siRNA击倒

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 ...

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

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Recruitment of transcriptional and epigenetic factors to their targets is a key step in their regulation. Prominently featured in recruitment are the ...

In vitro Reconstitution of the Active T. castaneum Telomerase

In vitro Reconstitution of the Active T. castaneum Telomerase

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

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

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Transposon  mutagenesis and single-gene deletion are two methods applied in genome-wide  gene knockout in bacteria 1,2. Although transposon mutagenesis is ...

Analysis of Global RNA Synthesis at the Single Cell Level following Hypoxia

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Hypoxia or lowering of the oxygen availability is involved in many physiological and pathological processes. At the molecular level, cells initiate a ...

siRNA Screening to Identify Ubiquitin and Ubiquitin-like System Regulators of Biological Pathways in Cultured Mammalian Cells

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Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules (UBLs) is emerging as a dynamic cellular signaling network that ...