Name: determining genome-wide transcript decay rates in proliferating and quiescent human fibroblasts
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Description: Watch this Scientific Journal Video about Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts at JoVE.com

文森特卡塞尔是丽塔. 艾伦基金会 (http://www.ritaallenfoundation.org) 的弥尔顿学者。这项工作的经费来自国家普通医学科学研究所授予的 P50 GM071508 (私家侦探大卫博特斯坦), PhRMA 基金会赠款 2007RSGl9572, 国家科学基金会授予 OCI-1047879 8月大卫,国立普通医学科学院 R01 GM081686, 国立普通医学科学院 R01 GM0866465, 伊莱 & #38; 伊蒂丝再生医学和 #38 的广泛中心; 干细胞研究, 虹膜康托妇女健康中心/加州大学洛杉矶分校 CTSI 国立卫生研究院格兰特 UL1TR000124 和白血病淋巴瘤协会这份出版物中报告的研究得到了国家卫生研究院国家癌症研究所的 P50CA092131。资助者在研究设计、数据收集和分析、决定出版或准备原稿方面没有作用。是 Eli 和 #38 的成员; 伊蒂丝广泛的再生医学和 #38 中心; 干细胞研究, 加州大学洛杉矶分校分子生物学研究所, 加州大学洛杉矶分校生物信息学部际计划。

所有的实验都是由普林斯顿大学和加州大学洛杉矶分校的机构评审委员会批准的。
1. 制备增殖和接触抑制成纤维细胞 ActD 时间课程
注意: 本协议使用 timecourse 四 timepoints。三生物独立样品可以收集每 timepoint 通过收集不同的组织培养板在一个实验, 或者实验可以重复多次与细胞的不同的文化。在我们的经验, 一个10厘米 (直径) 组织培养皿 (一盘) 提供足够的 RN...

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L., Robinson, D. G., Coller, H. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Widespread+changes+in+mRNA+stability+contribute+to+quiescence-specific+gene+expression+patterns+in+a+fibroblast+model+of+quiescence.">Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence.</a> BMC Genomics. 18 (1), 123 (2017).</li><li>Legesse-Miller, A., Elemento, O., Pfau, S. J., Forman, J. J., Tavazoie, S., Coller, H. 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静止可由外部信号诱发, 包括 mitogens 或血清的提取、细胞黏附缺乏和接触抑制。接触抑制是诱发静止的多种可能的方法之一, 是一种高度进化的保守过程, 细胞在反应细胞接触时退出增殖细胞周期。我们在这里的重点是接触抑制作为一个例子的方法来诱导平静。以前的研究报告说, 细胞接触可以影响 rna 生物25, 因此, 结果提供了一个静止方法的信息, 需要额外的研究来确定哪些变化...

成绩单的稳定状态反映了成绩单合成和成绩单衰减的贡献。调节和协调转录衰减是控制生物过程的重要机制1,2,3,4。例如, 成绩单衰变率已被证明是贡献的时间序列事件后, 激活的炎症细胞因子肿瘤坏死因子5。
我们以前已经表明, 在原始人成纤维细胞的增殖和平静之间的过渡与许多基因的转录水平的变化有关6。其中一些变化反映了这两个国家之间转录因子活动的差异。
成绩单的衰变率的变化也会导致在两个不同状态7,8中的成绩单的表达水平的变化。根据我们早先的发现, 扩散与静止之间的过渡与多个 rna9的级别的变化有关, 我们询问是否也有来自差异成绩单衰减的贡献增殖与静止成纤维细胞的基因表达。
为了监测成绩单的稳定性, 我们确定了在增殖与静止细胞中转录的全基因组的衰变率。为了达到这个目的, 我们通过引入一种新的转录抑制剂和监测个体转录在一段时间内消失的速率来监测增殖与静止成纤维细胞的衰变率。这种方法的优点是, 与简单监控总体基因表达的方法相比, 通过抑制新的转录合成, 我们将能够分别从它们的速率来确定这些转录的衰变率。转录.
ActD 治疗, 以抑制新的转录和确定成绩单衰变率已成功地应用于以往的多项研究。ActD 已经被用来解剖的重要性, RNA 的稳定性在转录丰度变化的结果, 从治疗与炎细胞因子5。同样的方法也被用来解剖的差异, 转录衰变率在增殖与分化的 C2C12 细胞, 因为他们采用了分化肌肉表型10。另外一个例子, 在多能和分化的小鼠胚胎干细胞中也检测到了全球 mRNA 半衰期11。在这些例子中, mRNA 衰变已被证明是非常重要的调节转录丰度和细胞向不同的细胞状态转变。
应用下面所述的方法, 我们发现, 当比较成纤维细胞在增殖和静态状态12时, 大约500基因的转录衰变率发生了变化。特别是, 我们发现 rna miR-29(在静止单元中 downregulated) 的目标在单元格过渡到静止时稳定。我们在这里描述的方法, 我们用来确定衰变率在增殖和静止细胞。这一方法是有用的比较全球 mRNA 衰变率在两个截然不同的, 但类似的条件, 当信息有关迅速腐烂的基因寻求。它也可以用来解决其他问题, 如细胞培养条件对转录衰变的影响, 例如, 在二维与三维的文化。衰变率可以被确定的基因组范围内的方法, 如微阵列或 RNA 序列. 或者, real-time qPCR 或北印迹可以用来确定一个基因的衰变率或型的型基础。这些速率可以用来计算每个被监测基因的半衰期, 并在两种情况下确定具有不同衰变率的基因。

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			<td height="42" style="height:42px;width:291px;">Centrifuges for microcentrifuge tubes capable of reaching 12,000 x g and 4&#176;C</td>
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			<td height="21" style="height:21px;width:291px;">Equipment for running agarose gels</td>
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			<td height="42" style="height:42px;width:291px;">Sterile tissue culture plates and conical tubes</td>
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			<td height="21" style="height:21px;width:291px;">Dulbecco&#39;s Modified Eagle Medium</td>
			<td style="width:163px;">Life Technologies</td>
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			<td height="21" style="height:21px;width:291px;">Fetal bovine serum</td>
			<td style="width:163px;">VWR</td>
			<td style="width:119px;">35-010-CV</td>
			<td style="width:237px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Sterile serological pipets, pipettors and pipet tips for tissue culture</td>
			<td style="width:163px;"></td>
			<td style="width:119px;"></td>
			<td style="width:237px;"></td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:291px;">Individually wrapped, disposable Rnase-free pipettes, pipette tips and tubes for RNA isolation and analysis</td>
			<td style="width:163px;"></td>
			<td style="width:119px;"></td>
			<td style="width:237px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Disposable gloves to be worn when handling reagents and RNA samples</td>
			<td style="width:163px;"></td>
			<td style="width:119px;"></td>
			<td style="width:237px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">RNaseZap</td>
			<td style="width:163px;">Invitrogen</td>
			<td style="width:119px;">AM9780</td>
			<td style="width:237px;">For decontaminating work surfaces from RNase</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">2.0 ml eppendorf tubes</td>
			<td style="width:163px;"></td>
			<td style="width:119px;"></td>
			<td style="width:237px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Trypsin-EDTA&#160; Solution 10X</td>
			<td style="width:163px;">Millipore Sigma</td>
			<td style="width:119px;">9002-07-07</td>
			<td style="width:237px;"></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:23px;width:291px;">Sterile PBS</td>
			<td style="width:163px;">Life Technologies</td>
			<td style="width:119px;">14190-250</td>
			<td style="width:237px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Trizol</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">15596018</td>
			<td style="width:237px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Actinomycin D</td>
			<td style="width:163px;">Millipore Sigma</td>
			<td style="width:119px;">A1410-2 mg</td>
			<td style="width:237px;">inhibits transcription</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Sterile DMSO</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td style="width:119px;">31-761-00ML</td>
			<td style="width:237px;">solvent for actinomycin D</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Chloroform</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">ICN19400225</td>
			<td style="width:237px;">MP Biomedicals, Inc product</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Isopropanol</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td style="width:119px;">BP2618500</td>
			<td style="width:237px;">molecular biology grade</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Ethanol</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td style="width:119px;">BP28184</td>
			<td style="width:237px;">molecular biology grade</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">RNase-free Glycogen (20 mg/ml aqueous solution)</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">R0551</td>
			<td style="width:237px;">carrier for RNA precipitation</td>
		</tr>
		<tr height="63">
			<td height="63" style="height:63px;width:291px;">TURBO DNA-free Kit</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">AM1907</td>
			<td style="width:237px;">removes DNA with DNase, then, in a subsequent step,&#160; inactivates DNA and removes divalent cations</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Agarose</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">ICN820721</td>
			<td style="width:237px;">MP Biomedicals, Inc product</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Loading dye for RNA gel</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">R0641</td>
			<td style="width:237px;">suitable even for denaturing electrophoresis</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Millenium RNA markers</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">AM7150</td>
			<td style="width:237px;">RNA ladder</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">One-color RNA Spike-in Kit</td>
			<td style="width:163px;">Agilent Technology</td>
			<td style="width:119px;">5188-5282</td>
			<td style="width:237px;">Example spike-in control for Agient microarray analysis</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Tris base</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td style="width:119px;">BP152-1</td>
			<td style="width:237px;">molecular biology grade, for TAE buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Glacial acetic acid</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td style="width:119px;">A38-500</td>
			<td style="width:237px;">for TAE buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">EDTA</td>
			<td style="width:163px;">Fisher Scientific</td>
			<td style="width:119px;">BP120-500</td>
			<td style="width:237px;">electrophoresis grade, for gels</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Ethidium bromide</td>
			<td style="width:163px;">Millipore Sigma</td>
			<td style="width:119px;">E7637</td>
			<td style="width:237px;">for molecular biology</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">External RNA Controls Consortium RNA Spike-in Mix</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td>4456740</td>
			<td style="width:237px;">Spike-in control for RNA Seq</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">TruSeq Stranded mRNA Library Preparation Kit A (48 samples, 12 indexes)</td>
			<td style="width:163px;">Illumina</td>
			<td style="width:119px;">RS-122-2101</td>
			<td style="width:237px;">for RNA Seq</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">96-well 0.3 ml PCR plate</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">AB-0600</td>
			<td style="width:237px;">for real-time qPCR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Microseal B adhesive seals</td>
			<td style="width:163px;">Bio-Rad</td>
			<td style="width:119px;">MSB1001</td>
			<td style="width:237px;">for real-time qPCR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Rnase/Dnase-free Reagent Reservoirs</td>
			<td style="width:163px;">VWR</td>
			<td style="width:119px;">89094-662</td>
			<td style="width:237px;">for real-time qPCR</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:291px;">Rnase/Dnase-free Eight tube strips and caps</td>
			<td style="width:163px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">AM12230</td>
			<td style="width:237px;">for real-time qPCR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">SuperScript Reverse Transcriptase</td>
			<td style="width:163px;">Invitrogen</td>
			<td style="width:119px;">18090010</td>
			<td style="width:237px;">for real-time qPCR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">AMPure XP Beads</td>
			<td style="width:163px;">Beckman Coulter</td>
			<td style="width:119px;">A63880</td>
			<td style="width:237px;">for real-time qPCR</td>
		</tr>
	</tbody>
</table>

determining genome-wide transcript decay rates in proliferating and quiescent human fibroblasts

静止是一种暂时的可逆状态, 其中细胞停止了细胞分裂, 但保留了增殖的能力。包括我们在内的多项研究表明, 静止与基因表达的广泛变化有关。其中一些变化发生在扩散相关转录因子的水平或活动的变化, 如 E2F 和 c-myc。我们已经证明, mRNA 的衰变也可以促进增殖和静止细胞之间基因表达的改变。在本协议中, 我们描述了建立人真皮包皮成纤维细胞增殖和静止培养的过程。然后, 我们描述的程序, 抑制新的转录在增殖和静止细胞与放线菌 D (ActD)。ActD 治疗是一种直接和可重复的方法, 游离新转录从成绩单衰变。ActD 治疗的一个缺点是, 由于 ActD 影响细胞的生存能力, 时间过程必须限制在短时间内。成绩单的水平被监测的时间, 以确定成绩单衰变率。这一过程允许鉴定的基因和异构体, 表现出差异衰变的增殖与静止成纤维细胞。

我们以前曾报道过在8小时的时间课程12中, 增殖和接触抑制主要人成纤维细胞的转录衰变率的微阵列分析结果。在补充表 1中提供了与增殖和接触抑制成纤维细胞比较的转录稳定性有显著变化的基因列表。荧光强度在时间零和在时间路线以后 ActD 治疗提供。基因被列入了名单上, 通过测定在增殖和接触抑制条件下有明显不同的斜坡的基因, 使用...

Watch this Scientific Journal Video about Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts at JoVE.com

Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts

我们描述了一种生成增殖和静止的主要人真皮成纤维细胞的协议, 监测转录衰变率, 并识别差异腐烂的基因。

增殖和静止人成纤维细胞的全基因组转录衰变率的测定

Quiescence is a temporary, reversible state in which cells have ceased cell division, but retain the capacity to proliferate. Multiple studies, including ...

Research

JoVE Journal

Genetics

siRNA Transfection and EMSA Analyses on Freshly Isolated Human Villous Cytotrophoblasts

在新鲜分离的人代绒毛滋养细胞转染和EMSA分析

Human primary villous cytotrophoblasts are a very useful source of primary cells to study placental functions and regulatory mechanisms, and to comprehend ...

科研

遗传学

Parallel Measurement of Circadian Clock Gene Expression and Hormone Secretion in Human Primary Cell Cultures

在人原代细胞培养生物钟基因表达及荷尔蒙分泌的并行测量

Circadian clocks are functional in all light-sensitive organisms, allowing for an adaptation to the external world by anticipating daily environmental ...

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement

通过DNA含量测定的哺乳动物复制时序的全基因组的测定

Replication of the genome occurs during S phase of the cell cycle in a highly regulated process that ensures the fidelity of DNA duplication. Each genomic ...

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae

与ChEC-seq的蛋白质-DNA相互作用的全基因组映射<em&gt;酿酒酵母（Saccharomyces cerevisiae）</em

Genome-wide mapping of protein-DNA interactions is critical for understanding gene regulation, chromatin remodeling, and other chromatin-resident ...

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

ATAC 基因组在原发性人类 T 淋巴细胞中的染色体全易接近染色质

Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a method used for the identification of open (accessible) regions ...

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

大范围早期果蝇胚胎的全基因组染色质构象捕获库的生成

Investigating the three-dimensional architecture of chromatin offers invaluable insight into the mechanisms of gene regulation. Here, we describe a ...

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

启动子捕获高分辨率, 全基因组的启动子交互分析

The three-dimensional organization of the genome is linked to its function. For example, regulatory elements such as transcriptional enhancers control the ...

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

全基因组对真核生物转录误差的监测

Accurate transcription is required for the faithful expression of genetic information. Surprisingly though, little is known about the mechanisms that ...

Determining the Egg Fertilization Rate of Bemisia tabaci Using a Cytogenetic Technique

Determining the Egg Fertilization Rate of Bemisia tabaci Using a Cytogenetic Technique

用细胞遗传学技术测定芽孢杆菌的受精率

A few species of sap-sucking whiteflies are some of the most damaging terrestrial pests worldwide because of the crop damage they inflict and plant ...

Isolation of Papillary and Reticular Fibroblasts from Human Skin by Fluorescence-activated Cell Sorting

荧光活化细胞分选分离人皮肤状和网状成纤维细胞

Fibroblasts are a highly heterogeneous cell population implicated in the pathogenesis of many human diseases. In human skin dermis, fibroblasts have ...