• 主题
高级搜索  >
历史搜索 清空历史
首页> 外文学位 >Methods for comprehensive transcriptome analysis using next-generation sequencing and application in hypertrophic cardiomyopathy.
【24h】

Methods for comprehensive transcriptome analysis using next-generation sequencing and application in hypertrophic cardiomyopathy.

机译：使用下一代测序技术进行全面转录组分析的方法，并应用于肥厚型心肌病。

获取原文
获取原文并翻译 | 示例
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Characterization of the RNA transcriptome by next-generation sequencing can produce an unprecedented yield of information that provides novel biologic insights. I describe four approaches for sequencing different aspects of the transcriptome and provide computational tools to analyze the resulting data. Methods that query the dynamic range of gene expression, low expressing transcripts, micro RNA levels, and start-site usage of transcripts are described.;Assessing changes in start-site usage can reveal major regulatory events that may be difficult to identify by standard gene expression analysis. By optimizing cDNA library construction steps to enhance for sequencing from 5' ends of transcripts, I developed a robust protocol to measure start-site usage of transcripts with high sensitivity. To identify genome-wide start-site usage changes between different biological specimens, I developed a computational approach that queries the distribution of reads at the 5' ends. This methodology is denoted as 5'RNAseq. Genome-wide 5'RNAseq of cardiac tissues from a mouse model of hypertrophic cardiomyopathy (HCM) identified Four-and-a-half LIM domains protein 1 (Fhl1) as the gene that exhibits the most marked change in start-site usage. Analysis of the specific cell populations in the heart revealed that the increased expression of Fhl1 and change in 5' regulation occurs in myocytes that become engulfed in fibrosis during disease progression. Further analyses of human ventricular specimens from subjects with a variety of cardiovascular pathologies revealed the identical Fhl1 start-site switch occurs in both primary and secondary cardiomyopathies.;Genetic ablation of Fhl1 in the mouse model of HCM resulted in markedly increased hypertrophy and histopathologic remodeling, indicating that Fhl1 acts as an adaptive modifier of HCM. This result contrasts with data from an earlier report that suggest that Fhl1 attenuates hypertrophy caused by pressure overload, and suggests that Fhl1 may be implicated in distinct responses to these different cardiac pathologies. As Fhl1 is encoded on chromosome X, the potentially protective role of Fhl1 in HCM may account for more severe clinical manifestations and outcomes in male patients with HCM and may provide novel therapeutic avenues to limit disease. More broadly, this work provides new tools that can be used to analyze transcriptomic information.
机译：通过下一代测序对RNA转录组进行表征可产生前所未有的信息产量，从而提供新颖的生物学见解。我描述了四种用于对转录组不同方面进行测序的方法，并提供了用于分析所得数据的计算工具。描述了查询基因表达动态范围，低表达转录本，微小RNA水平和转录本起始位点使用情况的方法;评估起始位点使用情况的变化可以揭示主要调控事件，这些事件可能很难用标准基因识别表达分析。通过优化cDNA文库构建步骤以增强从转录本5'端测序的能力，我开发了一种可靠的协议，可以高灵敏度地测量转录本的起始位点使用情况。为了确定不同生物学标本之间全基因组起始位点使用情况的变化，我开发了一种计算方法来查询5'末端读数的分布。该方法称为5'RNAseq。来自肥厚型心肌病（HCM）小鼠模型的心脏组织全基因组5'RNAseq鉴定出四个半LIM域蛋白1（Fhl1）是在起始位点使用中表现出最明显变化的基因。对心脏中特定细胞群的分析表明，Fhl1表达的增加和5'调节的改变发生在疾病过程中被纤维化吞噬的心肌细胞中。对来自具有各种心血管疾病的受试者的人的心室标本进行的进一步分析显示，原发性和继发性心肌病均发生相同的Fhl1起始位点转换。； HCM小鼠模型中Fhl1的基因切除导致肥大和组织病理学重构明显增加，指示Fhl1充当HCM的自适应修饰符。该结果与早期报道的数据相反，该报道表明Fhl1减轻了因压力超负荷引起的肥大，并暗示Fhl1可能涉及对这些不同心脏疾病的不同反应。由于Fhl1是在X染色体上编码的，因此Fhl1在HCM中的潜在保护作用可能解释了HCM男性患者中更严重的临床表现和结果，并且可能提供了限制疾病的新治疗途径。更广泛地说，这项工作提供了可用于分析转录组信息的新工具。

著录项

  • 作者

    Christodoulou, Danos C.;

  • 作者单位

    Harvard University.;

  • 授予单位 Harvard University.;
  • 学科 Genetics.
  • 学位 Ph.D.
  • 年度 2013
  • 页码 187 p.
  • 总页数 187
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号