| ACE-score-based Analysis of Temporal miRNA Targetomes During Human Cytomegalovirus Infection Using AGO-CLIP-seq
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Author:
Date:
2016-04-20
[Abstract] Although temporal regulation of gene expression during the course of infection is known to be critical for determining the outcome of host-virus interactions, systematic temporal analysis of the miRNA targetomes during productive viral infection has been technically challenging due to the large range of miRNA-mRNA cross-talks at the host-virus interface. High-confidence quantifying models of the suppression efficacy in targeting sites by integrating bioinformatics with Argonaute-crosslinking and immunoprecipitation followed by high-throughput sequencing (AGO-CLIP-seq) (Chi et al., 2009) data have been poorly developed. To accurately identify miRNA target sites and calculate the targeting efficacy of miRNA-target interactions, we developed a new bioinformatic quantitation method, ...
[摘要] 尽管已知在感染过程中基因表达的时间调节对于确定宿主 - 病毒相互作用的结果是至关重要的，但是在生产性病毒感染期间对miRNA targetomes的系统时间分析在技术上是具有挑战性的，因为大范围的miRNA- mRNA在主机 - 病毒接口交叉对话。数据通过将生物信息学与Argonaute-交联和免疫沉淀接着高通量测序（AGO-CLIP-seq）数据（Chi等人，2009）数据结合，已经不发达。为了准确地鉴定miRNA靶位点并计算miRNA-靶相互作用的靶向效果，我们开发了新的生物信息学定量方法，即AGO-CLIP-seq富集（ACE） - 评分算法（Kim等， 2015）。在我们的AGO-CLIP-seq分析中包括未感染的对照可以显着提高病毒或人miRNA的真实靶位点识别的准确性，并且在我们的ACE评分方法中提取生产性人巨细胞病毒（HCMV）感染期间的生理学显着变化。因此，我们建议我们新的基于ACE评分的方法可以应用于各种miRNA targetome研究，这将在其他类型的时间背景下进行，如发展阶段，细胞因子或病原体的免疫刺激和其他病毒。
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| ChIP-Seq in Candida albicans
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Author:
Date:
2014-06-20
[Abstract] Systems biology approaches can be used to study the regulatory interactions occurring between many components of the biological system at the whole-genome level and decipher the circuitries implicated in the regulation of cellular processes, including those imparting virulence to opportunistic fungi. Candida albicans (C. albicans) is a leading human fungal pathogen. It undergoes morphological switching between a budding yeast form and an elongated multicellular hyphal form. This transition is required for C. albicans’ ability to cause disease and is regulated through highly interconnected regulatory interactions between transcription factors (TFs) and target genes. The chromatin immunoprecipitation (ChIP)-High-throughput sequencing (Seq) technology (ChIP-Seq) is ...
[摘要] 系统生物学方法可以用于研究在全基因组水平上发生在生物系统的许多组分之间的调节相互作用，并且解释涉及细胞过程调节的电路，包括赋予机会性真菌的毒力的电路。 白色念珠菌（ C。albicans ）是一种主要的人类真菌病原体。它经历萌芽酵母形式和细长多细胞菌丝形式之间的形态学转换。此转换是 C所必需的。白色念珠菌引起疾病的能力，并且通过转录因子（TF）和靶基因之间高度相互关联的调节相互作用来调节。染色质免疫沉淀（ChIP） - 高通量测序（Seq）技术（ChIP-Seq）是解码转录调节网络的强有力的方法。该方案针对从丝状结构C制备ChIP DNA进行了优化。白色念珠菌细胞，然后进行高通量测序以鉴定调节酵母对菌丝转变的TF的靶标。
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