Picard Colette L, Gehring Mary
Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Methods Mol Biol. 2020;2093:173-201. doi: 10.1007/978-1-0716-0179-2_13.
Genomic imprinting is a phenomenon that occurs in flowering plants and mammals, whereby a gene is expressed in a parent-of-origin-specific manner. Although imprinting has now been examined genome-wide in a number of species using RNA-seq, the analyses used to assess imprinting vary between studies, making consistent comparisons between species difficult. Here we present a simple, easy-to-use bioinformatic pipeline for imprinting analyses suitable for any tissue, including plant endosperm. All relevant scripts can be downloaded. As an illustrative example, we reanalyze published data from A. thaliana and Z. mays endosperm using the pipeline and then demonstrate how to use the results to assess the conservation of imprinting between these species. We also introduce the Plant Imprinting Database, a repository for published imprinting datasets in plants that can be used to view, compare, and download data.
基因组印记是一种发生在开花植物和哺乳动物中的现象，即基因以亲本来源特异性的方式表达。尽管现在已经使用RNA测序在多个物种中对全基因组范围的印记进行了研究，但用于评估印记的分析方法在不同研究中有所不同，这使得不同物种之间难以进行一致的比较。在这里，我们提出了一种简单、易于使用的生物信息学流程，用于适用于任何组织（包括植物胚乳）的印记分析。所有相关脚本均可下载。作为一个说明性示例，我们使用该流程重新分析了来自拟南芥和玉米胚乳的已发表数据，然后展示了如何使用结果来评估这些物种之间印记的保守性。我们还介绍了植物印记数据库，这是一个用于存储已发表的植物印记数据集的资源库，可用于查看、比较和下载数据。
