通过染色质免疫沉淀测序（ChIP-Seq）数据生物信息学分析肝脏X受体（LXR）核受体顺反组。

Analysis of LXR Nuclear Receptor Cistrome Through ChIP-Seq Data Bioinformatics.

作者信息

de la Rosa Juan Vladimir, Ramón-Vázquez Ana, Tabraue Carlos, Castrillo Antonio

机构信息

Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Centro Mixto CSIC-Universidad Autónoma de Madrid, Madrid, Spain.

Unidad de Biomedicina IIBM-ULPGC (Unidad Asociada al CSIC), Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain.

出版信息

Methods Mol Biol. 2019;1951:99-109. doi: 10.1007/978-1-4939-9130-3_8.

DOI:10.1007/978-1-4939-9130-3_8

PMID:30825147

Abstract

Liver X receptors are members of the nuclear receptor superfamily of transcription factors. The LXR genes (NR1H2 and NR1H3) encode for two different proteins referred to as LXRα and LXRβ. Each LXR presents diverse tissue distribution but similar target DNA-binding elements and ligands. Both LXRs act as relevant transcriptional regulators of cholesterol metabolism in many tissues. Additionally, LXRs participate in innate immunity and inflammation. Therefore, in order to understand the molecular requirements that operate in LXR-dependent transcription, it is important to decipher LXR genomic binding properties. We have recently performed genome-wide binding analysis of LXR proteins. In this method paper, we describe a detailed computational protocol primarily based on HOMER software package for the analysis of ChIP-seq data.

摘要

肝脏X受体是转录因子核受体超家族的成员。LXR基因（NR1H2和NR1H3）编码两种不同的蛋白质，分别称为LXRα和LXRβ。每种LXR呈现出不同的组织分布，但具有相似的靶DNA结合元件和配体。两种LXR在许多组织中都是胆固醇代谢的相关转录调节因子。此外，LXR参与先天免疫和炎症反应。因此，为了了解LXR依赖性转录中起作用的分子要求，解读LXR基因组结合特性很重要。我们最近对LXR蛋白进行了全基因组结合分析。在本方法论文中，我们描述了一种主要基于HOMER软件包的详细计算方案，用于分析ChIP-seq数据。