Chromatin immunoprecipitation: advancing analysis of nuclear hormone signaling

Abstract

Recent decades have been filled with groundbreaking research in the field of endocrine hormone signaling. Pivotal events like the isolation and purification of the estrogen receptor, the cloning of glucocorticoid receptor cDNA, or dissemination of nuclear hormone receptor (NHR) DNA binding sequences are well recognized for their contributions. However, the novel genome-wide and gene-specific information obtained over the last decade describing NHR association with chromatin, cofactors, and epigenetic modifications, as well as their role in gene regulation, has been largely facilitated by the adaptation of the chromatin immunoprecipitation (ChIP) technique. Use of ChIP-based technologies has taken the field of hormone signaling from speculating about the transcription-enabling properties of acetylated chromatin and putative transcription (co-)factor genomic occupancy to demonstrating the detailed, stepwise mechanisms of factor binding and transcriptional initiation; from treating hormone-induced transcription as a steady-state event to understanding its dynamic and cyclic nature; from looking at the DNA sequences recognized by various DNA-binding domains in vitro to analyzing the cell-specific genome-wide pattern of nuclear receptor binding and interpreting its physiological implications. Not only have these events propelled hormone research, but, as some of the pioneering studies, have also contributed tremendously to the field of molecular endocrinology as a whole. In this review, we give a brief summary of some of the most important discoveries in hormone signaling using ChIP and other derivative techniques and speculate on what the future may hold.

Identification of estrogen-responsive genes based on the DNA binding properties of estrogen receptors using high-throughput sequencing technology

“…In addition to transcriptome analyses such as RNA-sequencing, CAGE sequencing [56] , and microarray analysis, mapping of ER binding sites (ERBSs) is being performed by ChIP-chip or ChIP sequencing (ChIP-seq) analysis, which is a deepsequencing technique for ChIP-derived DNA fragments [57] . Integrated studies of transcriptomes and transcription factor binding sites can provide useful information for ER-mediated gene regulation in a genome-wide manner [58] . In particular, the development of next-generation sequencing has allowed us to obtain DNA sequence information much more rapidly, and from across the genome.…”

TIP48/Reptin and H2A.Z Requirement for Initiating Chromatin Remodeling in Estrogen-Activated Transcription

“…Chromatin immunoprecipitation (ChIP) studies have provided extensive information on the recruitment of these complexes by the hormone bound estrogen receptor in ERα-positive breast cancer cells [5]. The first complex to occupy promoter sequences is the ATP-dependent SWI/SNF chromatin remodeling complex and its catalytic subunit Brg1.…”

Microfluidic Platforms for the Investigation of Intercellular Signalling Mechanisms

“…Commonly used techniques to assess such regulation involve analysing protein-DNA interactions, and include electrophoretic mobility shift assays, DNA footprinting assays, lucifer reporter assays and more recently, chromatin immuno-precipitation. [ 53 ] As a model for investigating the endocrine communication that occurs between the adrenal gland and liver for energy mobilisation, Mao and associates. [ 54 ] simulated the signalling events using embryonic kidney 293 cells and human hepatic L-02 cells.…”