New Technique Maps Hundreds of Proteins Simultaneously within Cell Nuclei

Amazing stuff! Could be a breakthrough!

"... Despite its importance, understanding gene regulation has been very challenging because previous methods to study regulatory proteins map them one at a time. ChIP–DIP now enables researchers to simultaneously map hundreds of DNA-associated regulatory proteins and take snapshots of how they change over time. ...

"We used ChIP–DIP to show how after an inflammatory event, cells of the immune system rapidly alter their histone proteins within a span of hours in order to activate inflammatory genes. We also used ChIP–DIP to identify combinations of proteins that regulate which genes are active or will become active in response to stress or during development. Previous consortium-based international projects have taken nearly a decade to conduct a few thousand experiments, but we have now done over 500 in the span of a few weeks." ..."

From the abstract:

"Gene expression is controlled by dynamic localization of thousands of regulatory proteins to precise genomic regions. Understanding this cell type-specific process has been a longstanding goal yet remains challenging because DNA–protein mapping methods generally study one protein at a time.

Here, to address this, we developed chromatin immunoprecipitation done in parallel (ChIP-DIP) to generate genome-wide maps of hundreds of diverse regulatory proteins in a single experiment. ChIP-DIP produces highly accurate maps within large pools (>160 proteins) for all classes of DNA-associated proteins, including modified histones, chromatin regulators and transcription factors and across multiple conditions simultaneously.

First, we used ChIP-DIP to measure temporal chromatin dynamics in primary dendritic cells following LPS stimulation.

Next, we explored quantitative combinations of histone modifications that define distinct classes of regulatory elements and characterized their functional activity in human and mouse cell lines.

Overall, ChIP-DIP generates context-specific protein localization maps at consortium scale within any molecular biology laboratory and experimental system."

New Technique Maps Hundreds of Proteins Simultaneously within Cell Nuclei - www.caltech.edu "Caltech researchers have developed a new method to map the positions of hundreds of DNA-associated proteins within cell nuclei all at the same time. The method, called ChIP–DIP (Chromatin ImmunoPrecipitation Done In Parallel), is a versatile tool for understanding the inner workings of the nucleus during different contexts, such as disease or development."

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements (no public access)

A schematic describing the ChIP-DIP process.