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2014 ; 70
(2-3
): 89-96
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Chromatin immunoprecipitation for human monocyte derived macrophages
#MMPMID25220915
Wooden J
; Ciborowski P
Methods
2014[Dec]; 70
(2-3
): 89-96
PMID25220915
show ga
The importance of Chromatin Immunoprecipitation (ChIP) technology has grown
exponentially along with an increased interest in epigenetic regulation. The
correlation of transcription factors with histone marks is now well established
as the center of epigenetic studies; therefore, precise knowledge about histone
marks is critical to unravel their molecular function and to understand their
role in biological systems. This knowledge constantly accumulates and is provided
openly in the expanding hubs of information such as the USCS Genome Browser.
Nevertheless, as we gain more knowledge, we realize that the DNA-protein
interactions are not driven by a "one size fits all" rule. Also, the diversity of
interactions between DNA, histones, and transcriptional regulators is much bigger
than previously considered. Besides a detailed protocol of sample preparation for
the ChIP assay from primary human monocyte-derived macrophages (MDM) [an
acceptable in vitro model for primary, human macrophage cells], we show that
differences between various types of cells exist. Furthermore, we can postulate
that such variations exist between transformed macrophage-like cell lines and
primary macrophages obtained from healthy volunteers. We found that the most
efficient fixation time for MDM is 10min. Finally, to perform multiple analytical
assays, we showed that even with thorough methodology, the yield of material
obtained from primary cells is the major challenge.