Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments

Transcription Factor Chromatin Immunoprecipitation in Endothelial Cells

Interactions between DNA and proteins are crucial for the regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful technique that allows the study of specific protein-DNA interactions in cultured cells and fresh or fixed tissue. Chromatin is isolated and sheared, and antibodies against the protein(s) of interest are used to isolate specific protein-DNA complexes. Subsequent analysis by real-time polymerase chain reaction (qPCR) or next-generation sequencing (NGS) allows identification and quantification of the co-purified DNA fragments, and NGS also gives insight into the genomic binding sites of a protein. Here we describe a cross-linking ChIP (X-ChIP) protocol, based around the example of a myc-tagged Proline-Rich Homeodomain (PRH) protein expressed in human umbilical vein endothelial cells. We also describe how to analyse specific known or suspected binding sites using quantitative PCR as well as how to analyse genome-wide binding from ChIP sequencing data.

Global Analyses to Identify Direct Transcriptional Targets of p53

The transcription factor p53 controls a gene expression program with pleiotropic effects on cell biology including cell cycle arrest and apoptosis. Identifying direct p53 target genes within this network and determining how they influence cell fate decisions downstream of p53 activation is a prerequisite for designing therapeutic approaches that target p53 to effectively kill cancer cells. Here we describe a comprehensive multi-omics approach for identifying genes that are direct transcriptional targets of p53. We provide detailed procedures for measuring global RNA polymerase activity, defining p53 binding sites across the genome, and quantifying changes in steady-state mRNA in response to p53 activation.

[The improvewment of DNA library construction in non-crosslinked chromatin immunoprecipitation coupled with next-generation sequencing]

OBJECTIVE

To optimize DNA library construction in non-crosslinked chromatin immunoprecipitation coupled with next-generation sequencing (Native ChIP-seq) to obtain high-quality Native ChIP-seq data.

METHODS

Human nasopharyngeal carcinoma HONE1 cell lysate was digested with MNase for release of the nucleosomes, and the histone-DNA complexes were immunoprecipitated with specific antibodies. The protein component in the precipitate was digested with proteinase K followed by DNA purification; the DNA library was constructed for sequence analysis.

RESULTS

Compared with the conventional DNA library construction, Tn5 transposase method allowed direct enrichment of the target DNA after Tn5 fragmentation, which was simple, time-saving and more efficient. The IGV visualized map showed that the information obtained by the two library construction methods was consistent. The sequencing data obtained by the two methods revealed more signal enrichment with Tn5 transposase library construction than with the conventional approach. H3K4me3 ChIP results showed a good reproducibility after Tn5 transposase library construction with a signal-to-noise ratio above 50%.

CONCLUSIONS

Tn5 transposase method improves the efficiency of DNA library construction and the results of subsequent sequence analysis, and is especially suitable for detecting histone modification in the DNA to provide a better technical option for epigenetic studies.

An improved method for quantitative ChIP studies of nuclear receptor function

Chromatin immunoprecipitation (ChIP) is a valuable tool for the endocrine researcher, providing a means to measure the recruitment of hormone-activated nuclear receptors, for example. However, the technique can be challenging to perform and has multiple experimental steps, risking introduction of error at each. The data produced can be challenging to interpret; several different methods are commonly used for normalising data and thus comparing between conditions. Absolute, sensitive quantification of protein-bound DNA is important for correct interpretation of the data. In addition, such quantification can help the investigator in troubleshooting experiments. Here, we outline a ChIP strategy combining droplet digital PCR for accurate quantification with an internal spike-in control for normalisation. This combination strengthens the reliability of ChIP data and allows the operator to optimise their protocol with greater confidence.