Chromatin immunoprecipitation (or ChIP) is a handy technique to study epigenetic profiles, but only if you have enough cells. The main problem with ChIP is that it can be a “greedy” technique that uses large numbers of cells while giving back the bare minimum of DNA as a result. This is problematic for the study of genome-wide epigenetic profiles in small populations of cells, such as cancer stem cells or the cells of the developing mouse blastocyst/embryo.
To solve this problem, researchers from the laboratories of Chang Lu and Kai Tan have come up with a “little” change to the ChIP process. Their new methodology, microfluidic oscillatory washing–based ChIP sequencing (MOWChIP-seq), generates reproducible results with as few as 100 cells and could represent a huge “little” step forward for the field.
Their new methodology involves the following steps.
- Fabrication of a microfluidic chamber of only 710 nanoliters in volume, where they placed a “packed bed” of magnetic beads conjugated to an antibody.
- Sonicated chromatin fragments were then passed through the packed bed at a slow rate to allow the immunoprecipitation of the desired target.
- Non-specific adsorbance was removed through short oscillatory washes created by pressure pulses.
- This allowed collection of a DNA concentration near the theoretical maximum, with a very low background level of contamination.
- Isolated ChIP DNA can be used for sequencing library construction without pre-amplification.
- Recovered DNA created reproducible ChIP-seq data over a wide range of input cells
- Results generated with 100–600 cell equivalents of chromatin either matched or surpassed other small-scale ChIP technologies using 5000 to 20,000 cell inputs.
- Direct ChIP on 100-600 cells using an optimized sonication technique derived good quality sequencing data that enabled analysis of important genome-wide features.
The authors went on to use this microfluidic technology to assess global histone modifications using small numbers of hematopoietic stem and progenitor cells (HSPCs) isolated from mouse fetal liver (FL). Again, the results were reproducible and consistent with known gene expression patterns. Excitingly, they were also able to distinguish previously unknown FL HSPC-specific enhancer elements.
This new microfluidic technique bypasses amplification steps, indexing, and pooling steps used in other ChIP strategies, and so may represent the best current technique for small-scale ChIP experiments. So have a little look and see how far your chromatin will now go at Nature Methods, July 2015.