Table 1.
Method name | Description | Number of cells | Application | Ref. |
---|---|---|---|---|
CChIP | Based on conventional NChIP but using ‘carrier’ chromatin, which allows detailed and reproducible epigenetic analysis of small numbers of cells | Procedure allows ChIP assays on as few as 100 cells and it can generate consistent results from 1000 cells | The procedure has been validated with primary mouse embryo material, but should be applicable to cells from various sources, including tissue biopsies and FACS-sorted cell populations. It may also be applicable to formaldehyde XChIP, thereby allowing the analysis of nonhistone proteins | [142] |
Q2ChIP | As an alternative to CChIP, Q2ChIP involves a chromatin preparation from a larger number of cells than CChIP, but includes chromatin dilution and aliquoting steps. In addition, Q2ChIP involves a crosslinking step, enabling the analysis of immunoprecipitation of transcription factors or other nonhistone DNA-bound proteins | 100,000 cells are used as starting material | Q2ChIP is suitable for analysis of both histone modifications and transcription factor binding from greatly reduced amounts of chromatin relative to conventional ChIP | [143] |
μChIP | The basis of the μChIP assay was the Q2ChIP assay with modifications. This 1D μChIP assay enables the analysis of histone or RNAPII binding throughout the human genome using high-density oligonucleotide arrays (ChIP-chip) | Chromatin is usually prepared from 1000 cells. | μChIP is applicable to small fresh tissue biopsies, and a crosslink-while-thawing procedure makes the assay suitable for frozen biopsies | [144,145] |
Microplate-based assay to enhance throughput: matrix ChIP | To increase the throughput and to simplify the assay, matrix ChIP, which utilizes surface-immobilized antibodies in a 96-well plate, was developed, where all steps from chromatin precipitation to PCR-ready DNA purification are carried out in microplate wells without sample transfers | Microplate-based number of cells | Application of all steps, from immunoprecipitation to DNA purification, is carried out in microplate wells without sample transfers, potentially enabling automation. A total of 96 ChIP assays for histone and various DNA-bound proteins can be conducted in a single day | [146] |
μChIP: Micro-chromatin immunoprecipitation; CChIP: Carrier chromatin immunoprecipitation; ChIP: Chromatin immunoprecipitation; FACS: Fluorescence-activated cell sorting; NChIP: Native chromatin immunoprecipitation; Q2ChIP: Quick and quantitative chromatin immunoprecipitation; RNAPII: RNA polymerase II; XChIP: Crosslinked chromatin.