ChIA-PET

ChIA-PET

Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a variation of Hi-C that features an immunoprecipitation step to map long-range DNA interactions , . In this method, DNA-protein complexes are crosslinked and fragmented. Specific antibodies are used to immunoprecipitate proteins of interest. Specific linkers are ligated to the DNA fragments, which ligate when in proximity. Linkers are then precipitated and digested with an enzyme and the DNA is sequenced. Deep sequencing provides base-pair resolution of ligated fragments. Hi-C and ChIA-PET currently provide the best balance of resolution and reasonable coverage in the human genome to map long-range interactions.

• ChIA-PET: Li G., Fullwood M. J., Xu H., Mulawadi F. H., Velkov S., et al. (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11: R22

1. Buisine N., Ruan X., Bilesimo P., Grimaldi A., Alfama G., et al. (2015) Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis. PLoS One 10: e0137526
2. Grubert F., Zaugg J. B., Kasowski M., Ursu O., Spacek D. V., et al. (2015) Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell 162: 1051-1065
3. Letourneau A., Cobellis G., Fort A., Santoni F., Garieri M., et al. (2015) HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells. PLoS One 10: e0126475
4. Reeder C., Closser M., Poh H. M., Sandhu K., Wichterle H., et al. (2015) High resolution mapping of enhancer-promoter interactions. PLoS One 10: e0122420
5. Dowen J. M., Fan Z. P., Hnisz D., Ren G., Abraham B. J., et al. (2014) Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 159: 374-387