Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET)

Methods Mol Biol. 2017;1468:63-89. doi: 10.1007/978-1-4939-4035-6_7.


Genomic DNA is dynamically associated with protein factors and folded to form chromatin fibers. The 3-dimensional (3D) configuration of the chromatin will enable the distal genetic elements to come into close proximity, allowing transcriptional regulation. Noncoding RNA can mediate the 3D structure of chromatin. Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a valuable and powerful technique in molecular biology which allows the study of unbiased, genome-wide de novo chromatin interactions with paired-end tags. Here, we describe the standard version of ChIA-PET and a Multiplex ChIA-PET version.

Keywords: Antibodies; Barcoded half-linkers; Chromatin immunoprecipitation (ChIP); Chromatin interactions; High-throughput sequencing; Multiplex ChIA-PET; Paired-end tags; Protein; Proximity ligation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Cells, Cultured
  • Chromatin / chemistry
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation
  • Gene Expression Regulation
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • K562 Cells
  • Nucleic Acid Conformation
  • RNA, Untranslated / metabolism*
  • Sequence Analysis, DNA / methods*


  • Chromatin
  • RNA, Untranslated