MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms

Genome Biol. 2019 Nov 25;20(1):251. doi: 10.1186/s13059-019-1868-z.


The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chromatin organization, yet introduce new computational challenges. Thus, we developed MIA-Sig, an algorithmic solution based on signal processing and information theory. We demonstrate its ability to de-noise the multiplex data, assess the statistical significance of chromatin complexes, and identify topological domains and frequent inter-domain contacts. On chromatin immunoprecipitation (ChIP)-enriched data, MIA-Sig can clearly distinguish the protein-associated interactions from the non-specific topological domains. Together, MIA-Sig represents a novel algorithmic framework for multiplex chromatin interaction analysis.

Keywords: 3D genomics; Algorithms; ChIA-Drop; Multiplex chromatin interactions; Signal processing.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromatin / metabolism*
  • Promoter Regions, Genetic
  • Signal Processing, Computer-Assisted*
  • Software*


  • Chromatin