HiCmaps

HiCmaps are standardized representations of chromatin interactions produced by Hi-C experiments. They capture the frequency with which pairs of genomic loci come into proximity in the three-dimensional nucleus, summarized as a two-dimensional contact map. A HiCmap is generated by sequencing crosslinked chromatin, mapping paired-end reads to a reference genome, assigning reads to genomic bins, and counting interactions between bin pairs. To reduce technical bias, HiCmaps are commonly normalized to correct for systematic effects such as distance-dependent decay, mappability, and fragment length, using methods like matrix balancing.

The resolution of a HiCmap depends on sequencing depth and bin size; finer resolutions (tens of kilobases) require deeper sequencing, while coarser analyses use larger bins. HiCmaps enable the identification of genome-wide features such as A/B compartments, topologically associating domains (TADs), and chromatin loops, and they provide insights into the organization of the genome in three dimensions. Researchers also use HiCmaps to compare chromatin architecture across cell types, developmental stages, or disease conditions, and to integrate these data with other assays such as ChIP-seq and RNA-seq to link structure with regulation and transcription.

Limitations of HiCmaps include sparse contact counts at high resolution, biases introduced during library preparation and sequencing, and the difficulty of translating contact frequencies into precise physical distances. Data are stored in specialized formats and deposited in public repositories, facilitating cross-study comparisons. HiCmaps thus serve as a foundational resource for studying the spatial organization of the genome and its functional implications.