Hi-C calibration by chemically induced chromosomal interactions.

Area of Science:

• Genomics
• Molecular Biology
• Biophysics

Background:

• Hi-C is a powerful tool for studying genome organization.
• Assessing Hi-C's quantitative properties like sensitivity and bias is challenging in vivo.
• The dynamic nature of chromosomal interactions complicates in vivo measurements.

Purpose of the Study:

• To quantitatively assess the sensitivity, bias, and linearity of the Hi-C assay.
• To establish a robust framework for calibrating Hi-C data.
• To understand the relationship between static chromosomal interactions and genome organization.

Main Methods:

• Chemically Induced Chromosomal Interaction (CICI) method was used to create stable interactions in yeast.
• Hi-C analysis was performed on engineered G1-phase budding yeast populations.
• Analysis focused on intra- and inter-chromosomal interactions across varying contact frequencies.

Main Results:

• Static intra-chromosomal loops do not form TADs but promote local 3D proximity (10-60 kb).
• Hi-C can detect interactions present in 5-10% of cells at moderate sequencing depths.
• The Hi-C assay shows no bias towards intra- vs. inter-chromosomal interactions.
• A linear relationship was observed between Hi-C signal intensity and contact frequency.

Conclusions:

• Hi-C is sensitive and quantitative, with a linear response to contact frequency.
• The study provides a framework for calibrating Hi-C data for more accurate genome organization studies.
• Findings clarify the intrinsic properties of Hi-C, aiding interpretation of genome conformation data.