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TADs as the Caller Calls Them.

¹Division of Gene Regulation, Oncode Institute and Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066CX, the Netherlands.

Journal of Molecular Biology

|October 27, 2019

Summary

Topologically associating domains (TADs) are key genome structures revealed by Hi-C. This review explores TAD formation, function, and proposes refining their definition to include the mechanisms that shape them.

Keywords:

3D genome Computational biology Gene regulation Hi-C Topologically associating domains

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Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

High-throughput sequencing and proximity ligation methods offer high-resolution insights into genome organization.
Topologically associating domains (TADs) are prominent features in Hi-C maps, characterized by increased self-interaction regions.
TADs exhibit strong evolutionary conservation and correlate with gene expression patterns.

Observation:

The precise definition and functional role of TADs remain subjects of ongoing debate.
Recent research presents a more complex understanding of TADs' involvement in gene regulation.

Findings:

This review covers the discovery and identification methods of TADs.
It examines the molecular mechanisms driving TAD formation.
Emerging data suggest a nuanced role for TADs in gene regulation.

Implications:

The findings advocate for incorporating formation mechanisms into the definition of TADs.
A deeper understanding of TADs can elucidate principles of genome organization and gene regulation.
This work provides a framework for future research into the functional significance of genome architecture.