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The spatial organization of transcriptional control

Nature Reviews Genetics volume 24, pages 53–68 (2023)Cite this article

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Abstract

In animals, the sequences for controlling gene expression do not concentrate just at the transcription start site of genes, but are frequently thousands to millions of base pairs distal to it. The interaction of these sequences with one another and their transcription start sites is regulated by factors that shape the three-dimensional (3D) organization of the genome within the nucleus. Over the past decade, indirect tools exploiting high-throughput DNA sequencing have helped to map this 3D organization, have identified multiple key regulators of its structure and, in the process, have substantially reshaped our view of how 3D genome architecture regulates transcription. Now, new tools for high-throughput super-resolution imaging of chromatin have directly visualized the 3D chromatin organization, settling some debates left unresolved by earlier indirect methods, challenging some earlier models of regulatory specificity and creating hypotheses about the role of chromatin structure in transcriptional regulation.

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Fig. 1: Contrasting views of enhancer-mediated transcription regulation based on 3C and Hi-C data.
Fig. 2: Open questions in the interpretation of population Hi-C data.
Fig. 3: Chromosome tracing disambiguates chromatin structure compared to generic super-resolution approaches.
Fig. 4: Overview of the chromosome-tracing procedure.
Fig. 5: Comparison of chromosome-tracing data and Hi-C data.
Fig. 6: Cell-type-specific topologically associating domains link cell-type-specific combinations of regulatory elements in Drosophila melanogaster embryos.

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Acknowledgements

The authors thank the members of the Boettiger laboratory for critical discussions and C. Walker for detailed feedback on the manuscript.

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    Antonina Hafner & Alistair Boettiger

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Glossary

Topologically associating domains

(TADs). These are defined on population-level contact-frequency maps as domains of higher interaction frequency within a region than between regions.

Mediator complex

A multisubunit protein complex that is a general regulator of transcription by RNA polymerase II.

Cohesin complex

A multisubunit protein complex that mediates sister-chromatid cohesion in mitosis and is essential for topologically associating domain (TAD) formation.

CTCF

The CCCTC binding factor (CTCF) is a zinc-finger transcription factor that is enriched at the boundaries of TADs.

Tethers

These are cis-regulatory elements that function to bring together distal DNA elements.

Phase separation

The process by which a mixture (such as oil and water) spontaneously separates into distinct phases, with molecules of one type separating from molecules of a second type.

Enthalpic

Interactions driven by the binding energy between molecules, such as homotypic interactions among chromatin states.

Loop extrusion

A model of how CTCF and cohesin are thought to form topologically associating domains (TADs), whereby cohesin is loaded onto the DNA and extrudes a loop until it is blocked by CTCF bound at the base of the loop.

Chromosome territories

Specific, largely non-overlapping areas in the nucleus that each chromosome occupies.

Diffraction limit

The distance limit below which two objects cannot be distinguished by conventional light microscopy. It depends on the wavelength of light and the objective used.

Fiducial markers

Markers used to correct for drift that may occur during an experiment. These can be fluorescent beads or labels on the DNA that remain constant throughout the imaging experiment.

Entropic

Changes that increase the number of accessible microstates in the system and do not require input energy.

Convolutional neural networks

(CNNs). Algorithms designed to learn from the data to uncover connections. CNNs are frequently used in image recognition and have been increasingly used to uncover relationships in biological data.

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Hafner, A., Boettiger, A. The spatial organization of transcriptional control. Nat Rev Genet 24, 53–68 (2023). https://doi.org/10.1038/s41576-022-00526-0

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