OPINION

Organizational principles of 3D genome architecture

Abstract

Studies of 3D chromatin organization have suggested that chromosomes are hierarchically organized into large compartments composed of smaller domains called topologically associating domains (TADs). Recent evidence suggests that compartments are smaller than previously thought and that the transcriptional or chromatin state is responsible for interactions leading to the formation of small compartmental domains in all organisms. In vertebrates, CTCF forms loop domains, probably via an extrusion process involving cohesin. CTCF loops cooperate with compartmental domains to establish the 3D organization of the genome. The continuous extrusion of the chromatin fibre by cohesin may also be responsible for the establishment of enhancer–promoter interactions and stochastic aspects of the transcription process. These observations suggest that the 3D organization of the genome is an emergent property of chromatin and its components, and thus may not be only a determinant but also a consequence of its function.

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Fig. 1: Current model of chromatin organization.
Fig. 2: New model of chromatin organization.
Fig. 3: Mechanisms of loop extrusion.
Fig. 4: Effects of CTCF, cohesin or WAPL depletion on 3D chromatin organization.
Fig. 5: CTCF loops and enhancer–promoter interactions.

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Acknowledgements

Work in the authors’ laboratory is supported by US Public Health Service Award R01 GM035463 (V.G.C.) and Pathway to Independence Award K99/R00 GM127671 (M.J.R.) from the US National Institutes of Health (NIH). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

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M.J.R. was involved in researching data for the article. Both authors were responsible for discussing content, writing the article and reviewing and/or editing the manuscript before submission.

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Correspondence to Victor G. Corces.

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Glossary

ChIA-PET

Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) utilizes chromatin immunoprecipitation followed by proximity ligation to identify chromatin interactions between loci bound by a protein of interest.

ChIP–exo and ChIP–nexus

Chromatin immunoprecipitation (ChIP) followed by exonuclease digestion (ChIP–exo) is a technique that is used in place of standard chromatin immunoprecipitation followed by sequencing (ChIP–seq) to identify protein binding sites at higher resolution. The higher resolution is achieved because exonuclease treatment trims stretches of flanking DNA that are not directly bound by the protein of interest. ChIP–nexus utilizes a different library preparation strategy to reportedly improve signal compared with ChIP–exo.

Compartmental domains

Domains in Hi-C data that are not formed by a CTCF loop and are formed instead by the segregation of active and inactive chromatin.

CTCF loops

Point-to-point interactions between loci that coincide with CTCF and cohesin occupancy and often contain CTCF motifs in convergent orientation. These appear as bright punctae corresponding to high-frequency interactions in Hi-C contact maps.

Directionality index

A common method of computationally identifying topologically associating domain (TAD) borders. A directionality is calculated for each binned genomic locus to describe the preference of interaction signal with bins on the right (positive directionality) or with bins on the left (negative directionality). TAD borders are defined at transitions between negative and positive directionality.

Gene loop

A loop formed by interactions between the transcription start site and the transcription termination site.

Global run-on sequencing

(GRO-seq). A method involving isolation of nascent transcripts and high-throughput sequencing to study active transcription genome-wide.

Hi-C

A method using proximity ligation and high-throughput sequencing to identify all interactions taking place throughout the genome.

Loop extrusion

A model in which chromatin is pulled through the cohesin or condensin ring to form loops.

Oligopaint

A method of labelling DNA using short fluorescently labelled oligonucleotides for high-resolution imaging of chromatin.

Ordinary domains

Domains observed in Hi-C data that are not spanned by a CTCF loop. They are probably the same as compartmental domains.

STORM

(Stochastic optical reconstruction microscopy). Super-resolution imaging using individual photo-switchable fluorophores.

Transcriptional states

The state of a locus based on the presence of chromatin-bound proteins or covalent histone modifications that correlate with gene silencing or active transcription.

Transcription factory

A distinct nuclear location where RNA polymerase II (RNAPII) accumulates on the basis of the observation that components of the transcription complex can be detected as discrete foci by microscopy. The transcription factory hypothesis suggests that genes are recruited to these nuclear locations in order to be transcribed.

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Rowley, M.J., Corces, V.G. Organizational principles of 3D genome architecture. Nat Rev Genet 19, 789–800 (2018). https://doi.org/10.1038/s41576-018-0060-8

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