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RNA polymerase II transcription compartments — from factories to condensates

Nature Reviews Genetics volume 26, pages 775–788 (2025)Cite this article

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Abstract

Transcription by RNA polymerase II is a fundamental step in gene regulation that mainly occurs in discrete nuclear foci, or transcription compartments, characterized by a high local concentration of polymerases and nascent RNA. Early studies referred to these foci as transcription factories, proposing that they harbour most transcriptional activity and all relevant protein machinery to produce mature RNAs. However, this model of transcriptional organization has long remained controversial owing to its mechanistic uncertainties. Recently, new insights into how these foci may form are being provided by studies of phase-separated transcriptional condensates that encompass RNA polymerases, transcription factors and RNA. Advances in 3D genomics and chromatin imaging are also deepening our understanding of how transcription compartments might facilitate communication between cis-regulatory elements in 3D nuclear space. In this Review, we contrast historical work on transcription factories with recent findings on transcriptional condensates to better understand the architecture and functional relevance of transcription compartments.

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Fig. 1: Basic organization of mammalian chromatin.
Fig. 2: Organization of transcription factories and phase-separated transcriptional condensates in mammalian cell nuclei.
Fig. 3: Different modes of enhancer–promoter 3D interactions.
Fig. 4: Features of an integrated transcription compartment model.

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Acknowledgements

The authors thank A. Marieke Oudelaar for critical reading of the manuscript and S. J. Wille for help with figures. Work in the laboratories of K.R. and A.P. is supported by the German Research Foundation (DFG) by the Priority Programs 2202 (Project 507951894 awarded to K.R. and 422389065 awarded to A.P.) and 2191 (Project 419067076 awarded to K.R. and 506296585 awarded to A.P.). Work in the laboratory of A.P. is also supported by the Collaborative Research Center 1565 (Project 469281184) and by the Lower Saxony Ministry for Science and Culture (NMWK) via the SPRUNG programme (Project 76211-1267/2023).

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Authors and Affiliations

  1. Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany

    Karsten Rippe

  2. Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), University of Heidelberg, Heidelberg, Germany

    Karsten Rippe

  3. Translational Epigenetics and Genome Architecture Group, Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany

    Argyris Papantonis

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  2. Argyris Papantonis
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Glossary

Active chromatin hub

A cluster of two or more transcribed genes that are co-regulated.

Genome architecture mapping

A method orthogonal to chromosome conformation capture in which the frequency of co-occurrence of DNA regions in thin cryosections of cell nuclei is used as a proxy of their spatial colocalization. This method does not require ligation of interacting DNA sequences and may, thus, provide information of multiway interactions among regions of interest.

High-throughput chromosome conformation capture

(Hi-C). A method to measure the frequency by which two genomic sequences are found in close spatial proximity. It relies on the ligation and pairwise detection of DNA by high-throughput sequencing.

Histone locus bodies

(HLBs). An assembly of transcription machinery and processing around the histone gene cluster. It drives the highly efficient, coordinated and cell-cycle-associated production of histone mRNAs. HLBs are stable and persist throughout the cell cycle, while uniquely integrating histone-specific processing machinery, such as NPAT, FLASH and U7 small nuclear ribonucleoprotein.

Intrinsically disordered regions

(IDRs). Segments of a protein that lack a defined higher-order structure under physiological conditions.

Liquid–liquid phase separation

The unmixing of proteins and RNA molecules from the surrounding nucleoplasm driven by multivalent interactions that form distinct, liquid-like droplets in the nucleus.

Multivalent

In the case of molecular interactions, multivalent refers to the ability of a molecule or complex to simultaneously interact with two or more other molecules/complexes owing to the presence of multiple interaction sites.

Nuclear speckles

Nuclear condensates, 100–2,000 nm in size, containing polyadenylated RNA and splicing factors that have been associated with the storage, processing and export of mRNAs.

Percolation

A phase transition in which an interconnected network of molecules forms through multivalent interactions. The concentration at which a system transitions from disconnected clusters to a single, system-spanning network is called the percolation limit or threshold.

Phase-separated transcriptional condensates

(PST-condensates). Accumulation of transcription-related factors that occur by a biophysical phase separation mechanism.

Phase separation

Transition in which molecules demix from their bulk environment into a dense condensate and a dilute surrounding phase to form bodies of distinct physicochemical properties.

Phase transition

Change in the physical state or organizational properties of a system. This term includes not only phase separation but also network transitions such as percolation.

RNAPII clusters

Local co-associations of two or more (active) RNA polymerase II (RNAPII) complexes.

Saturation concentration

(Csat). The concentration threshold above which phase separation occurs.

Super-enhancers

Clusters of closely spaced cis-regulatory elements typically controlling expression of cell identity genes.

Surface condensation

Initial phase of protein enrichment on the DNA or chromatin surface through multivalent interactions creates a thin, wetting layer, which can nucleate the formation of more defined, phase-separated protein clusters.

Transcription bodies

Large and long-lived focal nucleoplasmic sites of high transcriptional activity harbouring co-expressed genes (for example, the two characteristic bodies emerging upon genome activation during early zebrafish development).

Transcriptional condensates

Assemblies of transcription machinery components and related factors that may form through dynamic multivalent interactions by phase separation or other mechanisms.

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Rippe, K., Papantonis, A. RNA polymerase II transcription compartments — from factories to condensates. Nat Rev Genet 26, 775–788 (2025). https://doi.org/10.1038/s41576-025-00859-6

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