Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization

Sharma, Rajesh; Choi, Kyoung‐Jae; Quan, My Diem; Sharma, Sonum; Sankaran, Banumathi; Park, Hyekyung; LaGrone, Anel; Kim, Jean J.; MacKenzie, Kevin R.; Ferreon, Allan Chris M.; Kim, Choel; Ferreon, Josephine C.

doi:10.1038/s41467-021-25761-7

Cited by 56 publications

(55 citation statements)

References 84 publications

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“…In this work, we show that the ability of Sox2 to generate high forces through co-condensation with DNA critically relies on its IDRs; on the other hand, the DNA-binding HMGB domain of Sox2 alone is sufficient for condensation with DNA. This is reminiscent of recent findings with Klf4 and SMN proteins, 26,27 suggesting that condensate formation and force generation are two separable activities dependent on distinct domains of a given TF.…”

Section: Discussionsupporting

confidence: 67%

Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA

Nguyen

Chang

Watters

et al. 2022

Preprint

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Formation of biomolecular condensates constitutes an emerging mechanism for transcriptional regulation. Recent studies suggest that the co-condensation between transcription factors (TFs) and DNA can generate mechanical forces driving genome rearrangements. However, the reported forces generated by such protein-DNA co-condensation are typically below one piconewton (pN), questioning its physiological significance. Moreover, the force-generating capacity of these condensates in the chromatin context remains unknown. Using single-molecule biophysical techniques, we show that Sox2, a nucleosome-binding pioneer TF, forms co-condensates with DNA, thereby exerting considerable mechanical tension on DNA strands both in cis and trans. Sox2 can generate forces up to 7 pN—similar in magnitude to other cellular forces. Sox2:DNA condensates are highly stable, withstanding disruptive forces high enough to melt DNA. We find that the disordered domains of Sox2 are required for maximum force generation but not condensate formation per se. Finally, we show that nucleosomes dramatically attenuate the mechanical stress exerted by Sox2 via sequestering it from coalescing on bare DNA. Our findings reveal that TF-mediated DNA condensation can exert significant mechanical stress which can nonetheless be alleviated by the chromatin organization, suggesting a new function of eukaryotic chromatin in protecting the genome from potentially deleterious nuclear forces.

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Section: Discussionsupporting

confidence: 67%

Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA

Nguyen

Chang

Watters

et al. 2022

Preprint

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“…NANOG’s phase transition behaviour and mechanism are distinct from KLF4’s LLPS 9 . Liquids, solids and gels can develop from LLPS, depending on solution conditions, protein sequence and material properties 46 .…”

Section: Discussionmentioning

confidence: 98%

“…Liquids, solids and gels can develop from LLPS, depending on solution conditions, protein sequence and material properties 46 . KLF4’s LLPS results from recognition of the partial cognate sequence by the multivalent zinc fingers DNA-binding domain 9 . NANOG aggregation/condensation is mainly due to the oligomerization domain and behaves more like a functional amyloid (liquid-to-solid phase transition).…”

Section: Discussionmentioning

confidence: 99%

“…The pluripotent genome is shaped by the master transcription factors (TFs) NANOG and OCT4 8 . Recent studies, including ours 9 , have proposed that chromatin reorganization could occur through liquid–liquid phase separation (LLPS) 10 – 14 . We have demonstrated that KLF4 condensates facilitate NANOG expression, which explains the key role of KLF4 in induced cellular reprogramming 9 .…”

Section: Mainmentioning

confidence: 97%

“…Recent studies, including ours 9 , have proposed that chromatin reorganization could occur through liquid–liquid phase separation (LLPS) 10 – 14 . We have demonstrated that KLF4 condensates facilitate NANOG expression, which explains the key role of KLF4 in induced cellular reprogramming 9 . LLPS is enhanced by the disordered prion-like domains (PrDs) present in many RNA- and DNA-binding proteins 15 , 16 .…”

Section: Mainmentioning

confidence: 97%

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NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency

Choi

Quan

et al. 2022

Nat Cell Biol

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Human NANOG expression resets stem cells to ground-state pluripotency. Here we identify the unique features of human NANOG that relate to its dose-sensitive function as a master transcription factor. NANOG is largely disordered, with a C-terminal prion-like domain that phase-transitions to gel-like condensates. Full-length NANOG readily forms higher-order oligomers at low nanomolar concentrations, orders of magnitude lower than typical amyloids. Using single-molecule Förster resonance energy transfer and fluorescence cross-correlation techniques, we show that NANOG oligomerization is essential for bridging DNA elements in vitro. Using chromatin immunoprecipitation sequencing and Hi-C 3.0 in cells, we validate that NANOG prion-like domain assembly is essential for specific DNA recognition and distant chromatin interactions. Our results provide a physical basis for the indispensable role of NANOG in shaping the pluripotent genome. NANOG’s unique ability to form prion-like assemblies could provide a cooperative and concerted DNA bridging mechanism that is essential for chromatin reorganization and dose-sensitive activation of ground-state pluripotency.

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Spatial genome organization, TGFβ, and biomolecular condensates: Do they talk during development?

Vicioso-Mantis

Balbás

2022

BioEssays

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Cis‐regulatory elements govern gene expression programs to determine cell identity during development. Recently, the possibility that multiple enhancers are orchestrated in clusters of enhancers has been suggested. How these elements are arranged in the 3D space to control the activation of a specific promoter remains unclear. Our recent work revealed that the TGFβ pathway drives the assembly of enhancer clusters and precise gene activation during neurogenesis. We discovered that the TGFβ pathway coactivator JMJD3 was essential in maintaining these structures in the 3D space. To do that, JMJD3 required an intrinsically disordered region involved in forming phase‐separated biomolecular condensates found in the enhancer clusters. Our data support the existence of a relationship between 3D‐conformation of the chromatin, biomolecular condensates, and TGFβ‐driven response during mammalian neurogenesis. In this review, we discuss how signaling (TGFβ), epigenetics (JMJD3), and biochemical properties (biomolecular condensates nucleation) are coordinated to modulate the genome structure to guarantee proper neural development. Moreover, we comment on the potential underlying mechanisms and implications of the enhancer‐mediated regulation. Finally, we point out the knowledge gaps that still need to be addressed.

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Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization

Cited by 56 publications

References 84 publications

Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA

Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA

NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency

Spatial genome organization, TGFβ, and biomolecular condensates: Do they talk during development?

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