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Nucleosomes gate cofactor access to the transcription factor p53 P53-pos8-NCP

ABSTRACT: In solution crosslinking mass spectrometry of transcription factor p53 with the members of the ubiquitin proteasome system (UPS) on chromatin.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Jan Seebacher

LAB HEAD: Nicolas Thoma

PROVIDER: PXD054140 | Pride | 2025-07-31

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	2012_S01_XLMS_DSSO_2mM_201210_Id.Score_xlinks.xiNET.csv	Csv
	2012_S02_XLMS_DSSO_4mM_201210_Id.Score_xlinks.xiNET.csv	Csv
	L2_201210_JS_2012_S01_XLMS_DSSO_2mM.csv	Csv
	L2_201210_JS_2012_S01_XLMS_DSSO_2mM.fasta	Fasta
	L2_201210_JS_2012_S01_XLMS_DSSO_2mM.raw	Raw

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1 - 5 of 18

Publications

Nucleosomes specify co-factor access to p53.

Chakraborty Deyasini D Sandate Colby R CR Isbel Luke L Kempf Georg G Weiss Joscha J Cavadini Simone S Kater Lukas L Seebacher Jan J Kozicka Zuzanna Z Stoos Lisa L Grand Ralph S RS Schübeler Dirk D Michael Alicia K AK Thomä Nicolas H NH

Molecular cell 20250725 15

Pioneer transcription factors (TFs) engage chromatinized DNA motifs. However, it is unclear how the resultant TF-nucleosome complexes are decoded by co-factors. In humans, the TF p53 regulates cell-cycle progression, apoptosis, and the DNA damage response, with a large fraction of p53-bound sites residing in nucleosome-harboring inaccessible chromatin. We examined the interaction of chromatin-bound p53 with co-factors belonging to the ubiquitin proteasome system (UPS). At two distinct motif loca ...[more]

PMID: 40713947

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Nucleosomes gate cofactor access to the transcription factor p53 P53_USP7TRAF_FL_NCP

Project description:In solution crosslinking mass spectrometry of transcription factor p53 with the members of the ubiquitin proteasome system (UPS) on chromatin.

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Nucleosomes gate cofactor access to the transcription factor p53 [CUT&Run]

Project description:The transcription factor p53 regulates cell cycle progression, apoptosis, and the DNA damage response. A large fraction of p53 resides in inaccessible chromatin, where it is unclear how nucleosomes impact p53’s ability to engage cofactors. We examined the interaction of p53 with the members of the ubiquitin proteasome system (UPS) on chromatin. At two distinct motif locations (SHL-5.7, +5.9), the viral E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in vitro and in cells. The corresponding cryo-EM structure finds USP7 intricately engaged with p53 and nucleosomes, with the TRAF domain contacting the nucleosome at SHL-5.7 sandwiched between the p53 tetramerisation and DNA-binding domains. The structures of p53 bound to USP7/nucleosomes and E6AP illustrate how chromatin imposes a barrier for some, albeit not all p53 interactors. Our work suggests a conceptual framework for how nucleosomes govern TF/cofactor interactions.

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Nucleosomes gate cofactor access to the transcription factor p53 [ChIP-seq]

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Nucleosomes gate cofactor access to the transcription factor p53 [ChIP-seq]

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Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex

Project description:Deregulation of the ubiquitin ligase E6AP is causally linked to the development of human disease, including cervical cancer. In complex with the E6 oncoprotein of human papillomaviruses, E6AP targets the tumor suppressor p53 for degradation, thereby contributing to carcinogenesis. Moreover, E6 acts as a potent activator of E6AP by a yet unknown mechanism. However, structural information explaining how the E6AP-E6-p53 enzyme-substrate complex is assembled, and how E6 stimulates E6AP, is largely missing. We therefore developed and applied different approaches in structural mass spectrometry to show that binding of E6 induces conformational rearrangements in E6AP, which result in the positioning of E6 and p53 in the immediate vicinity of the catalytic centre of E6AP. Our data provides structural and functional insights into the dynamics of the full-length E6AP-E6-p53 enzyme-substrate complex and reveals how E6 can both stimulate the ubiquitin ligase activity of E6AP and facilitate the transfer of ubiquitin from E6AP onto p53.

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