Choudhary
Laboratory
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Deciphering cell signaling networks through innovative proteomics and genomics.
Acetylation of histones and non-histone proteins is not a mere consequence of ongoing transcription.
Liebner T et al. Nature Communication. (2024 June) [Pubmed]
Using MS and genomics approaches, we show that acute transcription inhibition does not cause global changes in histone acetylation, while CBP/p300 inhibition induces selective alterations in the histone acetylome, indicating that acetyltransferases remain active in the absence of ongoing transcription. Our results challenge the prevailing view that histone acetylation is mainly a consequence of transcription.
Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties.
Prus G et al. Cell. (2024 May) [Pubmed]
We present a global, quantitative analysis of ubiquitylation site occupancy and half-life across the proteome. By showing that site occupancy, turnover rate, and sensitivity to proteasome inhibition together distinguish ubiquitylation sites involved in proteasomal degradation from those mediating cellular signaling, we also uncover a surveillance mechanism that rapidly and site-indiscriminately deubiquitylates all ubiquitin-activating (E1) and ubiquitin-conjugating (E2) enzymes.
Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes.
Narita T, Higashijima Y et al. Nature Genetics. (2023 April) [Pubmed]
We identify multisite lysine acetylation on the histone H2B N-terminus (H2BNTac) as a precise signature of active enhancers. H2BNTac, catalyzed specifically by CBP/p300 marks endogenously active enhancers as well as CBP/p300-dependent gene promoters, and its signal intensity accurately predicts real-time enhancer strength and CBP/p300 target genes.
Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release.
Narita T et al. Mol Cell. (2021 May) [Pubmed]
We revealed that pre-initiation complex assembly is a dynamically controlled step in the transcription cycle, and that p300/CBP-catalyzed acetylation serves as a signal that specifically promotes transcription initiation at enhancer-regulated genes. We propose that p300/CBP acetyltransferase activity operates via a “recruit-and-release” mechanism that simultaneously promotes RNAPII recruitment and pause release, thereby enabling kinetic activation of enhancer-mediated transcription.
Time-resolved analysis reveals rapid dynamics and broad Scope of the CBP/p300 acetylome.
Weinert BT, Narita T et al. Cell. (2018 May) [Pubmed]
By combining quantitative proteomics with specific CBP/p300 catalytic inhibitors, bromodomain inhibitors, and genetic knockout cells, we reveal a comprehensive map of regulated acetylation sites and their dynamic turnover rates. CBP/p300 regulates a much larger number of acetylation sites than known previously, and CBP/p300-catalyzed rapid acetylation is essential for gene transcription. The entire resource dataset is freely accessible at:
p300DBGlobal mapping of the endogenous DNA damage repair networks identifies Shieldin as a novel protein complex in DNA damage repair.
Gupta R et al. Cell. (2018 May) [Pubmed]
Using a novel proteomic approach we reveal a comprehensive map of protein interaction of key DNA damage repair proteins. We show that the novel protein complex shieldin is an essential downstream effector of 53BP1 in regulating NHEJ, antibody class-switching and sensitivity to PARP inhibitors. Identification of Shieldin provides new insights into the evolution of vertebrate-specific DDR pathways with key relevance for understanding antibody diversification and PARP inhibitor resistance.
A fully-funded postdoc position is available in the Group.
We offer exciting scientific environment and cutting-edge technologies for identifying and investigating novel regulatory mechanisms of cell signaling. More details about the position can be found here.
Interested candidates can also directly contact Chuna Choudhary:
chuna.choudhary@cpr.ku.dk