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The mass spectrometry analysis of CTDP1 function

ABSTRACT: We previously identified an interaction between the RNA polymerase II (Pol II) subunit RPB7 and the phosphatase CTDP1 in regulating transcription termination-reinitiation. Here, we establish that CTDP1 dephosphorylates a unique Pol II phospho-isoform modified at Tyr1, Ser5, and Ser7 of its C-terminal domain. This activity is critical for recruiting the Mediator complex and modulating transcriptional efficiency. Furthermore, by integrating phosphoproteomic and immunoprecipitation-mass spectrometry data, we reveal that CTDP1 also governs the phosphorylation of numerous RNA splicing factors. Our findings position CTDP1 as a master coordinator that integrates transcription with RNA splicing.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Cell Culture, Embryonic Stem Cell

SUBMITTER: Haonan Zheng

LAB HEAD: Xiong Ji

PROVIDER: PXD071392 | Pride | 2026-07-10

REPOSITORIES: Pride

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			Action	DRS
	ZHN_20240306_WT1_MT2_INPUT5.xlsx	Xlsx
	ZHN_20240306_WT1_MT2_INPUT5.zip	Other
	ZHN_20240508_S200.zip	Other
	ZHN_20240508_S200_Rep1_2024.05.09.filtered_cross-linked_sites.csv	Csv
	ZHN_20240508_S200_Rep2_2024.05.09.filtered_cross-linked_sites.csv	Csv

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CTDP1 governs a unique RNAPII phospho-form and coordinates Mediator recruitment, transcription efficiency, and splicing

Project description:We previously reported that the RNA polymerase II (Pol II) subunit RPB7 interacts with the phosphatase CTDP1 to regulate transcription termination-reinitiation. Here, we demonstrate that CTDP1 specifically dephosphorylates a unique phospho-isoform of Pol II, which is modified at tyrosine 1, serine 5, and serine 7 (Tyr1, Ser5, Ser7) of its C-terminal domain. Functionally, this regulation is critical for the recruitment of the Mediator complex to chromatin and for modulating Pol II transcriptional efficiency. Furthermore, by integrating phosphoproteomic and immunoprecipitation-mass spectrometry data, we show that CTDP1 also regulates the phosphorylation of numerous RNA splicing factors. Consequently, depletion of CTDP1 disrupts gene expression oscillations, leading to increased intron retention and aberrant splicing of cassette exons. These findings suggest that CTDP1 serves as a key integrator of transcription and splicing, potentially contributing to the regulation of circadian rhythms and the cell cycle.

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CTDP1 and RPB7 stabilize and license Pol II termination to reinitiation [PRO-seq]

Project description:The regulations of RNA Pol II initiation, elongation, and termination have been extensively investigated in mammalian cells, but how RNA Pol II terminates and then reinitiates a new round of transcription remains elusive. Here, we found that RPB7 loss triggers the degradation of RNA Pol II. Strikingly, RPB7 degradation combines knock out of E3 ligase Cullin 3 led to the accumulation of phosphorylated Pol II in the soluble fractions and Pol II reinitiation failure. The stability of recycled Pol II is dependent on the loop domain of RPB7 and the dephosphorylation of Pol II CTD. Termination-reinitiation recycling requires RPB7, CTD phosphatase subunit 1 (CTDP1), and stabilization of Pol II. Our study demonstrates that RPB7/CTDP1 controls the dephosphorylation and stabilization of RNA Pol II to permit RNA Pol II termination to reinitiation recycle in mammalian cells.

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RPB7/CTDP1 stabilizes and licenses Pol II termination to reinitiation [ChAR-Seq]

Project description:The regulations of transcription process have been extensively investigated, but how RNA Pol II terminates and reinitiates a new round of transcription remains elusive. Here, we found that RPB7 loss triggers the degradation of RNA Pol II. RPB7 degradation combing knock out of E3 ligase Cullin 3 led to the accumulation of phosphorylated Pol II in the soluble fractions and Pol II reinitiation failure. The stability of recycled Pol II is dependent on the loop-region and dimerization of RPB7 and the phosphorylation state of Pol II CTD. Site-specific cancer mutations in the RPB7 loop-region caused the dysregulations of specific gene expression. Moreover, the loss of RPB7 or CTD phosphatase subunit 1 (CTDP1) result in the defects in Pol II termination-reinitiation recycle. Together, our study demonstrates that RPB7/CTDP1 controls the dephosphorylation and stabilization of RNA Pol II to permit RNA Pol II termination to reinitiation recycle in mammalian cells.

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RPB7/CTDP1 stabilizes and licenses Pol II termination to reinitiation [ChIP-Seq]

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