CDKL5 kinase controls transcription-coupled responses to DNA damage

Taran Khanam; Ivan Muñoz; Florian Weiland; Thomas Carroll; Michael Morgan; Barbara N. Borsos; Vasiliki Pantazi; Meghan Slean; Miroslav Novak; Rachel Toth; Paul Appleton; Tibor Pankotai; Houjiang Zhou; John Rouse

doi:10.15252/embj.2021108271

CDKL5 kinase controls transcription-coupled responses to DNA damage

Taran Khanam, Ivan Muñoz, Florian Weiland, Thomas Carroll, Michael Morgan, Barbara N. Borsos, Vasiliki Pantazi, Meghan Slean, Miroslav Novak, Rachel Toth, Paul Appleton, Tibor Pankotai, Houjiang Zhou, John Rouse

King Abdullah University of Science and Technology

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Abstract

Mutations in the gene encoding the CDKL5 kinase are among the most common genetic causes of childhood epilepsy and can also give rise to the severe neurodevelopmental condition CDD (CDKL5 deficiency disorder). Despite its importance for human health, the phosphorylation targets and cellular roles of CDKL5 are poorly understood, especially in the cell nucleus. Here, we report that CDKL5 is recruited to sites of DNA damage in actively transcribed regions of the nucleus. A quantitative phosphoproteomic screen for nuclear CDKL5 substrates reveals a network of transcriptional regulators including Elongin A (ELOA), phosphorylated on a specific CDKL5 consensus motif. Recruitment of CDKL5 and ELOA to damaged DNA, and subsequent phosphorylation of ELOA, requires both active transcription and the synthesis of poly(ADP-ribose) (PAR), to which CDKL5 can bind. Critically, CDKL5 kinase activity is essential for the transcriptional silencing of genes induced by DNA double-strand breaks. Thus, CDKL5 is a DNA damage-sensing, PAR-controlled transcriptional modulator, a finding with implications for understanding the molecular basis of CDKL5-related diseases.

Original language	English (US)
Journal	EMBO JOURNAL
DOIs	https://doi.org/10.15252/embj.2021108271
State	Published - Oct 4 2021

Bibliographical note

KAUST Repository Item: Exported on 2021-10-11
Acknowledgements: We thank the technical support of the MRC-PPU including the DNA Sequencing Service, Tissue Culture team, Reagents and Services team, and the PPU Mass-Spectrometry team. We also thank Fiona Brown and James Hastie for ELOA phospho-Ser antibody production and purification. We are grateful to Jessica Downs, Simon Boulton and Roger Greenberg for the U-2-OS cells harbouring the FokI silencing reporter and to Nick Lakin for -disrupted U-2-OS cells. We are grateful to Graeme Ball for help with microscopy data analysis. We thank Luis Sanchez-Pulido and Chis Ponting for help with bioinformatics analyses. We thank Petr Walczysko and William Moore for their generous help with generating OMERO figures. We are grateful to members of the Rouse laboratory for useful discussions. BBN and TP were funded by the National Research, Development and Innovation Office grant GINOP-2.2.1-15-2017-00052, EFOP 3.6.3-VEKOP-16-2017-00009, NKFI-FK 132080, the János Bolyai Research Scholarship of the Hungarian Academy of Sciences BO/27/20, UNKP-20-5-SZTE-265, EMBO short-term fellowship 8513 and the Tempus Foundation. This work was supported by the Medical Research Council (grant number: MC_UU_12016/1; TK, IM, JR) and the pharmaceutical companies supporting the Division of Signal Transduction Therapy Unit (Boehringer Ingelheim, GlaxoSmithKline and Merck KGaA). 311 PARP

ASJC Scopus subject areas

General Neuroscience
General Biochemistry, Genetics and Molecular Biology
Molecular Biology
General Immunology and Microbiology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.15252/embj.2021108271

https://repository.kaust.edu.sa/bitstream/10754/672464/1/embj.2021108271.pdf

Cite this

@article{58b8b09d427a47699a871b2b60287def,

title = "CDKL5 kinase controls transcription-coupled responses to DNA damage",

abstract = "Mutations in the gene encoding the CDKL5 kinase are among the most common genetic causes of childhood epilepsy and can also give rise to the severe neurodevelopmental condition CDD (CDKL5 deficiency disorder). Despite its importance for human health, the phosphorylation targets and cellular roles of CDKL5 are poorly understood, especially in the cell nucleus. Here, we report that CDKL5 is recruited to sites of DNA damage in actively transcribed regions of the nucleus. A quantitative phosphoproteomic screen for nuclear CDKL5 substrates reveals a network of transcriptional regulators including Elongin A (ELOA), phosphorylated on a specific CDKL5 consensus motif. Recruitment of CDKL5 and ELOA to damaged DNA, and subsequent phosphorylation of ELOA, requires both active transcription and the synthesis of poly(ADP-ribose) (PAR), to which CDKL5 can bind. Critically, CDKL5 kinase activity is essential for the transcriptional silencing of genes induced by DNA double-strand breaks. Thus, CDKL5 is a DNA damage-sensing, PAR-controlled transcriptional modulator, a finding with implications for understanding the molecular basis of CDKL5-related diseases.",

author = "Taran Khanam and Ivan Mu{\~n}oz and Florian Weiland and Thomas Carroll and Michael Morgan and Borsos, {Barbara N.} and Vasiliki Pantazi and Meghan Slean and Miroslav Novak and Rachel Toth and Paul Appleton and Tibor Pankotai and Houjiang Zhou and John Rouse",

note = "KAUST Repository Item: Exported on 2021-10-11 Acknowledgements: We thank the technical support of the MRC-PPU including the DNA Sequencing Service, Tissue Culture team, Reagents and Services team, and the PPU Mass-Spectrometry team. We also thank Fiona Brown and James Hastie for ELOA phospho-Ser antibody production and purification. We are grateful to Jessica Downs, Simon Boulton and Roger Greenberg for the U-2-OS cells harbouring the FokI silencing reporter and to Nick Lakin for -disrupted U-2-OS cells. We are grateful to Graeme Ball for help with microscopy data analysis. We thank Luis Sanchez-Pulido and Chis Ponting for help with bioinformatics analyses. We thank Petr Walczysko and William Moore for their generous help with generating OMERO figures. We are grateful to members of the Rouse laboratory for useful discussions. BBN and TP were funded by the National Research, Development and Innovation Office grant GINOP-2.2.1-15-2017-00052, EFOP 3.6.3-VEKOP-16-2017-00009, NKFI-FK 132080, the J{\'a}nos Bolyai Research Scholarship of the Hungarian Academy of Sciences BO/27/20, UNKP-20-5-SZTE-265, EMBO short-term fellowship 8513 and the Tempus Foundation. This work was supported by the Medical Research Council (grant number: MC_UU_12016/1; TK, IM, JR) and the pharmaceutical companies supporting the Division of Signal Transduction Therapy Unit (Boehringer Ingelheim, GlaxoSmithKline and Merck KGaA). 311 PARP",

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T1 - CDKL5 kinase controls transcription-coupled responses to DNA damage

AU - Khanam, Taran

AU - Muñoz, Ivan

AU - Weiland, Florian

AU - Carroll, Thomas

AU - Morgan, Michael

AU - Borsos, Barbara N.

AU - Pantazi, Vasiliki

AU - Slean, Meghan

AU - Novak, Miroslav

AU - Toth, Rachel

AU - Appleton, Paul

AU - Pankotai, Tibor

AU - Zhou, Houjiang

AU - Rouse, John

N1 - KAUST Repository Item: Exported on 2021-10-11 Acknowledgements: We thank the technical support of the MRC-PPU including the DNA Sequencing Service, Tissue Culture team, Reagents and Services team, and the PPU Mass-Spectrometry team. We also thank Fiona Brown and James Hastie for ELOA phospho-Ser antibody production and purification. We are grateful to Jessica Downs, Simon Boulton and Roger Greenberg for the U-2-OS cells harbouring the FokI silencing reporter and to Nick Lakin for -disrupted U-2-OS cells. We are grateful to Graeme Ball for help with microscopy data analysis. We thank Luis Sanchez-Pulido and Chis Ponting for help with bioinformatics analyses. We thank Petr Walczysko and William Moore for their generous help with generating OMERO figures. We are grateful to members of the Rouse laboratory for useful discussions. BBN and TP were funded by the National Research, Development and Innovation Office grant GINOP-2.2.1-15-2017-00052, EFOP 3.6.3-VEKOP-16-2017-00009, NKFI-FK 132080, the János Bolyai Research Scholarship of the Hungarian Academy of Sciences BO/27/20, UNKP-20-5-SZTE-265, EMBO short-term fellowship 8513 and the Tempus Foundation. This work was supported by the Medical Research Council (grant number: MC_UU_12016/1; TK, IM, JR) and the pharmaceutical companies supporting the Division of Signal Transduction Therapy Unit (Boehringer Ingelheim, GlaxoSmithKline and Merck KGaA). 311 PARP

PY - 2021/10/4

Y1 - 2021/10/4

N2 - Mutations in the gene encoding the CDKL5 kinase are among the most common genetic causes of childhood epilepsy and can also give rise to the severe neurodevelopmental condition CDD (CDKL5 deficiency disorder). Despite its importance for human health, the phosphorylation targets and cellular roles of CDKL5 are poorly understood, especially in the cell nucleus. Here, we report that CDKL5 is recruited to sites of DNA damage in actively transcribed regions of the nucleus. A quantitative phosphoproteomic screen for nuclear CDKL5 substrates reveals a network of transcriptional regulators including Elongin A (ELOA), phosphorylated on a specific CDKL5 consensus motif. Recruitment of CDKL5 and ELOA to damaged DNA, and subsequent phosphorylation of ELOA, requires both active transcription and the synthesis of poly(ADP-ribose) (PAR), to which CDKL5 can bind. Critically, CDKL5 kinase activity is essential for the transcriptional silencing of genes induced by DNA double-strand breaks. Thus, CDKL5 is a DNA damage-sensing, PAR-controlled transcriptional modulator, a finding with implications for understanding the molecular basis of CDKL5-related diseases.

AB - Mutations in the gene encoding the CDKL5 kinase are among the most common genetic causes of childhood epilepsy and can also give rise to the severe neurodevelopmental condition CDD (CDKL5 deficiency disorder). Despite its importance for human health, the phosphorylation targets and cellular roles of CDKL5 are poorly understood, especially in the cell nucleus. Here, we report that CDKL5 is recruited to sites of DNA damage in actively transcribed regions of the nucleus. A quantitative phosphoproteomic screen for nuclear CDKL5 substrates reveals a network of transcriptional regulators including Elongin A (ELOA), phosphorylated on a specific CDKL5 consensus motif. Recruitment of CDKL5 and ELOA to damaged DNA, and subsequent phosphorylation of ELOA, requires both active transcription and the synthesis of poly(ADP-ribose) (PAR), to which CDKL5 can bind. Critically, CDKL5 kinase activity is essential for the transcriptional silencing of genes induced by DNA double-strand breaks. Thus, CDKL5 is a DNA damage-sensing, PAR-controlled transcriptional modulator, a finding with implications for understanding the molecular basis of CDKL5-related diseases.

UR - http://hdl.handle.net/10754/672464

UR - https://onlinelibrary.wiley.com/doi/10.15252/embj.2021108271

UR - http://www.scopus.com/inward/record.url?scp=85116117426&partnerID=8YFLogxK

U2 - 10.15252/embj.2021108271

DO - 10.15252/embj.2021108271

M3 - Article

C2 - 34605059

SN - 1460-2075

JO - EMBO JOURNAL

JF - EMBO JOURNAL

ER -

CDKL5 kinase controls transcription-coupled responses to DNA damage

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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