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Feng F, Gao Y, Zhao Q, Luo T, Yang Q, Zhao N, Xiao Y, Han Y, Pan J, Feng S, Zhang L, Wu M. Single-electron transfer between sulfonium and tryptophan enables site-selective photo crosslinking of methyllysine reader proteins. Nat Chem 2024; 16:1267-1277. [PMID: 39079947 DOI: 10.1038/s41557-024-01577-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 06/12/2024] [Indexed: 08/15/2024]
Abstract
The identification of readers, an important class of proteins that recognize modified residues at specific sites, is essential to uncover the biological roles of post-translational modifications. Photoreactive crosslinkers are powerful tools for investigating readers. However, existing methods usually employ synthetically challenging photoreactive warheads, and their high-energy intermediates generated upon irradiation, such as nitrene and carbene, may cause substantial non-specific crosslinking. Here we report dimethylsulfonium as a methyllysine mimic that binds to specific readers and subsequently crosslinks to a conserved tryptophan inside the binding pocket through single-electron transfer under ultraviolet irradiation. The crosslinking relies on a protein-templated σ-π electron donor-acceptor interaction between sulfonium and indole, ensuring excellent site selectivity for tryptophan in the active site and orthogonality to other methyllysine readers. This method could escalate the discovery of methyllysine readers from complex cell samples. Furthermore, this photo crosslinking strategy could be extended to develop other types of microenvironment-dependent conjugations to site-specific tryptophan.
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Affiliation(s)
- Feng Feng
- Department of Chemistry, Zhejiang University, Hangzhou, China
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Yingxiao Gao
- Department of Chemistry, Fudan University, Shanghai, China
| | - Qun Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ting Luo
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Qingyun Yang
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Nan Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yihang Xiao
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yusong Han
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Jinheng Pan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, China
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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2
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Gold S, Shilatifard A. Therapeutic targeting of BET bromodomain and other epigenetic acetylrecognition domain-containing factors. Curr Opin Genet Dev 2024; 86:102181. [PMID: 38564841 DOI: 10.1016/j.gde.2024.102181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
Development of cancer therapies targeting chromatin modifiers and transcriptional regulatory factors is rapidly expanding to include new targets and novel targeting strategies. At the same time, basic molecular research continues to refine our understanding of the epigenetic mechanisms regulating transcription, gene expression, and oncogenesis. This mini-review focuses on cancer therapies targeting the chromatin-associated factors that recognize histone lysine acetylation. Recently reported safety and efficacy are discussed for inhibitors targeting the bromodomains of bromodomain and extraterminal domain (BET) family proteins. In light of recent results indicating that the transcriptional regulator BRD4-PTEFb can function independently of BRD4's bromodomains, the clinical trial performance of these BET inhibitors is placed in a broader context of existing and potential strategies for targeting BRD4-PTEFb. Recently developed therapies targeting bromodomain-containing factors within the SWI/SNF (BAF) family of chromatin remodeling complexes are discussed, as is the potential for targeting the bromodomain-containing transcription factor TAF1 and the YEATS acetylrecognition domain-containing factor GAS41. Recent findings regarding the selectivity and combinatorial specificity of acetylrecognition are highlighted. In conclusion, the potential for further development is discussed with a focus on proximity-based therapies targeting this class of epigenetic factors.
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Affiliation(s)
- Sarah Gold
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. https://twitter.com/@rwx_life
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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3
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Gendosz de Carrillo D, Kocikowska O, Rak M, Krzan A, Student S, Jędrzejowska-Szypułka H, Pawletko K, Lasek-Bal A. The Relevance of Reperfusion Stroke Therapy for miR-9-3p and miR-9-5p Expression in Acute Stroke-A Preliminary Study. Int J Mol Sci 2024; 25:2766. [PMID: 38474013 DOI: 10.3390/ijms25052766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Reperfusion stroke therapy is a modern treatment that involves thrombolysis and the mechanical removal of thrombus from the extracranial and/or cerebral arteries, thereby increasing penumbra reperfusion. After reperfusion therapy, 46% of patients are able to live independently 3 months after stroke onset. MicroRNAs (miRNAs) are essential regulators in the development of cerebral ischemia/reperfusion injury and the efficacy of the applied treatment. The first aim of this study was to examine the change in serum miRNA levels via next-generation sequencing (NGS) 10 days after the onset of acute stroke and reperfusion treatment. Next, the predictive values of the bioinformatics analysis of miRNA gene targets for the assessment of brain ischemic response to reperfusion treatment were explored. Human serum samples were collected from patients on days 1 and 10 after stroke onset and reperfusion treatment. The samples were subjected to NGS and then validated using qRT-PCR. Differentially expressed miRNAs (DEmiRNAs) were used for enrichment analysis. Hsa-miR-9-3p and hsa-miR-9-5p expression were downregulated on day 10 compared to reperfusion treatment on day 1 after stroke. The functional analysis of miRNA target genes revealed a strong association between the identified miRNA and stroke-related biological processes related to neuroregeneration signaling pathways. Hsa-miR-9-3p and hsa-miR-9-5p are potential candidates for the further exploration of reperfusion treatment efficacy in stroke patients.
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Affiliation(s)
- Daria Gendosz de Carrillo
- Department of Physiology, Faculty of Medicine, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
| | - Olga Kocikowska
- Department of Physiology, Faculty of Medicine, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
- Department of Engineering and Systems Biology, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Małgorzata Rak
- Department of Physiology, Faculty of Medicine, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
| | - Aleksandra Krzan
- Department of Neurology, School of Health Sciences, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
- Department of Neurology, Upper-Silesian Medical Center of the Silesian Medical University, 40-752 Katowice, Poland
| | - Sebastian Student
- Department of Engineering and Systems Biology, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, 44-100 Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Halina Jędrzejowska-Szypułka
- Department of Physiology, Faculty of Medicine, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
| | - Katarzyna Pawletko
- Department of Physiology, Faculty of Medicine, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
- Department for Experimental Medicine, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
| | - Anetta Lasek-Bal
- Department of Neurology, School of Health Sciences, Medical University of Silesia in Katowice, 40-752 Katowice, Poland
- Department of Neurology, Upper-Silesian Medical Center of the Silesian Medical University, 40-752 Katowice, Poland
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4
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Marunde MR, Fuchs HA, Burg JM, Popova IK, Vaidya A, Hall NW, Weinzapfel EN, Meiners MJ, Watson R, Gillespie ZB, Taylor HF, Mukhsinova L, Onuoha UC, Howard SA, Novitzky K, McAnarney ET, Krajewski K, Cowles MW, Cheek MA, Sun ZW, Venters BJ, Keogh MC, Musselman CA. Nucleosome conformation dictates the histone code. eLife 2024; 13:e78866. [PMID: 38319148 PMCID: PMC10876215 DOI: 10.7554/elife.78866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized 'codes' that are read by specialized regions (reader domains) in chromatin-associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP: histone PTM] specificities, and thus decipher the histone code and guide epigenetic therapies. However, this has largely been done using the reductive approach of isolated reader domains and histone peptides, which cannot account for any higher-order factors. Here, we show that the [BPTF PHD finger and bromodomain: histone PTM] interaction is dependent on nucleosome context. The tandem reader selectively associates with nucleosomal H3K4me3 and H3K14ac or H3K18ac, a combinatorial engagement that despite being in cis is not predicted by peptides. This in vitro specificity of the BPTF tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. We propose that regulatable histone tail accessibility and its impact on the binding potential of reader domains necessitates we refine the 'histone code' concept and interrogate it at the nucleosome level.
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Affiliation(s)
| | - Harrison A Fuchs
- Department of Biochemistry, University of Iowa Carver College of MedicineAuroraUnited States
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel HillChapel HillUnited States
| | | | | | | | | | | | - Catherine A Musselman
- Department of Biochemistry, University of Iowa Carver College of MedicineAuroraUnited States
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical CampusAuroraUnited States
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5
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Han D, Schaffner SH, Davies JP, Benton ML, Plate L, Nordman JT. BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels. Proc Natl Acad Sci U S A 2023; 120:e2305092120. [PMID: 37722046 PMCID: PMC10523488 DOI: 10.1073/pnas.2305092120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/11/2023] [Indexed: 09/20/2023] Open
Abstract
Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3 (Bromodomain and WD repeat-containing protein 3), a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased H3K4me1 (H3 lysine 4 monomethylation) levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. Here, we show that depleting BRWD3 not only causes an increase in H3K4me1 levels but also causes a decrease in H3K4me3 (H3 lysine 4 trimethylation) levels, indicating that BRWD3 influences H3K4 methylation more broadly. Using immunoprecipitation coupled to quantitative mass spectrometry, we identified an interaction between BRWD3 and the H3K4-specific lysine demethylase 5 (KDM5/Lid), an enzyme that removes tri- and dimethyl marks from H3K4. Moreover, analysis of ChIP-seq (chromatin immunoprecipitation sequencing) data revealed that BRWD3 and KDM5 are significantly colocalized throughout the genome and H3K4me3 are highly enriched at BRWD3 binding sites. We show that BRWD3 promotes K48-linked polyubiquitination and degradation of KDM5 and that KDM5 degradation is dependent on both BRWD3 and Cul4. Critically, depleting KDM5 fully restores altered H3K4me3 levels and partially restores H3K4me1 levels upon BRWD3 depletion. Together, our results demonstrate that BRWD3 regulates KDM5 activity to balance H3K4 methylation levels.
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Affiliation(s)
- Dongsheng Han
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37212
| | | | - Jonathan P. Davies
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37212
| | | | - Lars Plate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37212
- Department of Chemistry, Vanderbilt University, Nashville, TN37212
| | - Jared T. Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37212
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6
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Jo JH, Park JU, Kim YM, Ok SM, Kim DK, Jung DH, Kim HJ, Seong HA, Cho HJ, Nah J, Kim S, Fu H, Redon CE, Aladjem MI, Jang SM. RepID represses megakaryocytic differentiation by recruiting CRL4A-JARID1A at DAB2 promoter. Cell Commun Signal 2023; 21:219. [PMID: 37612584 PMCID: PMC10463337 DOI: 10.1186/s12964-023-01246-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/23/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Megakaryocytes (MKs) are platelet precursors, which arise from hematopoietic stem cells (HSCs). While MK lineage commitment and differentiation are accompanied by changes in gene expression, many factors that modulate megakaryopoiesis remain to be uncovered. Replication initiation determinant protein (RepID) which has multiple histone-code reader including bromodomain, cryptic Tudor domain and WD40 domains and Cullin 4-RING E3 ubiquitin ligase complex (CRL4) recruited to chromatin mediated by RepID have potential roles in gene expression changes via epigenetic regulations. We aimed to investigate whether RepID-CRL4 participates in transcriptional changes required for MK differentiation. METHODS The PCR array was performed using cDNAs derived from RepID-proficient or RepID-deficient K562 erythroleukemia cell lines. Correlation between RepID and DAB2 expression was examined in the Cancer Cell Line Encyclopedia (CCLE) through the CellMinerCDB portal. The acceleration of MK differentiation in RepID-deficient K562 cells was determined by estimating cell sizes as well as counting multinucleated cells known as MK phenotypes, and by qRT-PCR analysis to validate transcripts of MK markers using phorbol 12-myristate 13-acetate (PMA)-mediated MK differentiation condition. Interaction between CRL4 and histone methylation modifying enzymes were investigated using BioGRID database, immunoprecipitation and proximity ligation assay. Alterations of expression and chromatin binding affinities of RepID, CRL4 and histone methylation modifying enzymes were investigated using subcellular fractionation followed by immunoblotting. RepID-CRL4-JARID1A-based epigenetic changes on DAB2 promoter were analyzed by chromatin-immunoprecipitation and qPCR analysis. RESULTS RepID-deficient K562 cells highly expressing MK markers showed accelerated MKs differentiation exhibiting increases in cell size, lobulated nuclei together with reaching maximum levels of MK marker expression earlier than RepID-proficient K562 cells. Recovery of WD40 domain-containing RepID constructs in RepID-deficient background repressed DAB2 expression. CRL4A formed complex with histone H3K4 demethylase JARID1A in soluble nucleus and loaded to the DAB2 promoter in a RepID-dependent manner during proliferation condition. RepID, CRL4A, and JARID1A were dissociated from the chromatin during MK differentiation, leading to euchromatinization of the DAB2 promoter. CONCLUSION This study uncovered a role for the RepID-CRL4A-JARID1A pathway in the regulation of gene expression for MK differentiation, which can form the basis for the new therapeutic approaches to induce platelet production. Video Abstract.
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Affiliation(s)
- Jae-Hyun Jo
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jong-Uk Park
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Yeong-Mu Kim
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Seon-Mi Ok
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Dong-Kyu Kim
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Dong-Hyun Jung
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hye-Ji Kim
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hyun-A Seong
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Hyo Je Cho
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Jihoon Nah
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Sangjune Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892-4255, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892-4255, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892-4255, USA
| | - Sang-Min Jang
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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7
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Aguilar R, Khan L, Arslanovic N, Birmingham K, Kasliwal K, Posnikoff S, Chakraborty U, Hickman AR, Watson R, Ezell RJ, Willis HE, Cowles MW, Garner R, Shim A, Gutierrez I, Marunde MR, Keogh MC, Tyler JK. Multivalent binding of the tardigrade Dsup protein to chromatin promotes yeast survival and longevity upon exposure to oxidative damage. RESEARCH SQUARE 2023:rs.3.rs-3182883. [PMID: 37546815 PMCID: PMC10402244 DOI: 10.21203/rs.3.rs-3182883/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Tardigrades are remarkable in their ability to survive extreme environments. The damage suppressor (Dsup) protein is thought responsible for their extreme resistance to reactive oxygen species (ROS) generated by irradiation. Here we show that expression of Ramazzottius varieornatus Dsup in Saccharomyces cerevisiae reduces oxidative DNA damage and extends the lifespan of budding yeast exposed to chronic oxidative genotoxicity. This protection from ROS requires either the Dsup HMGN-like domain or sequences C-terminal to same. Dsup associates with no apparent bias across the yeast genome, using multiple modes of nucleosome binding; the HMGN-like region interacts with both the H2A/H2B acidic patch and H3/H4 histone tails, while the C-terminal region binds DNA. These findings give precedent for engineering an organism by physically shielding its genome to promote survival and longevity in the face of oxidative damage.
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Affiliation(s)
- Rhiannon Aguilar
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | | | - Nina Arslanovic
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Kaylah Birmingham
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Pharmacology Graduate Program, New York, NY 10065 United States
| | - Kritika Kasliwal
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Spike Posnikoff
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | - Ujani Chakraborty
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | | | | | | | | | | | - Richard Garner
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Abraham Shim
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
- Weill Cornell Medicine, Biochemistry, Cellular, and Molecular Biology Graduate Program, New York, NY 10065, USA
| | - Ignacio Gutierrez
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
| | | | | | - Jessica K. Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY 10065, USA
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8
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Isbel L, Iskar M, Durdu S, Weiss J, Grand RS, Hietter-Pfeiffer E, Kozicka Z, Michael AK, Burger L, Thomä NH, Schübeler D. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. Nat Struct Mol Biol 2023:10.1038/s41594-023-01021-8. [PMID: 37386214 DOI: 10.1038/s41594-023-01021-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 05/15/2023] [Indexed: 07/01/2023]
Abstract
The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are unusually diverse with regard to their chromatin features, including histone modifications, raising the possibility that the local chromatin environment can contextualize p53 regulation. Here, we show that epigenetic characteristics of closed chromatin, such as DNA methylation, do not influence the binding of p53 across the genome. Instead, the ability of p53 to open chromatin and activate its target genes is locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated histone 3 lysine 4 (H3K4), thereby preferentially localizing to those p53 sites that reside in closed chromatin, whereas it is deterred from accessible chromatin by H3K4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to affect gene expression as a function of the local chromatin state. These findings link H3K4 methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors that locally modulate TF function.
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Affiliation(s)
- Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Murat Iskar
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sevi Durdu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Joscha Weiss
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Eric Hietter-Pfeiffer
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Zuzanna Kozicka
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Alicia K Michael
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Faculty of Sciences, University of Basel, Basel, Switzerland.
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9
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Jo JH, Ok SM, Kim DK, Kim YM, Park JU, Jung DH, Kim HJ, Seong HA, Cho HJ, Nah J, Kim S, Fu H, Redon CE, Aladjem MI, Jang SM. RepID represses megakaryocytic differentiation by recruiting CRL4A-JARID1A at DAB2 promoter. RESEARCH SQUARE 2023:rs.3.rs-3045396. [PMID: 37461562 PMCID: PMC10350187 DOI: 10.21203/rs.3.rs-3045396/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Background Megakaryocytes (MKs) are platelet precursors, which arise from hematopoietic stem cells (HSCs). While MK lineage commitment and differentiation are accompanied by changes in gene expression, many factors that modulate megakaryopoiesis remain to be uncovered. Replication origin binding protein (RepID) which has multiple histone-code reader including bromodomain, cryptic Tudor domain and WD40 domains and Cullin 4-RING ubiquitin ligase complex (CRL4) recruited to chromatin mediated by RepID have potential roles in gene expression changes via epigenetic regulations. We aimed to investigate whether RepID-CRL4 participates in transcriptional changes required for MK differentiation. Methods The PCR array was performed using cDNAs derived from RepID-proficient or RepID-deficient K562 erythroleukemia cell lines. Correlation between RepID and DAB2 expression was examined in the Cancer Cell Line Encyclopedia (CCLE) through the CellMinerCDB portal. The acceleration of MK differentiation in RepID-deficient K562 cells was determined by estimating cell sizes as well as counting multinucleated cells known as MK phenotypes, and by qRT-PCR analysis to validate transcripts of MK markers using phorbol 12-myristate 13-acetate (PMA)-mediated MK differentiation condition. Interaction between CRL4 and histone methylation modifying enzymes were investigated using BioGRID database, immunoprecipitation and proximity ligation assay. Alterations of expression and chromatin binding affinities of RepID, CRL4 and histone methylation modifying enzymes were investigated using subcellular fractionation followed by immunoblotting. RepID-CRL4-JARID1A-based epigenetic changes on DAB2 promoter were analyzed by chromatin-immunoprecipitation and qPCR analysis. Results RepID-deficient K562 cells highly expressing MK markers showed accelerated MKs differentiation exhibiting increases in cell size, lobulated nuclei together with reaching maximum levels of MK marker expression earlier than RepID-proficient K562 cells. Recovery of WD40 domain-containing RepID constructs in RepID-deficient background repressed DAB2 expression. CRL4A formed complex with histone H3K4 demethylase JARID1A in soluble nucleus and loaded to the DAB2 promoter in a RepID-dependent manner during proliferation condition. RepID, CRL4A, and JARID1A were dissociated from the chromatin during MK differentiation, leading to euchromatinization of the DAB2 promoter. Conclusion This study uncovered a role for the RepID-CRL4A-JARID1A pathway in the regulation of gene expression for MK differentiation, which can form the basis for the new therapeutic approaches to induce platelet production.
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10
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Jain K, Marunde MR, Burg JM, Gloor SL, Joseph FM, Poncha KF, Gillespie ZB, Rodriguez KL, Popova IK, Hall NW, Vaidya A, Howard SA, Taylor HF, Mukhsinova L, Onuoha UC, Patteson EF, Cooke SW, Taylor BC, Weinzapfel EN, Cheek MA, Meiners MJ, Fox GC, Namitz KEW, Cowles MW, Krajewski K, Sun ZW, Cosgrove MS, Young NL, Keogh MC, Strahl BD. An acetylation-mediated chromatin switch governs H3K4 methylation read-write capability. eLife 2023; 12:e82596. [PMID: 37204295 PMCID: PMC10229121 DOI: 10.7554/elife.82596] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/18/2023] [Indexed: 05/20/2023] Open
Abstract
In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g. K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has a broader extension. Here, we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on the cis H3 tail, as determined with fully-defined heterotypic nucleosomes. In vivo, H3 tail acetylation is directly and dynamically coupled with cis H3K4 methylation levels. Together, these observations reveal an acetylation 'chromatin switch' on the H3 tail that modulates read-write accessibility in nucleosomes and resolves the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.
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Affiliation(s)
- Kanishk Jain
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| | | | | | | | - Faith M Joseph
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Karl F Poncha
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | | | | | | | | | | | | | | | | | | | - Spencer W Cooke
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
| | - Bethany C Taylor
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | | | | | - Geoffrey C Fox
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
| | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
| | | | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology, Upstate Medical UniversitySyracuseUnited States
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | | | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill of MedicineChapel HillUnited States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, School of MedicineChapel HillUnited States
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11
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Nussinov R, Yavuz BR, Arici MK, Demirel HC, Zhang M, Liu Y, Tsai CJ, Jang H, Tuncbag N. Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK. Biophys Rev 2023; 15:163-181. [PMID: 37124926 PMCID: PMC10133437 DOI: 10.1007/s12551-023-01054-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) and cancer share proteins, pathways, and mutations. Their clinical symptoms are different. However, individuals with NDDs have higher probabilities of eventually developing cancer. Here, we review the literature and ask how the shared features can lead to different medical conditions and why having an NDD first can increase the chances of malignancy. To explore these vital questions, we focus on dysregulated PI3K/mTOR, a major brain cell growth pathway in differentiation, and MAPK, a critical pathway in proliferation, a hallmark of cancer. Differentiation is governed by chromatin organization, making aberrant chromatin remodelers highly likely agents in NDDs. Dysregulated chromatin organization and accessibility influence the lineage of specific cell brain types at specific embryonic development stages. PAK1, with pivotal roles in brain development and in cancer, also regulates MAPK. We review, clarify, and connect dysregulated pathways with dysregulated proliferation and differentiation in cancer and NDDs and highlight PAK1 role in brain development and MAPK regulation. Exactly how PAK1 activation controls brain development, and why specific chromatin remodeler components, e.g., BAF170 encoded by SMARCC2 in autism, await clarification.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Bengi Ruken Yavuz
- Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - M Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Habibe Cansu Demirel
- Department of Chemical and Biological Engineering, College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702 USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Nurcan Tuncbag
- Department of Chemical and Biological Engineering, College of Engineering, Koc University, 34450 Istanbul, Turkey
- School of Medicine, Koc University, 34450 Istanbul, Turkey
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12
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Han D, Schaffner SH, Davies JP, Lauren Benton M, Plate L, Nordman JT. BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534572. [PMID: 37034668 PMCID: PMC10081218 DOI: 10.1101/2023.03.28.534572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3, a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased in H3K4me1 levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. Here, we show that depleting BRWD3 not only causes an increase in H3K4me1 levels, but also causes a decrease in H3K4me3 levels, indicating that BRWD3 influences H3K4 methylation more broadly. Using immunoprecipitation coupled to quantitative mass spectrometry, we identified an interaction between BRWD3 and the H3K4-specific demethylase 5 (KDM5/Lid), an enzyme that removes tri- and di- methyl marks from H3K4. Moreover, analysis of ChIP-seq data revealed that BRWD3 and KDM5 are significantly co- localized throughout the genome and that sites of H3K4me3 are highly enriched at BRWD3 binding sites. We show that BRWD3 promotes K48-linked polyubiquitination and degradation of KDM5 and that KDM5 degradation is dependent on both BRWD3 and Cul4. Critically, depleting KDM5 fully restores altered H3K4me3 levels and partially restores H3K4me1 levels upon BRWD3 depletion. Together, our results demonstrate that BRWD3 regulates KDM5 activity to balance H3K4 methylation levels.
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Affiliation(s)
- Dongsheng Han
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37212, USA
| | | | - Jonathan P. Davies
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37212, USA
| | | | - Lars Plate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37212, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37212, USA
| | - Jared T. Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37212, USA
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13
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Barchi M, Guida E, Dolci S, Rossi P, Grimaldi P. Endocannabinoid system and epigenetics in spermatogenesis and testicular cancer. VITAMINS AND HORMONES 2023; 122:75-106. [PMID: 36863802 DOI: 10.1016/bs.vh.2023.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
In mammals, male germ cell development starts during fetal life and is carried out in postnatal life with the formation of sperms. Spermatogenesis is the complex and highly orderly process during which a group of germ stem cells is set at birth, starts to differentiate at puberty. It proceeds through several stages: proliferation, differentiation, and morphogenesis and it is strictly regulated by a complex network of hormonal, autocrine and paracrine factors and it is associated with a unique epigenetic program. Altered epigenetic mechanisms or inability to respond to these factors can impair the correct process of germ development leading to reproductive disorders and/or testicular germ cell cancer. Among factors regulating spermatogenesis an emerging role is played by the endocannabinoid system (ECS). ECS is a complex system comprising endogenous cannabinoids (eCBs), their synthetic and degrading enzymes, and cannabinoid receptors. Mammalian male germ cells have a complete and active ECS which is modulated during spermatogenesis and that crucially regulates processes such as germ cell differentiation and sperm functions. Recently, cannabinoid receptor signaling has been reported to induce epigenetic modifications such as DNA methylation, histone modifications and miRNA expression. Epigenetic modifications may also affect the expression and function of ECS elements, highlighting the establishment of a complex mutual interaction. Here, we describe the developmental origin and differentiation of male germ cells and testicular germ cell tumors (TGCTs) focusing on the interplay between ECS and epigenetic mechanisms involved in these processes.
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Affiliation(s)
- Marco Barchi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Eugenia Guida
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Susanna Dolci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Pellegrino Rossi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Paola Grimaldi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
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14
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Joseph FM, Young NL. Histone variant-specific post-translational modifications. Semin Cell Dev Biol 2023; 135:73-84. [PMID: 35277331 PMCID: PMC9458767 DOI: 10.1016/j.semcdb.2022.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 01/12/2023]
Abstract
Post-translational modifications (PTMs) of histones play a key role in DNA-based processes and contribute to cell differentiation and gene function by adding an extra layer of regulation. Variations in histone sequences within each family of histones expands the chromatin repertoire and provide further mechanisms for regulation and signaling. While variants are known to be present in certain genomic loci and carry out important functions, much remains unknown about variant-specific PTMs and their role in regulating chromatin. This ambiguity is in part due to the limited technologies and appropriate reagents to identify and quantitate variant-specific PTMs. Nonetheless, histone variants are an integral portion of the chromatin system and the understanding of their modifications and resolving how PTMs function differently on specific variants is paramount to the advancement of the field. Here we review the current knowledge on post-translational modifications specific to histone variants, with an emphasis on well-characterized PTMs of known function. While not every possible PTM is addressed, we present key variant-specific PTMs and what is known about their function and mechanisms in convenient reference tables.
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Affiliation(s)
- Faith M Joseph
- Translational Biology and Molecular Medicine Graduate Program, USA
| | - Nicolas L Young
- Translational Biology and Molecular Medicine Graduate Program, USA; Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
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15
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Zukin SA, Marunde MR, Popova IK, Soczek KM, Nogales E, Patel AB. Structure and flexibility of the yeast NuA4 histone acetyltransferase complex. eLife 2022; 11:e81400. [PMID: 36263929 PMCID: PMC9643008 DOI: 10.7554/elife.81400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 protein complex acetylates histones H4 and H2A to activate both transcription and DNA repair. We report the 3.1-Å resolution cryo-electron microscopy structure of the central hub of NuA4, which flexibly tethers the histone acetyltransferase (HAT) and Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) modules. The hub contains the large Tra1 subunit and a core that includes Swc4, Arp4, Act1, Eaf1, and the C-terminal region of Epl1. Eaf1 stands out as the primary scaffolding factor that interacts with the Tra1, Swc4, and Epl1 subunits and contributes the conserved HSA helix to the Arp module. Using nucleosome-binding assays, we find that the HAT module, which is anchored to the core through Epl1, recognizes H3K4me3 nucleosomes with hyperacetylated H3 tails, while the TINTIN module, anchored to the core via Eaf1, recognizes nucleosomes that have hyperacetylated H2A and H4 tails. Together with the known interaction of Tra1 with site-specific transcription factors, our data suggest a model in which Tra1 recruits NuA4 to specific genomic sites then allowing the flexible HAT and TINTIN modules to select nearby nucleosomes for acetylation.
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Affiliation(s)
- Stefan A Zukin
- College of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Irina K Popova
- EpiCypher, Inc, Research Triangle ParkDurhamUnited States
| | - Katarzyna M Soczek
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Avinash B Patel
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
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16
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Tirado-Class N, Hathaway C, Chung WK, Dungrawala H. PHIP variants associated with Chung-Jansen syndrome disrupt replication fork stability and genome integrity. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006212. [PMID: 35863899 PMCID: PMC9528965 DOI: 10.1101/mcs.a006212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022] Open
Abstract
Chung-Jansen syndrome (CJS) is a rare, autosomal dominant disorder characterized by developmental delay, intellectual disability/cognitive impairment, behavioral challenges, obesity, and dysmorphic features. CJS is associated with heterozygous variants in PHIP (Pleckstrin-Homology Interacting Protein), a gene that encodes one of several substrate receptors for Cullin4-RING (CRL4) E3 ubiquitin ligase complex. Full length PHIP, also called DCAF14, was recently identified to function as a replication stress response protein. Herein, we report the identification of two PHIP missense variants identified by exome sequencing in unrelated individuals with CJS. The variants p.D488V and p.E963G occur in different functional elements of DCAF14- WD40 repeat domain and pleckstrin homology-binding region (PBR), respectively. Using DNA fiber assays, we reveal that cells expressing either variant exhibit defective replication fork progression in conditions of replication stress. Furthermore, unlike wild type DCAF14, both variants fail to accomplish DNA replication after exposure to genotoxic stress indicating a critical role of DCAF14 in protecting stalled replication forks. Thus, we have identified replication defects associated with CJS variants and predict replication-associated genome instability with CJS syndrome.
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