1
|
Gordon JM, Phizicky DV, Schärfen L, Brown CL, Arias Escayola D, Kanyo J, Lam TT, Simon MD, Neugebauer KM. Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics. Nucleic Acids Res 2024; 52:9886-9903. [PMID: 38943343 PMCID: PMC11381358 DOI: 10.1093/nar/gkae562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/23/2024] [Accepted: 06/28/2024] [Indexed: 07/01/2024] Open
Abstract
Polyadenylation controls mRNA biogenesis, nucleo-cytoplasmic export, translation and decay. These processes are interdependent and coordinately regulated by poly(A)-binding proteins (PABPs), yet how PABPs are themselves regulated is not fully understood. Here, we report the discovery that human nuclear PABPN1 is phosphorylated by mitotic kinases at four specific sites during mitosis, a time when nucleoplasm and cytoplasm mix. To understand the functional consequences of phosphorylation, we generated a panel of stable cell lines inducibly over-expressing PABPN1 with point mutations at these sites. Phospho-inhibitory mutations decreased cell proliferation, highlighting the importance of PABPN1 phosphorylation in cycling cells. Dynamic regulation of poly(A) tail length and RNA stability have emerged as important modes of gene regulation. We therefore employed long-read sequencing to determine how PABPN1 phospho-site mutants affected poly(A) tails lengths and TimeLapse-seq to monitor mRNA synthesis and decay. Widespread poly(A) tail lengthening was observed for phospho-inhibitory PABPN1 mutants. In contrast, expression of phospho-mimetic PABPN1 resulted in shorter poly(A) tails with increased non-A nucleotides, in addition to increased transcription and reduced stability of a distinct cohort of mRNAs. Taken together, PABPN1 phosphorylation remodels poly(A) tails and increases mRNA turnover, supporting the model that enhanced transcriptome dynamics reset gene expression programs across the cell cycle.
Collapse
Affiliation(s)
- Jackson M Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - David V Phizicky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Courtney L Brown
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dahyana Arias Escayola
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06520, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
2
|
Ishtayeh H, Galves M, Barnatan TT, Berdichevsky Y, Amer‐Sarsour F, Pasmanik‐Chor M, Braverman I, Blumen SC, Ashkenazi A. Oculopharyngeal muscular dystrophy mutations link the RNA-binding protein HNRNPQ to autophagosome biogenesis. Aging Cell 2023; 22:e13949. [PMID: 37559347 PMCID: PMC10577562 DOI: 10.1111/acel.13949] [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: 02/25/2023] [Revised: 06/22/2023] [Accepted: 07/15/2023] [Indexed: 08/11/2023] Open
Abstract
Autophagy is an intracellular degradative process with an important role in cellular homeostasis. Here, we show that the RNA binding protein (RBP), heterogeneous nuclear ribonucleoprotein Q (HNRNPQ)/SYNCRIP is required to stimulate early events in autophagosome biogenesis, in particular the induction of VPS34 kinase by ULK1-mediated beclin 1 phosphorylation. The RBPs HNRNPQ and poly(A) binding protein nuclear 1 (PABPN1) form a regulatory network that controls the turnover of distinct autophagy-related (ATG) proteins. We also show that oculopharyngeal muscular dystrophy (OPMD) mutations engender a switch from autophagosome stimulation to autophagosome inhibition by impairing PABPN1 and HNRNPQ control of the level of ULK1. The overexpression of HNRNPQ in OPMD patient-derived cells rescues the defective autophagy in these cells. Our data reveal a regulatory mechanism of autophagy induction that is compromised by PABPN1 disease mutations, and may thus further contribute to their deleterious effects.
Collapse
Affiliation(s)
- Hasan Ishtayeh
- The Department of Cell and Developmental Biology, Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Margarita Galves
- The Department of Cell and Developmental Biology, Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Tania T. Barnatan
- The Department of Cell and Developmental Biology, Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Yevgeny Berdichevsky
- The Department of Cell and Developmental Biology, Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Fatima Amer‐Sarsour
- The Department of Cell and Developmental Biology, Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Metsada Pasmanik‐Chor
- Bioinformatics Unit, G.S. Wise Faculty of Life ScienceTel Aviv UniversityTel AvivIsrael
| | - Itzhak Braverman
- Department of Otolaryngology, Head and Neck SurgeryHillel Yaffe Medical CenterHaderaIsrael
- Rappaport Faculty of Medicine, TechnionHaifaIsrael
| | - Sergiu C. Blumen
- Rappaport Faculty of Medicine, TechnionHaifaIsrael
- Department of NeurologyHillel Yaffe Medical CenterHaderaIsrael
| | - Avraham Ashkenazi
- The Department of Cell and Developmental Biology, Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Sagol School of NeuroscienceTel Aviv UniversityTel AvivIsrael
| |
Collapse
|
3
|
Kases K, Schubert E, Hajikhezri Z, Larsson M, Devi P, Darweesh M, Andersson L, Akusjärvi G, Punga T, Younis S. The RNA-binding protein ZC3H11A interacts with the nuclear poly(A)-binding protein PABPN1 and alters polyadenylation of viral transcripts. J Biol Chem 2023; 299:104959. [PMID: 37356722 PMCID: PMC10371797 DOI: 10.1016/j.jbc.2023.104959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023] Open
Abstract
Nuclear mRNA metabolism is regulated by multiple proteins, which either directly bind to RNA or form multiprotein complexes. The RNA-binding protein ZC3H11A is involved in nuclear mRNA export, NF-κB signaling, and is essential during mouse embryo development. Furthermore, previous studies have shown that ZC3H11A is important for nuclear-replicating viruses. However, detailed biochemical characterization of the ZC3H11A protein has been lacking. In this study, we established the ZC3H11A protein interactome in human and mouse cells. We demonstrate that the nuclear poly(A)-binding protein PABPN1 interacts specifically with the ZC3H11A protein and controls ZC3H11A localization into nuclear speckles. We report that ZC3H11A specifically interacts with the human adenovirus type 5 (HAdV-5) capsid mRNA in a PABPN1-dependent manner. Notably, ZC3H11A uses the same zinc finger motifs to interact with PABPN1 and viral mRNA. Further, we demonstrate that the lack of ZC3H11A alters the polyadenylation of HAdV-5 capsid mRNA. Taken together, our results suggest that the ZC3H11A protein may act as a novel regulator of polyadenylation of nuclear mRNA.
Collapse
Affiliation(s)
- Katharina Kases
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Schubert
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zamaneh Hajikhezri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Priya Devi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mahmoud Darweesh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Department of Microbiology and Immunology, Al-Azhr University, Assiut, Egypt
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; Division of Immunology and Rheumatology, Stanford University, Stanford, California, USA.
| |
Collapse
|
4
|
Zhen N, Zhu J, Mao S, Zhang Q, Gu S, Ma J, Zhang Y, Yin M, Li H, Huang N, Wu H, Sun F, Ying B, Zhou L, Pan Q. Alternative Splicing of lncRNAs From SNHG Family Alters snoRNA Expression and Induces Chemoresistance in Hepatoblastoma. Cell Mol Gastroenterol Hepatol 2023; 16:735-755. [PMID: 37478905 PMCID: PMC10520360 DOI: 10.1016/j.jcmgh.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND & AIMS Hepatoblastoma (HB) is a common pediatric malignant liver tumor that is characterized by a low level of genetic mutations. Alternative splicing (AS) has been shown to be closely associated with cancer progression, especially in tumors with a low mutational burden. However, the role of AS in HB remains unknown. METHODS Transcriptome sequencing was performed on 5 pairs of HB tissues and matched non-tumor tissues to delineate the AS landscape in HB. AS events were validated in 92 samples from 46 patients. RNA pull-down and RNA immunoprecipitation assays were carried out to identify splicing factors that regulate the AS of small nucleolar RNA host genes (SNHG). Patient-derived organoids (PDOs) were established to investigate the role of the splicing factor polyadenylate-binding nuclear protein 1 (PABPN1). RESULTS This study uncovered aberrant alternative splicing in HB, including lncRNAs from SNHG family that undergo intron retention in HB. Further investigations revealed that PABPN1, a significantly upregulated RNA binding protein, interacts with splicing machinery in HB, inducing the intron retention of these SNHG RNAs and the downregulation of intronic small nucleolar RNAs (snoRNAs). Functionally, PABPN1 acts as an oncofetal splicing regulator in HB by promoting cell proliferation and DNA damage repair via inducing the intron retention of SNHG19. Knock-down of PABPN1 increases the cisplatin sensitivity of HB PDOs. CONCLUSIONS Our findings revealed the role of intron retention in regulating snoRNA expression in hepatoblastoma, explained detailed regulatory mechanism between PABPN1 and the intron retention of SNHG RNAs, and provided insight into the development of new HB treatment options.
Collapse
Affiliation(s)
- Ni Zhen
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiabei Zhu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Siwei Mao
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Song Gu
- Department of Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Ma
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- Department of Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People's Hospital, Shanghai, China
| | - Minzhi Yin
- Department of Pathology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haojie Li
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Nan Huang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Han Wu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fenyong Sun
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Lin Zhou
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China; Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Hainan, China.
| |
Collapse
|
5
|
Chen L, Dong W, Zhou M, Yang C, Xiong M, Kazobinka G, Chen Z, Xing Y, Hou T. PABPN1 regulates mRNA alternative polyadenylation to inhibit bladder cancer progression. Cell Biosci 2023; 13:45. [PMID: 36879298 PMCID: PMC9987104 DOI: 10.1186/s13578-023-00997-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/24/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND About 10-20% of patients with bladder cancer (BC) progress to muscle-invasive diseases, of which the underlying key molecular events have yet to be addressed. RESULTS Here, we identified poly(A) binding protein nuclear 1 (PABPN1), a general factor of alternative polyadenylation (APA), was downregulated in BC. Overexpression and knockdown of PABPN1 significantly decreased and increased BC aggressiveness, respectively. Mechanistically, we provide evidence that the preference of PABPN1-bound polyadenylation signals (PASs) depends on the relative location between canonical and non-canonical PASs. PABPN1 shapes inputs converging on Wnt signaling, cell cycle, and lipid biosynthesis. CONCLUSIONS Together, these findings provide insights into how PABPN1-mediated APA regulation contributes to BC progression, and suggest that pharmacological targeting PABPN1 might have therapeutic potential in patients with BC.
Collapse
Affiliation(s)
- Liang Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wei Dong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Menghao Zhou
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chenlu Yang
- Department of Gynecology and Obstetrics, Women and Children Hospital of Guangdong Province, Guangzhou, 510080, China
| | - Ming Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Gallina Kazobinka
- Urology Unit, La Nouvelle Polyclinique Centrale de Bujumbura, Bujumbura, 378, Burundi
| | - Zhaohui Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yifei Xing
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Teng Hou
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China. .,Department of Urology, South China Hospital, Medical School, Shenzhen University, Shenzhen, 518116, China.
| |
Collapse
|
6
|
Zhao Y, Li L, Wang X, He S, Shi W, Chen S. Temporal Proteomic and Phosphoproteomic Analysis of EV-A71-Infected Human Cells. J Proteome Res 2022; 21:2367-2384. [DOI: 10.1021/acs.jproteome.2c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Zhao
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Xinhui Wang
- CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, Jiangsu, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
| | - Sudan He
- CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, Jiangsu, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
| | - Weifeng Shi
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou 213003, Jiangsu, China
| | - She Chen
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| |
Collapse
|
7
|
Hadar A, Voinsky I, Parkhomenko O, Puzianowska‐Kuźnicka M, Kuźnicki J, Gozes I, Gurwitz D. Higher ATM expression in lymphoblastoid cell lines from centenarian compared with younger women. Drug Dev Res 2022; 83:1419-1424. [PMID: 35774024 PMCID: PMC9545764 DOI: 10.1002/ddr.21972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 11/11/2022]
Abstract
With increased life expectancies in developed countries, cancer rates are becoming more common among the elderly. Cancer is typically driven by a combination of germline and somatic mutations accumulating during an individual's lifetime. Yet, many centenarians reach exceptionally old age without experiencing cancer. It was suggested that centenarians have more robust DNA repair and mitochondrial function, allowing improved maintenance of DNA stability. In this study, we applied real-time quantitative PCR to examine the expression of ATM in lymphoblastoid cell lines (LCLs) from 15 healthy female centenarians and 24 younger female donors aged 21-88 years. We observed higher ATM mRNA expression of in LCLs from female centenarians compared with both women aged 21-48 years (FD = 2.0, p = .0016) and women aged 56-88 years (FD = 1.8, p = .0094. Positive correlation was found between ATM mRNA expression and donors age (p = .0028). Levels of hsa-miR-181a-5p, which targets ATM, were lower in LCLs from centenarians compared with younger women. Our findings suggest a role for ATM in protection from age-related diseases, possibly reflecting more effective DNA repair, thereby reducing somatic mutation accumulation during aging. Further studies are required for analyzing additional DNA repair pathways in biosamples from centenarians and younger age men and women.
Collapse
Affiliation(s)
- Adva Hadar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Irena Voinsky
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Olga Parkhomenko
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Monika Puzianowska‐Kuźnicka
- Department of Human EpigeneticsMossakowski Medical Research InstituteWarsawPoland
- Department of Geriatrics and GerontologyMedical Centre of Postgraduate EducationWarsawPoland
| | - Jacek Kuźnicki
- The International Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Illana Gozes
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Sagol School of NeuroscienceTel Aviv UniversityTel AvivIsrael
| | - David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Sagol School of NeuroscienceTel Aviv UniversityTel AvivIsrael
| |
Collapse
|
8
|
Schwein PA, Ge Y, Yang B, D’Souza A, Mody A, Shen D, Woo CM. Writing and Erasing O-GlcNAc on Casein Kinase 2 Alpha Alters the Phosphoproteome. ACS Chem Biol 2022; 17:1111-1121. [PMID: 35467332 DOI: 10.1021/acschembio.1c00987] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
O-GlcNAc is an essential carbohydrate modification that intersects with phosphorylation signaling pathways via crosstalk on protein substrates or by direct modification of the kinases that write the phosphate modification. Casein kinase 2 alpha (CK2α), the catalytic subunit of the ubiquitously expressed and constitutively active kinase CK2, is modified by O-GlcNAc, but the effect of this modification on the phosphoproteome in cells is unknown. Here, we apply complementary targeted O-GlcNAc editors, nanobody-OGT and -splitOGA, to selectively write and erase O-GlcNAc from a tagged CK2α to measure the effects on the phosphoproteome in cells. These tools effectively and selectively edit the Ser347 glycosite on CK2α. Using quantitative phosphoproteomics, we report 51 phosphoproteins whose enrichment changes as a function of editing O-GlcNAc on CK2α, including HDAC1, HDAC2, ENSA, SMARCAD1, and PABPN1. Specific phosphosites on HDAC1 Ser393 and HDAC2 Ser394, both reported CK2 substrates, are significantly enhanced by O-GlcNAcylation of CK2α. These data will propel future studies on the crosstalk between O-GlcNAc and phosphorylation.
Collapse
Affiliation(s)
- Paul A. Schwein
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Yun Ge
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Alexandria D’Souza
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Alison Mody
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
9
|
Ruta V, Pagliarini V, Sette C. Coordination of RNA Processing Regulation by Signal Transduction Pathways. Biomolecules 2021; 11:biom11101475. [PMID: 34680108 PMCID: PMC8533259 DOI: 10.3390/biom11101475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.
Collapse
Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Correspondence:
| |
Collapse
|
10
|
Zhao LW, Fan HY. Revisiting poly(A)-binding proteins: Multifaceted regulators during gametogenesis and early embryogenesis. Bioessays 2021; 43:e2000335. [PMID: 33830517 DOI: 10.1002/bies.202000335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/27/2022]
Abstract
Post-transcriptional regulation faces a distinctive challenge in gametes. Transcription is limited when the germ cells enter the division phase due to condensed chromatin, while gene expression during gamete maturation, fertilization, and early cleavage depends on existing mRNA post-transcriptional coordination. The dynamics of the 3'-poly(A) tail play crucial roles in defining mRNA fate. The 3'-poly(A) tail is covered with poly(A)-binding proteins (PABPs) that help to mediate mRNA metabolism and recent work has shed light on the number and function of germ cell-specific expressed PABPs. There are two structurally different PABP groups distinguished by their cytoplasmic and nuclear localization. Both lack catalytic activity but are coupled with various roles through their interaction with multifunctional partners during mRNA metabolism. Here, we present a synopsis of PABP function during gametogenesis and early embryogenesis and describe both conventional and current models of the functions and regulation of PABPs, with an emphasis on the physiological significance of how germ cell-specific PABPs potentially affect human fertility.
Collapse
Affiliation(s)
- Long-Wen Zhao
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
11
|
Schlam‐Babayov S, Bensimon A, Harel M, Geiger T, Aebersold R, Ziv Y, Shiloh Y. Phosphoproteomics reveals novel modes of function and inter-relationships among PIKKs in response to genotoxic stress. EMBO J 2021; 40:e104400. [PMID: 33215756 PMCID: PMC7809795 DOI: 10.15252/embj.2020104400] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 01/10/2023] Open
Abstract
The DNA damage response (DDR) is a complex signaling network that relies on cascades of protein phosphorylation, which are initiated by three protein kinases of the family of PI3-kinase-related protein kinases (PIKKs): ATM, ATR, and DNA-PK. ATM is missing or inactivated in the genome instability syndrome, ataxia-telangiectasia (A-T). The relative shares of these PIKKs in the response to genotoxic stress and the functional relationships among them are central questions in the genome stability field. We conducted a comprehensive phosphoproteomic analysis in human wild-type and A-T cells treated with the double-strand break-inducing chemical, neocarzinostatin, and validated the results with the targeted proteomic technique, selected reaction monitoring. We also matched our results with 34 published screens for DDR factors, creating a valuable resource for identifying strong candidates for novel DDR players. We uncovered fine-tuned dynamics between the PIKKs following genotoxic stress, such as DNA-PK-dependent attenuation of ATM. In A-T cells, partial compensation for ATM absence was provided by ATR and DNA-PK, with distinct roles and kinetics. The results highlight intricate relationships between these PIKKs in the DDR.
Collapse
Affiliation(s)
- Sapir Schlam‐Babayov
- The David and Inez Myers Laboratory of Cancer GeneticsDepartment of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Ariel Bensimon
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Present address:
CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Michal Harel
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Tamar Geiger
- Department of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Faculty of ScienceUniversity of ZurichZurichSwitzerland
| | - Yael Ziv
- The David and Inez Myers Laboratory of Cancer GeneticsDepartment of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| | - Yosef Shiloh
- The David and Inez Myers Laboratory of Cancer GeneticsDepartment of Human Molecular Genetics and BiochemistryTel Aviv University School of MedicineTel AvivIsrael
| |
Collapse
|
12
|
Xu W, Comhair SAA, Chen R, Hu B, Hou Y, Zhou Y, Mavrakis LA, Janocha AJ, Li L, Zhang D, Willard BB, Asosingh K, Cheng F, Erzurum SC. Integrative proteomics and phosphoproteomics in pulmonary arterial hypertension. Sci Rep 2019; 9:18623. [PMID: 31819116 PMCID: PMC6901481 DOI: 10.1038/s41598-019-55053-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023] Open
Abstract
Pulmonary arterial endothelial cells (PAEC) are mechanistically linked to origins of pulmonary arterial hypertension (PAH). Here, global proteomics and phosphoproteomics of PAEC from PAH (n = 4) and healthy lungs (n = 5) were performed using LC-MS/MS to confirm known pathways and identify new areas of investigation in PAH. Among PAH and control cells, 170 proteins and 240 phosphopeptides were differentially expressed; of these, 45 proteins and 18 phosphopeptides were located in the mitochondria. Pathologic pathways were identified with integrative bioinformatics and human protein-protein interactome network analyses, then confirmed with targeted proteomics in PAH PAEC and non-targeted metabolomics and targeted high-performance liquid chromatography of metabolites in plasma from PAH patients (n = 30) and healthy controls (n = 12). Dysregulated pathways in PAH include accelerated one carbon metabolism, abnormal tricarboxylic acid (TCA) cycle flux and glutamate metabolism, dysfunctional arginine and nitric oxide pathways, and increased oxidative stress. Functional studies in cells confirmed abnormalities in glucose metabolism, mitochondrial oxygen consumption, and production of reactive oxygen species in PAH. Altogether, the findings indicate that PAH is typified by changes in metabolic pathways that are primarily found in mitochondria.
Collapse
Affiliation(s)
- Weiling Xu
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America.
| | - Suzy A A Comhair
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ruoying Chen
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Bo Hu
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Yuan Hou
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Yadi Zhou
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Lori A Mavrakis
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Allison J Janocha
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Ling Li
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Dongmei Zhang
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Belinda B Willard
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Kewal Asosingh
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Feixiong Cheng
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Serpil C Erzurum
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States of America. .,Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, United States of America.
| |
Collapse
|
13
|
Domingo-Prim J, Endara-Coll M, Bonath F, Jimeno S, Prados-Carvajal R, Friedländer MR, Huertas P, Visa N. EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks. Nat Commun 2019; 10:2135. [PMID: 31086179 PMCID: PMC6513946 DOI: 10.1038/s41467-019-10153-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
The exosome is a ribonucleolytic complex that plays important roles in RNA metabolism. Here we show that the exosome is necessary for the repair of DNA double-strand breaks (DSBs) in human cells and that RNA clearance is an essential step in homologous recombination. Transcription of DSB-flanking sequences results in the production of damage-induced long non-coding RNAs (dilncRNAs) that engage in DNA-RNA hybrid formation. Depletion of EXOSC10, an exosome catalytic subunit, leads to increased dilncRNA and DNA-RNA hybrid levels. Moreover, the targeting of the ssDNA-binding protein RPA to sites of DNA damage is impaired whereas DNA end resection is hyper-stimulated in EXOSC10-depleted cells. The DNA end resection deregulation is abolished by transcription inhibitors, and RNase H1 overexpression restores the RPA recruitment defect caused by EXOSC10 depletion, which suggests that RNA clearance of newly synthesized dilncRNAs is required for RPA recruitment, controlled DNA end resection and assembly of the homologous recombination machinery.
Collapse
Affiliation(s)
- Judit Domingo-Prim
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Endara-Coll
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sonia Jimeno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Sevilla, Spain.,Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Rosario Prados-Carvajal
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Sevilla, Spain.,Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Sevilla, Spain.,Departamento de Genética, Universidad de Sevilla, 41080, Sevilla, Spain
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
| |
Collapse
|
14
|
Harish P, Dickson G, Malerba A. Advances in emerging therapeutics for oculopharyngeal muscular dystrophy. Expert Opin Orphan Drugs 2018. [DOI: 10.1080/21678707.2018.1536542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Pradeep Harish
- School of Biological Sciences, Centres of Gene and Cell therapy and Biomedical sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - George Dickson
- School of Biological Sciences, Centres of Gene and Cell therapy and Biomedical sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Alberto Malerba
- School of Biological Sciences, Centres of Gene and Cell therapy and Biomedical sciences, Royal Holloway University of London, Egham, Surrey, UK
| |
Collapse
|