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Liu Y, Zheng L, Li Y, Ma L, Zheng N, Liu X, Zhao Y, Yu L, Liu N, Liu S, Zhang K, Zhou J, Wei M, Yang C, Yang G. Neratinib impairs function of m6A recognition on AML1-ETO pre-mRNA and induces differentiation of t (8;21) AML cells by targeting HNRNPA3. Cancer Lett 2024; 594:216980. [PMID: 38797229 DOI: 10.1016/j.canlet.2024.216980] [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: 12/05/2023] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
Acute myeloid leukemia (AML) is frequently linked to genetic abnormalities, with the t (8; 21) translocation, resulting in the production of a fusion oncoprotein AML1-ETO (AE), being a prevalent occurrence. This protein plays a pivotal role in t (8; 21) AML's onset, advancement, and recurrence, making it a therapeutic target. However, the development of drug molecules targeting AML1-ETO are markedly insufficient, especially used in clinical treatment. In this study, it was uncovered that Neratinib could significantly downregulate AML1-ETO protein level, subsequently promoting differentiation of t (8; 21) AML cells. Based on "differentiated active" probes, Neratinib was identified as a functional inhibitor against HNRNPA3 through covalent binding. The further studies demonstrated that HNRNPA3 function as a putative m6A reader responsible for recognizing and regulating the alternative splicing of AML-ETO pre-mRNA. These findings not only contribute to a novel insight to the mechanism governing post-transcriptional modification of AML1-ETO transcript, but also suggest that Neratinib would be promising therapeutic potential for t (8; 21) AML treatment.
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MESH Headings
- Humans
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Quinolines/pharmacology
- Cell Differentiation/drug effects
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- RNA Precursors/metabolism
- RNA Precursors/genetics
- Heterogeneous-Nuclear Ribonucleoprotein Group A-B/metabolism
- Heterogeneous-Nuclear Ribonucleoprotein Group A-B/genetics
- Translocation, Genetic/drug effects
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Adenosine/pharmacology
- Alternative Splicing/drug effects
- Cell Line, Tumor
- Animals
- Mice
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Affiliation(s)
- Yulin Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Liting Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Ying Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Lan Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Nan Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Xinhua Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Yanli Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Li Yu
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, PR China
| | - Ning Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Shuangwei Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Kun Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Jingfeng Zhou
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, PR China.
| | - Mingming Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Guang Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
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Thibault PA, Ganesan A, Kalyaanamoorthy S, Clarke JPWE, Salapa HE, Levin MC. hnRNP A/B Proteins: An Encyclopedic Assessment of Their Roles in Homeostasis and Disease. BIOLOGY 2021; 10:biology10080712. [PMID: 34439945 PMCID: PMC8389229 DOI: 10.3390/biology10080712] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022]
Abstract
The hnRNP A/B family of proteins is canonically central to cellular RNA metabolism, but due to their highly conserved nature, the functional differences between hnRNP A1, A2/B1, A0, and A3 are often overlooked. In this review, we explore and identify the shared and disparate homeostatic and disease-related functions of the hnRNP A/B family proteins, highlighting areas where the proteins have not been clearly differentiated. Herein, we provide a comprehensive assembly of the literature on these proteins. We find that there are critical gaps in our grasp of A/B proteins' alternative splice isoforms, structures, regulation, and tissue and cell-type-specific functions, and propose that future mechanistic research integrating multiple A/B proteins will significantly improve our understanding of how this essential protein family contributes to cell homeostasis and disease.
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Affiliation(s)
- Patricia A. Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Aravindhan Ganesan
- ArGan’s Lab, School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Subha Kalyaanamoorthy
- Department of Chemistry, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Joseph-Patrick W. E. Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Hannah E. Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Michael C. Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; (P.A.T.); (J.-P.W.E.C.); (H.E.S.)
- Department of Medicine, Neurology Division, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
- Correspondence:
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Amano N, Matsumoto K, Shimizu Y, Nakamura M, Tsumura H, Ishii D, Sato Y, Iwamura M. High HNRNPA3 expression is associated with lymph node metastasis and poor prognosis in patients treated with radical cystectomy. Urol Oncol 2020; 39:196.e1-196.e7. [PMID: 33160845 DOI: 10.1016/j.urolonc.2020.10.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/25/2020] [Accepted: 10/24/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVE We sought to identify heterogeneous nuclear ribonucleoprotein A3 (HNRNPA3) expression in bladder cancer and its relationship to clinicopathological findings and prognosis. METHODS Immunohistochemical staining for HNRNPA3 was performed on 122 archived radical cystectomy specimens, with immunoreactivity being stratified on a 0 to 3 scale. The percentage of HNRNPA3 expressing tumor cells was calculated and multiplied by the staining score over an average of 5 areas to obtain a semiquantitative H-score (maximum value: 300). HNRNPA3 expression was categorized as high (≥80) or low (<80). RESULTS The patients' median age was 70 years, and the median follow-up period was 39.4 months. High HNRNPA3 expression was significantly associated with lymph node metastasis (P= 0.014) and S100A8, S100A9 and uroplakin III expression (P= 0.028, 0.002, and 0.047, respectively). Log-rank tests indicated that high HNRNPA3 expression was significantly associated with disease progression and cancer-specific death (P= 0.013 and 0.006, respectively). In the Cox proportional hazards regression analysis, only lymph node metastasis was associated with disease progression and cancer-specific survival. CONCLUSION HNRNPA3 may be a new biomarker to predict biologically aggressive cancers and determine the appropriate treatment modality in patients after radical cystectomy.
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Affiliation(s)
- Noriyuki Amano
- Department of Urology, School of Medicine, Kitasato University, Sagamihara, Japan
| | - Kazumasa Matsumoto
- Department of Urology, School of Medicine, Kitasato University, Sagamihara, Japan.
| | - Yuriko Shimizu
- Department of Urology, School of Medicine, Kitasato University, Sagamihara, Japan
| | - Marie Nakamura
- Department of Urology, School of Medicine, Kitasato University, Sagamihara, Japan
| | - Hideyasu Tsumura
- Department of Urology, School of Medicine, Kitasato University, Sagamihara, Japan
| | - Daisuke Ishii
- Department of Urology, School of Medicine, Kitasato University, Sagamihara, Japan
| | - Yuichi Sato
- Department of Urology, School of Medicine, Kitasato University, Sagamihara, Japan
| | - Masatsugu Iwamura
- Department of Urology, School of Medicine, Kitasato University, Sagamihara, Japan
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4
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Girbes Minguez M, Wolters-Eisfeld G, Lutz D, Buck F, Schachner M, Kleene R. The cell adhesion molecule L1 interacts with nuclear proteins via its intracellular domain. FASEB J 2020; 34:9869-9883. [PMID: 32533745 DOI: 10.1096/fj.201902242r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 02/05/2023]
Abstract
Proteolytic cleavage of the cell adhesion molecule L1 (L1) in brain tissue and in cultured cerebellar neurons results in the generation and nuclear import of a 30 kDa fragment comprising most of L1's C-terminal, intracellular domain. In search of molecules that interact with this domain, we performed affinity chromatography with the recombinant intracellular L1 domain and a nuclear extract from mouse brains, and identified potential nuclear L1 binding partners involved in transcriptional regulation, RNA processing and transport, DNA repair, chromatin remodeling, and nucleocytoplasmic transport. By co-immunoprecipitation and enzyme-linked immunosorbent assay using recombinant proteins, we verified the direct interaction between L1 and the nuclear binding partners non-POU domain containing octamer-binding protein and splicing factor proline/glutamine-rich. The proximity ligation assay confirmed this close interaction in cultures of cerebellar granule cells. Our findings suggest that L1 fragments regulate multiple nuclear functions in the nervous system. We discuss possible physiological and pathological roles of these interactions in regulation of chromatin structure, gene expression, RNA processing, and DNA repair.
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Affiliation(s)
- Maria Girbes Minguez
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gerrit Wolters-Eisfeld
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - David Lutz
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Buck
- Zentrum für Diagnostik, Institut für Klinische Chemie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Melitta Schachner
- Center for Neuroscience, Shantou University Medical College, Shantou, China
- Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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5
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Heterogeneous Nuclear Ribonucleoproteins A1 and A2 Function in Telomerase-Dependent Maintenance of Telomeres. Cancers (Basel) 2019; 11:cancers11030334. [PMID: 30857208 PMCID: PMC6468650 DOI: 10.3390/cancers11030334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 11/17/2022] Open
Abstract
The A/B subfamily of heterogeneous nuclear ribonucleoproteins (hnRNPs A/B), which includes hnRNP A1, A2/B1, and A3, plays an important role in cell proliferation. The simultaneous suppression of hnRNP A1/A2, but not the suppression of hnRNP A1 or A2 alone, has been shown to inhibit cell proliferation and induce apoptosis in cancer cells, but not in mortal normal cells. However, the molecular basis for such a differential inhibition of cell proliferation remains unknown. Here, we show that the simultaneous suppression of hnRNP A1 and hnRNP A2 resulted in dysfunctional telomeres and induced DNA damage responses in cancer cells. The inhibition of apoptosis did not alleviate the inhibition of cell proliferation nor the formation of dysfunctional telomeres in cancer cells depleted of hnRNP A1/A2. Moreover, while proliferation of mortal normal fibroblasts was not sensitive to the depletion of hnRNP A1/A2, the ectopic expression of hTERT in normal fibroblasts rendered these cells sensitive to proliferation inhibition, which was associated with the production of dysfunctional telomeres. Our study demonstrates that hnRNP A1 and A2 function to maintain telomeres in telomerase-expressing cells only, suggesting that the maintenance of functional telomeres in telomerase-expressing cancer cells employs factors that differ from those used in the telomerase-negative normal cells.
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6
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Lin CL, Taggart AJ, Lim KH, Cygan KJ, Ferraris L, Creton R, Huang YT, Fairbrother WG. RNA structure replaces the need for U2AF2 in splicing. Genome Res 2016; 26:12-23. [PMID: 26566657 PMCID: PMC4691745 DOI: 10.1101/gr.181008.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 11/10/2015] [Indexed: 01/21/2023]
Abstract
RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear introns that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complementary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of introns does not require U2AF2, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes.
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Affiliation(s)
- Chien-Ling Lin
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Allison J Taggart
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kian Huat Lim
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kamil J Cygan
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
| | - Luciana Ferraris
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Robbert Creton
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Yen-Tsung Huang
- Departments of Epidemiology and Biostatistics, Brown University, Providence, Rhode Island 02912, USA
| | - William G Fairbrother
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
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Yeh YM, Chen CY, Huang PR, Hsu CW, Wu CC, Wang TCV. Proteomic analyses of genes regulated by heterogeneous nuclear ribonucleoproteins A/B in Jurkat cells. Proteomics 2014; 14:1357-66. [PMID: 24634410 DOI: 10.1002/pmic.201300549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/20/2014] [Accepted: 03/04/2014] [Indexed: 11/06/2022]
Abstract
Several lines of evidence suggest that hnRNPs A/B (hnRNPs A1, A2/B1, and A3) play an important role in proliferation, although the functional overlap among members of hnRNPs A/B remains largely unknown. In this study, we have employed RNAi knockdown and proteomic approaches to investigate the biological functions of hnRNPs A/B. Depletion of hnRNP A2, but not A1 or A3, produced a significant inhibition of cellular proliferation in Jurkat cells. Analysis of the proteomes in the cells depleted for hnRNP A1, A2, or A3 has identified a total of 167 differentially expressed proteins in the depleted cells. Network analysis of the proteins altered in the cells depleted for hnRNP A2 revealed that the biological processes likely affected by these proteins are related to cell cycle, cytoskeleton rearrangement, and transcription regulation. Indeed, we have confirmed that the level of RhoA and CrkL was selectively reduced in the cells depleted of hnRNP A2, but not in the cells depleted for hnRNP A1 or A3. Therefore, we suggest that the reduced proliferation observed in the cells depleted of hnRNP A2 may result from its effects on cell adhesion processes in the Jurkat cells.
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Affiliation(s)
- Yuan-Ming Yeh
- Department of Molecular and Cellular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
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He Q, Chen L, Xu Y, Yu W. Identification of centromeric and telomeric DNA-binding proteins in rice. Proteomics 2013; 13:826-32. [PMID: 23303719 DOI: 10.1002/pmic.201100416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/22/2012] [Accepted: 11/25/2012] [Indexed: 12/17/2022]
Abstract
Centromeres and telomeres are DNA/protein complexes and essential functional components of eukaryotic chromosomes. Previous studies have shown that rice centromeres and telomeres are occupied by CentO (rice centromere satellite DNA) satellite and G-rich telomere repeats, respectively. However, the protein components are not fully understood. DNA-binding proteins associated with centromeric or telomeric DNAs will most likely be important for the understanding of centromere and telomere structure and functions. To capture DNA-specific binding proteins, affinity pull-down technique was applied in this study to isolate rice centromeric and telomeric DNA-binding proteins. Fifty-five proteins were identified for their binding affinity to rice CentO repeat, and 80 proteins were identified for their binding to telomere repeat. One CentO-binding protein, Os02g0288200, was demonstrated to bind to CentO specifically by in vitro assay. A conserved domain, DUF573 with unknown functions was identified in this protein, and proven to be responsible for the specific binding to CentO in vitro. Four proteins identified as telomere DNA-binding proteins in this study were reported by different groups previously. These results demonstrate that DNA affinity pull-down technique is effective in the isolation of sequence-specific binding proteins and will be applicable in future studies of centromere and telomere proteins.
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Affiliation(s)
- Qi He
- State Key Laboratory for Agrobiotechnology, Institute of Plant Molecular Biology and Agricultural Biotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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Telomere- and telomerase-interacting protein that unfolds telomere G-quadruplex and promotes telomere extension in mammalian cells. Proc Natl Acad Sci U S A 2012. [PMID: 23184978 DOI: 10.1073/pnas.1200232109] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Telomere extension by telomerase is essential for chromosome stability and cell vitality. Here, we report the identification of a splice variant of mammalian heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2), hnRNP A2*, which binds telomeric DNA and telomerase in vitro. hnRNP A2* colocalizes with telomerase in Cajal bodies and at telomeres. In vitro assays show that hnRNP A2* actively unfolds telomeric G-quadruplex DNA, exposes 5 nt of the 3' telomere tail and substantially enhances the catalytic activity and processivity of telomerase. The expression level of hnRNP A2* in tissues positively correlates with telomerase activity, and overexpression of hnRNP A2* leads to telomere elongation in vivo. Thus, hnRNP A2* plays a positive role in unfolding telomere G-quadruplexes and in enhancing telomere extension by telomerase.
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Zheng D, Chen CYA, Shyu AB. Unraveling regulation and new components of human P-bodies through a protein interaction framework and experimental validation. RNA (NEW YORK, N.Y.) 2011; 17:1619-34. [PMID: 21750099 PMCID: PMC3162328 DOI: 10.1261/rna.2789611] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The cellular factors involved in mRNA degradation and translation repression can aggregate into cytoplasmic domains known as GW bodies or mRNA processing bodies (P-bodies). However, current understanding of P-bodies, especially the regulatory aspect, remains relatively fragmentary. To provide a framework for studying the mechanisms and regulation of P-body formation, maintenance, and disassembly, we compiled a list of P-body proteins found in various species and further grouped both reported and predicted human P-body proteins according to their functions. By analyzing protein-protein interactions of human P-body components, we found that many P-body proteins form complex interaction networks with each other and with other cellular proteins that are not recognized as P-body components. The observation suggests that these other cellular proteins may play important roles in regulating P-body dynamics and functions. We further used siRNA-mediated gene knockdown and immunofluorescence microscopy to demonstrate the validity of our in silico analyses. Our combined approach identifies new P-body components and suggests that protein ubiquitination and protein phosphorylation involving 14-3-3 proteins may play critical roles for post-translational modifications of P-body components in regulating P-body dynamics. Our analyses provide not only a global view of human P-body components and their physical interactions but also a wealth of hypotheses to help guide future research on the regulation and function of human P-bodies.
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Affiliation(s)
- Dinghai Zheng
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
| | - Chyi-Ying A. Chen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, Houston, Texas 77021, USA
- Corresponding author.E-mail .
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Abstract
The hnRNPs (heterogeneous nuclear ribonucleoproteins) are RNA-binding proteins with important roles in multiple aspects of nucleic acid metabolism, including the packaging of nascent transcripts, alternative splicing and translational regulation. Although they share some general characteristics, they vary greatly in terms of their domain composition and functional properties. Although the traditional grouping of the hnRNPs as a collection of proteins provided a practical framework, which has guided much of the research on them, this approach is becoming increasingly incompatible with current knowledge about their structural and functional divergence. Hence, we review the current literature to examine hnRNP diversity, and discuss how this impacts upon approaches to the classification of RNA-binding proteins in general.
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12
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Huang PR, Hung SC, Wang TCV. Telomeric DNA-binding activities of heterogeneous nuclear ribonucleoprotein A3 in vitro and in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:1164-74. [PMID: 20600361 DOI: 10.1016/j.bbamcr.2010.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 06/07/2010] [Accepted: 06/14/2010] [Indexed: 10/19/2022]
Abstract
Telomeres are dynamic DNA-protein complexes that protect the ends of linear chromosome. Telomere-binding proteins play crucial role in the maintenance of telomeres. HnRNP A3 has been shown recently to bind specifically to single-stranded telomeric DNA in vitro, although its in vivo telomere function remains unknown. In this study, the DNA-binding properties of hnRNP A3 in vitro as well as its putative role of telomere maintenance in vivo were investigated. The minimal sequence for hnRNP A3 binding to DNA was determined as an undecamer with the following consensus sequence 5'-[T/C]AG[G/T]NN[T/C]AG[G/T]N-3'. Confocal microscopy and chromatin-immunoprecipitation (ChIP) analyses showed that hnRNP A3 is associated with telomere in vivo. Knocking-down the expression of hnRNP A3 had no effect on telomere length maintenance and did not affect cell proliferation. In contrast, overexpression of hnRNP A3 resulted in the production of steady-state short telomeres in OECM1 cells. These results suggest that hnRNP A3 is associated with telomere in vivo and acts as a negative regulator of telomere length maintenance.
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Affiliation(s)
- Pei-Rong Huang
- Department of Molecular and Cellular Biology, Chang Gung University, Tao-Yuan. Taiwan
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13
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TERRA transcripts are bound by a complex array of RNA-binding proteins. Nat Commun 2010; 1:33. [PMID: 20975687 DOI: 10.1038/ncomms1032] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 06/02/2010] [Indexed: 11/08/2022] Open
Abstract
Telomeres are transcribed from the telomeric C-rich strand, giving rise to UUAGGG repeat-containing telomeric transcripts or TERRA, which are novel structural components of telomeres. TERRA abundance is highly dependent on developmental status (including nuclear reprogramming), telomere length, cellular stresses, tumour stage and chromatin structure. However, the molecular mechanisms and factors controlling TERRA levels are still largely unknown. In this study, we identify a set of RNA-binding proteins, which endogenously bind and regulate TERRA in the context of primary mouse embryonic fibroblasts. The identification was carried out by biotin pull-down assays followed by LC-MALDI TOF/TOF mass spectrometry. Different members of the heterogeneous nuclear ribonucleoprotein family are among the ribonucleoprotein family that bind more abundantly to TERRA. Downregulation of TERRA-bound RBPs by small interfering RNA further shows that they can impact on TERRA abundance, their location and telomere lengthening. These findings anticipate an impact of TERRA-associated RBPs on telomere biology and telomeres diseases, such as cancer and aging.
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Krüger AC, Raarup MK, Nielsen MM, Kristensen M, Besenbacher F, Kjems J, Birkedal V. Interaction of hnRNP A1 with telomere DNA G-quadruplex structures studied at the single molecule level. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1343-50. [DOI: 10.1007/s00249-010-0587-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 12/07/2009] [Accepted: 02/12/2010] [Indexed: 10/19/2022]
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A gene expression signature classifying telomerase and ALT immortalization reveals an hTERT regulatory network and suggests a mesenchymal stem cell origin for ALT. Oncogene 2009; 28:3765-74. [PMID: 19684619 PMCID: PMC2875172 DOI: 10.1038/onc.2009.238] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Telomere length is maintained by two known mechanisms, the activation of telomerase or alternative lengthening of telomeres (ALT). The molecular mechanisms regulating the ALT phenotype are poorly understood and it is unknown how the decision of which pathway to activate is made at the cellular level. We have shown earlier that active repression of telomerase gene expression by chromatin remodelling of the promoters is one mechanism of regulation; however, other genes and signalling networks are likely to be required to regulate telomerase and maintain the ALT phenotype. Using gene expression profiling, we have uncovered a signature of 1305 genes to distinguish telomerase-positive and ALT cell lines. By combining this with the gene expression profiles of liposarcoma tissue samples, we refined this signature to 297 genes. A network analysis of known interactions between genes within this signature revealed a regulatory signalling network consistent with a model of human telomerase reverse transcriptase (hTERT) repression in ALT cell lines and liposarcomas. This network expands on our existing knowledge of hTERT regulation and provides a platform to understand differential regulation of hTERT in different tumour types and normal tissues. We also show evidence to suggest a novel mesenchymal stem cell origin for ALT immortalization in cell lines and mesenchymal tissues.
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Chambery A, Colucci-D’Amato L, Vissers JPC, Scarpella S, Langridge JI, Parente A. Proteomic Profiling of Proliferating and Differentiated Neural mes-c-myc A1 Cell Line from Mouse Embryonic Mesencephalon by LC−MS. J Proteome Res 2008; 8:227-38. [DOI: 10.1021/pr800454n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Angela Chambery
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Luca Colucci-D’Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Johannes P. C. Vissers
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Simona Scarpella
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - James I. Langridge
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Augusto Parente
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
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Friend LR, Han SP, Rothnagel JA, Smith R. Differential subnuclear localisation of hnRNPs A/B is dependent on transcription and cell cycle stage. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1783:1972-80. [PMID: 18588922 DOI: 10.1016/j.bbamcr.2008.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/23/2008] [Accepted: 05/23/2008] [Indexed: 01/31/2023]
Abstract
The heterogeneous nuclear ribonucleoproteins A1, A2/B1 and A3 (hnRNPs A/B) are involved in many nuclear functions that are confined to distinct regions within the nucleus. To characterise and compare the distribution of the hnRNPs A/B in these subnuclear compartments, their colocalisation with spliceosomal components, nascent transcripts and other nuclear markers in HeLa cells was investigated by immunostaining and transfection of GFP constructs. The mechanisms of this localisation were further explored by treating cells with detergent, nucleases and transcription inhibitors. We have also examined the dynamics of A2/B1 throughout the cell cycle. Our results show that hnRNPs A/B have different subnuclear localisations, with A1 differentially localised to the nuclear envelope, and A2/B1 and A3 enriched around nucleoli. This pattern of distribution was dependent on RNA integrity and active transcription. The hnRNPs A/B preferentially colocalised with a subset of splicing factors. Significantly, only rarely did transcription factories colocalise with high levels of these hnRNPs. Moreover, localisation of A2/B1 changed with cell cycle stage. Our findings show that the subnuclear localisation of the hnRNPs A/B is differentially, spatially and temporally regulated, and suggest that this localisation may be relevant to their nuclear functions.
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Affiliation(s)
- Lexie R Friend
- School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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