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Miyake T, McDermott JC. Nucleolar localization of c-Jun. FEBS J 2021; 289:748-765. [PMID: 34499807 DOI: 10.1111/febs.16187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023]
Abstract
Nucleoli are well defined for their function in ribosome biogenesis, but only a small fraction of the nucleolar proteome has been characterized. Here, we report that the proto-oncogene, c-Jun, is targeted to the nucleolus. Using live cell imaging in myogenic cells, we document that the c-Jun basic domain contains a unique, evolutionarily conserved motif that determines nucleolar targeting. Fos family Jun dimer partners, such as Fra2, while nuclear, do not co-localize with c-Jun in the nucleolus. A point mutation in c-Jun that mimics Fra2 (M260E) in its Nucleolar Localization sequence (NoLS) results in loss of c-Jun nucleolar targeting while still preserving nuclear localization. Fra2 can sequester c-Jun in the nucleoplasm, indicating that the stoichiometric ratio of heterodimeric partners regulates c-Jun nucleolar targeting. Finally, nucleolar localization of c-Jun modulates nucleolar architecture and ribosomal RNA accumulation. These studies highlight a novel role for Jun family proteins in the nucleolus, having potential implications for a diverse array of AP-1-regulated cellular processes.
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Affiliation(s)
- Tetsuaki Miyake
- Department of Biology, York University, Toronto, ON, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada
| | - John C McDermott
- Department of Biology, York University, Toronto, ON, Canada.,Muscle Health Research Centre (MHRC), York University, Toronto, ON, Canada.,Centre for Research in Biomolecular Interactions (CRBI), York University, Toronto, ON, Canada.,Centre for Research in Mass Spectrometry (CRMS), York University, Toronto, ON, Canada
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2
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Vahidnezhad H, Youssefian L, Saeidian AH, Boyden LM, Touati A, Harvey N, Naji M, Zabihi M, Barzegar M, Sotoudeh S, Liu L, Guy A, Kariminejad A, Zeinali S, Choate KA, McGrath JA, Uitto J. Kindler epidermolysis bullosa-like skin phenotype and downregulated basement membrane zone gene expression in poikiloderma with neutropenia and a homozygous USB1 mutation. Matrix Biol 2021; 99:43-57. [PMID: 34004352 DOI: 10.1016/j.matbio.2021.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 11/24/2022]
Abstract
Epidermolysis bullosa (EB) is a genotypically heterogeneous group of disorders characterized by cutaneous blistering and erosions with a tremendous spectrum of severity. One of the distinct forms of EB, Kindler EB (KEB), manifests with blistering and poikiloderma; this subtype of EB is caused by mutations in the FERMT1 gene encoding kindlin-1. In this study, we investigated a patient clinically diagnosed as KEB with reduced FERMT1 gene expression and intensity of immunostaining for kindlin-1. Transmission electron microscopy showed lamina densa reduplication, frequently observed in KEB. However, no mutations were identified in FERMT1 in this patient with consanguineous parents, and this gene resided outside of genomic regions of homozygosity (ROH). Instead, whole-exome sequencing and homozygosity mapping identified a homozygous sequence variant at the +4 position of intron 2 in the USB1 gene, encoding an exoribonuclease required for processing of U6 snRNA, a critical component of spliceosomes. Examination of the patient's RNA by RNA-Seq confirmed the pathogenicity of this variant, causing aberrant splicing predicted to result in loss of function of USB1. Mutations in this gene have been reported in patients with poikiloderma and neutropenia, with a few reported cases in association with skin fragility, a condition distinct from the KEB phenotype. Transcriptome analysis revealed that several genes, expressed in the cutaneous basement membrane zone and previously associated with different subtypes of EB, were differentially downregulated at the mRNA level. EB-associated mRNA downregulation was confirmed at protein levels by skin immunofluorescence. These observations provide a novel mechanism for blistering and erosions in the skin as a result reduced presence of adhesion complexes critical for stable association of epidermis and dermis at the level of cutaneous basement membrane zone.
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Affiliation(s)
- Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, United States
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, United States
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, United States; Genetics, Genomics, and Cancer Biology PhD Program, Jefferson College of Life Sciences, Thomas Jefferson University, Philadelphia, PA, United States
| | - Lynn M Boyden
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Andrew Touati
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Nailah Harvey
- Philadelphia College of Osteopathic Medicine, Philadelphia, PA, United States
| | - Mahtab Naji
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, United States
| | | | | | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Lu Liu
- Viapath, St Thomas' Hospital, London, United Kingdom
| | - Alyson Guy
- Viapath, St Thomas' Hospital, London, United Kingdom
| | | | - Sirous Zeinali
- Kawsar Human Genetics Research Center, Tehran, Iran; Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Keith A Choate
- Departments of Dermatology, Genetics, and Pathology, Yale University School of Medicine, New Haven, CT 06510, United States
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London, Guy's Campus, London, United Kingdom
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States; Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, United States.
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3
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Zhang X, Zhang J, Liu Y, Li J, Tan J, Song Z. Bcl-2 Associated Athanogene 2 (BAG2) is Associated With Progression and Prognosis of Hepatocellular Carcinoma: A Bioinformatics-Based Analysis. Pathol Oncol Res 2021; 27:594649. [PMID: 34257542 PMCID: PMC8262200 DOI: 10.3389/pore.2021.594649] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 02/12/2021] [Indexed: 12/28/2022]
Abstract
Background: Bcl-2 associated athanogene2 (BAG2) is reported to act as an oncogene or a tumor-suppressor in tumors in a context-dependent way; however, its function in hepatocellular carcinoma (HCC) remains unclear. Methods: Immunohistochemistry (IHC) staining, cell counting kit-8 (CCK-8) assay, apoptotic assay, cell invasion assay and a set of bioinformatics tools were integrated to analyze the role of BAG2 in hepatocellular carcinoma. Results: BAG2 was significantly up-regulated in HCC. Prognostic analysis indicated that HCC patients with high expression of BAG2 had significantly shorter overall survival, progression free survival and disease specific survival. Besides, silencing BAG2 in HCC cells impaired cell proliferation, facilitated apoptosis and repressed invasion of the cells. Bioinformatics analysis showed that BAG2 might regulate ribosome biogenesis in HCC. Conclusion: This study revealed that the up-regulated BAG2 in HCC was associated with a worse prognosis and might favor the progression of the disease.
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Affiliation(s)
- Xi Zhang
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Junjun Zhang
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yang Liu
- Department of Pathology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jie Li
- Department of Information Science and Engineering, Hunan University of Chinese Medicine, Changsha, China
| | - Juan Tan
- Department of Pathology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
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Zhang XO, Gingeras TR, Weng Z. Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Genome Res 2019; 29:1402-1414. [PMID: 31413151 PMCID: PMC6724667 DOI: 10.1101/gr.249789.119] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/24/2019] [Indexed: 01/09/2023]
Abstract
Alu elements are one of the most successful families of transposons in the human genome. A portion of Alu elements is transcribed by RNA Pol III, whereas the remaining ones are part of Pol II transcripts. Because Alu elements are highly repetitive, it has been difficult to identify the Pol III–transcribed elements and quantify their expression levels. In this study, we generated high-resolution, long-genomic-span RAMPAGE data in 155 biosamples all with matching RNA-seq data and built an atlas of 17,249 Pol III–transcribed Alu elements. We further performed an integrative analysis on the ChIP-seq data of 10 histone marks and hundreds of transcription factors, whole-genome bisulfite sequencing data, ChIA-PET data, and functional data in several biosamples, and our results revealed that although the human-specific Alu elements are transcriptionally repressed, the older, expressed Alu elements may be exapted by the human host to function as cell-type–specific enhancers for their nearby protein-coding genes.
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Affiliation(s)
- Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Abstract
Most RNA polymerases can initiate transcription from diverse DNA template sequences with relatively few outright sequence restraints. Recent reports have demonstrated that failure to subdue the promiscuity of RNA polymerase in vivo can severely impede cell function. This phenomenon appears common to all cell types with undesirable effects ranging from growth inhibition in prokaryotes to cancer in higher organisms. Here we discuss similarities and differences in strategies employed by cells to minimise spurious transcription across life's domains.
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Affiliation(s)
- Joseph T Wade
- a Wadsworth Center , New York State Department of Health , Albany , NY , USA.,b Department of Biomedical Sciences , School of Public Health, University at Albany, SUNY , Albany , NY , USA
| | - David C Grainger
- c Institute of Microbiology and Infection, School of Biosciences, University of Birmingham , Edgbaston, Birmingham , UK
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