1
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Sardar S, McNair CM, Ravindranath L, Chand SN, Yuan W, Bogdan D, Welti J, Sharp A, Ryan NK, Knudsen LA, Schiewer MJ, DeArment EG, Janas T, Su XA, Butler LM, de Bono JS, Frese K, Brooks N, Pegg N, Knudsen KE, Shafi AA. AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer. Oncogene 2024:10.1038/s41388-024-03148-4. [PMID: 39266679 DOI: 10.1038/s41388-024-03148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/20/2024] [Accepted: 08/28/2024] [Indexed: 09/14/2024]
Abstract
Castration resistant prostate cancer (CRPC) remains an incurable disease stage with ineffective treatments options. Here, the androgen receptor (AR) coactivators CBP/p300, which are histone acetyltransferases, were identified as critical mediators of DNA damage repair (DDR) to potentially enhance therapeutic targeting of CRPC. Key findings demonstrate that CBP/p300 expression increases with disease progression and selects for poor prognosis in metastatic disease. CBP/p300 bromodomain inhibition enhances response to standard of care therapeutics. Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed that CBP/p300 regulates DDR. Further mechanistic investigation showed that CBP/p300 attenuation via therapeutic targeting and genomic knockdown decreases homologous recombination (HR) factors in vitro, in vivo, and in human prostate cancer (PCa) tumors ex vivo. Similarly, CBP/p300 expression in human prostate tissue correlates with HR factors. Lastly, targeting CBP/p300 impacts HR-mediate repair and patient outcome. Collectively, these studies identify CBP/p300 as drivers of PCa tumorigenesis and lay the groundwork to optimize therapeutic strategies for advanced PCa via CBP/p300 inhibition, potentially in combination with AR-directed and DDR therapies.
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Affiliation(s)
- Sumaira Sardar
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | | | - Lakshmi Ravindranath
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Saswati N Chand
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom
| | - Denisa Bogdan
- The Institute of Cancer Research, London, United Kingdom
| | - Jon Welti
- The Institute of Cancer Research, London, United Kingdom
| | - Adam Sharp
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Natalie K Ryan
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Liam A Knudsen
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Matthew J Schiewer
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Elise G DeArment
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Thomas Janas
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Xiaofeng A Su
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lisa M Butler
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Johann S de Bono
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Kris Frese
- CellCentric Ltd., Cambridge, United Kingdom
| | | | - Neil Pegg
- CellCentric Ltd., Cambridge, United Kingdom
| | | | - Ayesha A Shafi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA.
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2
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Sardar S, McNair CM, Ravindranath L, Chand SN, Yuan W, Bogdan D, Welti J, Sharp A, Ryan NK, Schiewer MJ, DeArment EG, Janas T, Su XA, Butler LM, de Bono JS, Frese K, Brooks N, Pegg N, Knudsen KE, Shafi AA. AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592966. [PMID: 38766099 PMCID: PMC11100730 DOI: 10.1101/2024.05.07.592966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Castration resistant prostate cancer (CRPC) remains an incurable disease stage with ineffective treatments options. Here, the androgen receptor (AR) coactivators CBP/p300, which are histone acetyltransferases, were identified as critical mediators of DNA damage repair (DDR) to potentially enhance therapeutic targeting of CRPC. Key findings demonstrate that CBP/p300 expression increases with disease progression and selects for poor prognosis in metastatic disease. CBP/p300 bromodomain inhibition enhances response to standard of care therapeutics. Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed that CBP/p300 regulates DDR. Further mechanistic investigation showed that CBP/p300 attenuation via therapeutic targeting and genomic knockdown decreases homologous recombination (HR) factors in vitro, in vivo, and in human prostate cancer (PCa) tumors ex vivo. Similarly, CBP/p300 expression in human prostate tissue correlates with HR factors. Lastly, targeting CBP/p300 impacts HR-mediate repair and patient outcome. Collectively, these studies identify CBP/p300 as drivers of PCa tumorigenesis and lay the groundwork to optimize therapeutic strategies for advanced PCa via CBP/p300 inhibition, potentially in combination with AR-directed and DDR therapies.
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Affiliation(s)
- Sumaira Sardar
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
| | - Christopher M. McNair
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, 19107, USA
| | - Lakshmi Ravindranath
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
| | - Saswati N. Chand
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, 19107, USA
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom
| | - Denisa Bogdan
- The Institute of Cancer Research, London, United Kingdom
| | - Jon Welti
- The Institute of Cancer Research, London, United Kingdom
| | - Adam Sharp
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Natalie K. Ryan
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Matthew J. Schiewer
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, 19107, USA
| | - Elise G. DeArment
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
| | - Thomas Janas
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
| | - Xiaofeng A. Su
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lisa M. Butler
- South Australian Immunogenomics Cancer Institute, The University of Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Johann S. de Bono
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Kris Frese
- CellCentric Ltd., Cambridge, United Kingdom
| | | | - Neil Pegg
- CellCentric Ltd., Cambridge, United Kingdom
| | - Karen E. Knudsen
- The American Cancer Society, Philadelphia, Pennsylvania, 19103, USA
| | - Ayesha A. Shafi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20817, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, 20817 USA
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3
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Zhang M, Huang H, Li J, Wu Q. ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry. Cell Rep 2024; 43:113663. [PMID: 38206813 DOI: 10.1016/j.celrep.2023.113663] [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: 09/20/2023] [Revised: 11/28/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
The transcription factor ZNF143 contains a central domain of seven zinc fingers in a tandem array and is involved in 3D genome construction. However, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes a diverse range of genomic sites directly within enhancers and promoters and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites, and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF degradation, reveals that ZNF143 and CTCF collaborate to regulate higher-order topological chromatin organization. Finally, CTCF depletion enlarges direct ZNF143 chromatin looping. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate CTCF/cohesin configuration and TAD (topologically associating domain) formation, whereas directional recognition of genomic DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.
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Affiliation(s)
- Mo Zhang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Haiyan Huang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China.
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4
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Rad SMAH, Halpin JC, Tawinwung S, Suppipat K, Hirankarn N, McLellan AD. MicroRNA‐mediated metabolic reprogramming of chimeric antigen receptor T cells. Immunol Cell Biol 2022; 100:424-439. [PMID: 35507473 PMCID: PMC9322280 DOI: 10.1111/imcb.12551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Seyed Mohammad Ali Hosseini Rad
- Department of Microbiology and Immunology School of Biomedical Science University of Otago Dunedin Otago New Zealand
- Center of Excellence in Immunology and Immune‐mediated Diseases Chulalongkorn University Bangkok Thailand
- Department of Microbiology Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Joshua Colin Halpin
- Department of Microbiology and Immunology School of Biomedical Science University of Otago Dunedin Otago New Zealand
| | - Supannikar Tawinwung
- Center of Excellence in Immunology and Immune‐mediated Diseases Chulalongkorn University Bangkok Thailand
- Department of Pharmacology and Physiology Faculty of Pharmaceutical Sciences Chulalongkorn University Bangkok Thailand
| | - Koramit Suppipat
- Center of Excellence in Immunology and Immune‐mediated Diseases Chulalongkorn University Bangkok Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune‐mediated Diseases Chulalongkorn University Bangkok Thailand
- Department of Microbiology Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Alexander D McLellan
- Department of Microbiology and Immunology School of Biomedical Science University of Otago Dunedin Otago New Zealand
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5
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Islam S, Tekman M, Flanagan SE, Guay-Woodford L, Hussain K, Ellard S, Kleta R, Bockenhauer D, Stanescu H, Iancu D. Founder mutation in the PMM2 promotor causes hyperinsulinemic hypoglycaemia/polycystic kidney disease (HIPKD). Mol Genet Genomic Med 2021; 9:e1674. [PMID: 33811480 PMCID: PMC8683636 DOI: 10.1002/mgg3.1674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 01/03/2023] Open
Abstract
Background Polycystic kidney disease with hyperinsulinaemic hypoglycaemia (HIPKD) is a recently described disease caused by a single nucleotide variant, c.‐167G>T, in the promoter region of PMM2 (encoding phosphomannomutase 2), either in homozygosity or compound heterozygosity with a pathogenic coding variant in trans. All patients identified so far are of European descent, suggesting a possible founder effect. Methods We generated high density genotyping data from 11 patients from seven unrelated families, and used this information to identify a common haplotype that included the promoter variant. We estimated the age of the promoter mutation with DMLE+ software, using demographic parameters corresponding to the European population. Results All patients shared a 0.312 Mb haplotype which was absent in 503 European controls available in the 1000 Genomes Project. The age of this mutation was estimated as 105–110 generations, indicating its occurrence around 600 BC, a time of intense migration, which might explain the presence of the same mutations in Europeans around the globe. Conclusion The shared unique haplotype among seemingly unrelated patients is consistent with a founder effect in Europeans.
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Affiliation(s)
- Sumaya Islam
- Department Renal Medicine, University College London, London, UK
| | - Mehmet Tekman
- Department Renal Medicine, University College London, London, UK
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Lisa Guay-Woodford
- Center for Translational Research, Children's National Hospital Health System, Washington, DC, USA
| | - Khalid Hussain
- Department of Endocrinology, Sidra Medicine, Doha, Qatar
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Robert Kleta
- Department Renal Medicine, University College London, London, UK.,Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Detlef Bockenhauer
- Department Renal Medicine, University College London, London, UK.,Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Horia Stanescu
- Department Renal Medicine, University College London, London, UK
| | - Daniela Iancu
- Department Renal Medicine, University College London, London, UK
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6
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Al-Obaide MAI, Al-Obaidi II, Vasylyeva TL. Unexplored regulatory sequences of divergently paired GLA and HNRNPH2 loci pertinent to Fabry disease in human kidney and skin cells: Presence of an active bidirectional promoter. Exp Ther Med 2020; 21:154. [PMID: 33456521 PMCID: PMC7792484 DOI: 10.3892/etm.2020.9586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/01/2020] [Indexed: 12/21/2022] Open
Abstract
Fabry disease (FD) is a rare hereditary disorder characterized by a wide range of symptoms caused by a variety of mutations in the galactosidase α (GLA) gene. The heterogeneous nuclear ribonucleoprotein (HNRNPH2) gene is divergently paired with GLA on chromosome X and is thought to be implicated in FD. However, insufficient information is available on the regulatory mechanisms associated with the expression of HNRNPH2 and the GLA loci. Therefore, the current study performed bioinformatics analyses to assess the GLA and HNRNPH2 loci and investigate the regulatory mechanisms involved in the expression of each gene. The regulatory mechanisms underlying GLA and HNRNPH2 were revealed. The expression of each gene was associated with a bidirectional promoter (BDP) characterized by the absence of TATA box motifs and the presence of specific transcription factor binding sites (TFBSs) and a CpG Island (CGI). The nuclear run-on transcription assay confirmed the activity of BDP GLA and HNRNPH2 transcription in 293T. Methylation-specific PCR analysis demonstrated a statistically significant variation in the DNA methylation pattern of BDP in several cell lines, including human adult epidermal keratinocytes (AEKs), human renal glomerular endothelial cells, human renal epithelial cells and 293T cells. The highest observed significance was demonstrated in AEKs (P<0.05). The results of the chromatin-immunoprecipitation assay using 293T cells identified specific TFBS motifs for Yin Yang 1 and nuclear respiratory factor 1 transcription factors in BDPs. The National Center for Biotechnology Information-single nucleotide polymorphism database revealed pathogenic variants in the BDP sequence. Additionally, a previously reported variant associated with a severe heterozygous female case of GLA FD was mapped in BDP. The results of the present study suggested that the expression of the divergent paired loci, GLA and HNRNPH2, were controlled by BDP. Mutations in BDP may also serve a role in FD and may explain clinical disease diversity.
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Affiliation(s)
- Mohammed A Ibrahim Al-Obaide
- Department of Pediatrics, School of Medicine, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Ibtisam I Al-Obaidi
- Department of Pediatrics, School of Medicine, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
| | - Tetyana L Vasylyeva
- Department of Pediatrics, School of Medicine, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA
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7
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He K, Rad SMAH, Poudel A, McLellan AD. Compact Bidirectional Promoters for Dual-Gene Expression in a Sleeping Beauty Transposon. Int J Mol Sci 2020; 21:ijms21239256. [PMID: 33291599 PMCID: PMC7731152 DOI: 10.3390/ijms21239256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Promoter choice is an essential consideration for transgene expression in gene therapy. The expression of multiple genes requires ribosomal entry or skip sites, or the use of multiple promoters. Promoter systems comprised of two separate, divergent promoters may significantly increase the size of genetic cassettes intended for use in gene therapy. However, an alternative approach is to use a single, compact, bidirectional promoter. We identified strong and stable bidirectional activity of the RPBSA synthetic promoter comprised of a fragment of the human Rpl13a promoter, together with additional intron/exon structures. The Rpl13a-based promoter drove long-term bidirectional activity of fluorescent proteins. Similar results were obtained for the EF1-α and LMP2/TAP1 promoters. However, in a lentiviral vector, the divergent bidirectional systems failed to produce sufficient titres to translate into an expression system for dual chimeric antigen receptor (CAR) expression. Although bidirectional promoters show excellent applicability to drive short RNA in Sleeping Beauty transposon systems, their possible use in the lentiviral applications requiring longer and more complex RNA, such as dual-CAR cassettes, is limited.
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8
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Huning L, Kunkel GR. The ubiquitous transcriptional protein ZNF143 activates a diversity of genes while assisting to organize chromatin structure. Gene 2020; 769:145205. [PMID: 33031894 DOI: 10.1016/j.gene.2020.145205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
Zinc Finger Protein 143 (ZNF143) is a pervasive C2H2 zinc-finger transcriptional activator protein regulating the efficiency of eukaryotic promoter regions. ZNF143 is able to activate transcription at both protein coding genes and small RNA genes transcribed by either RNA polymerase II or RNA polymerase III. Target genes regulated by ZNF143 are involved in an array of different cellular processes including both cancer and development. Although a key player in regulating eukaryotic genes, the molecular mechanism by with ZNF143 binds and activates genes transcribed by two different polymerases is still relatively unknown. In addition to its role as a transcriptional regulator, recent genomics experiments have implicated ZNF143 as a potential co-factor involved in chromatin looping and establishing higher order structure within the genome. This review focuses primarily on possible activation mechanisms of promoters by ZNF143, with less emphasis on the role of ZNF143 in cancer and development, and its function in establishing higher order chromatin contacts within the genome.
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Affiliation(s)
- Laura Huning
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | - Gary R Kunkel
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
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9
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The roles of long noncoding RNAs in breast cancer metastasis. Cell Death Dis 2020; 11:749. [PMID: 32929060 PMCID: PMC7490374 DOI: 10.1038/s41419-020-02954-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most significant threat to female health. Breast cancer metastasis is the major cause of mortality in breast cancer patients. To fully unravel the molecular mechanisms that underlie the breast cancer cell metastasis is critical for developing strategies to improve survival and prognosis in breast cancer patients. Recent studies have revealed that the long noncoding RNAs (lncRNAs) are involved in breast cancer metastasis through a variety of molecule mechanisms, though the precise functional details of these lncRNAs are yet to be clarified. In the present review, we focus on the functions of lncRNAs in breast cancer invasion and metastasis, with particular emphasis on the functional properties, the regulatory factors, the therapeutic promise, as well as the future challenges in studying these lncRNA.
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10
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Ye B, Yang G, Li Y, Zhang C, Wang Q, Yu G. ZNF143 in Chromatin Looping and Gene Regulation. Front Genet 2020; 11:338. [PMID: 32318100 PMCID: PMC7154149 DOI: 10.3389/fgene.2020.00338] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/20/2020] [Indexed: 01/02/2023] Open
Abstract
ZNF143, a human homolog of the transcriptional activator Staf, is a C2H2-type protein consisting of seven zinc finger domains. As a transcription factor (TF), ZNF143 is sequence specifically binding to chromatin and activates the expression of protein-coding and non-coding genes on a genome scale. Although it is ubiquitous expressed, its expression in cancer cells and tissues is usually higher than that in normal cells and tissues. Therefore, abnormal expression of ZNF143 is related to cancer cell survival, proliferation, differentiation, migration, and invasion, suggesting that new small molecules can be designed by targeting ZNF143 as it may be a good potential biomarker and therapeutic target for related cancers. However, the mechanism on how ZNF143 regulates its targeting gene remains unclear. Recently, with the development of chromatin conformation capture (3C) and its derivatives, and high-throughput sequencing technology, new findings have been obtained in the study of ZNF143. Pioneering studies have showed that ZNF143 binds directly to promoters and contributes to chromatin interactions connecting promoters to distal regulatory elements, such as enhancers. Further, it has proved that ZNF143 is involved in CCCTC-binding factor (CTCF) in establishing the conserved chromatin loops by cooperating with cohesin and other partners. These results indicate that ZNF143 is a key loop formation factor. In addition, we report ZNF143 is dynamically bound to chromatin during the cell cycle demonstrated that it is a potential mitotic bookmarking factor. It may be associated with CTCF for mitosis-to-G1 phase transition and chromatin loop re-establishment in early G1 phase. In the future, researchers could further clarify the fine mechanism of ZNF143 in mediating chromatin loops with the help of CUT&RUN (CUT&Tag) and Cut-C technology. Thus, in this review, we summarize the research progress of TF ZNF143 in detail and also predict the potential functions of ZNF143 in cell fate and identity based on our recent discoveries.
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Affiliation(s)
- Bingyu Ye
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
| | - Ganggang Yang
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
| | - Yuanmeng Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Chunyan Zhang
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
| | - Qiwen Wang
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, Henan Normal University, Xinxiang, China.,Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Henan Normal University, Xinxiang, China.,College of Life Sciences, Henan Normal University, Xinxiang, China.,Institute of Biomedical Science, Henan Normal University, Xinxiang, China.,Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), Henan Normal University, Xinxiang, China
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11
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ZNF143 Suppresses Cell Apoptosis and Promotes Proliferation in Gastric Cancer via ROS/p53 Axis. DISEASE MARKERS 2020; 2020:5863178. [PMID: 32076462 PMCID: PMC7017572 DOI: 10.1155/2020/5863178] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022]
Abstract
Aim This study was aimed at identifying the role of zinc finger protein 143 (ZNF143) in gastric cancer (GC) progression. Methods The impact of ZNF143 on the proliferation ability and apoptosis of GC cells was detected. The expression of ZNF143 and related targeted genes was determined using Western blot analysis. The reactive oxygen species (ROS) level of GC cells was examined using the ROS generation assay. The role of ZNF143 in the proliferation of GC cells in vivo was examined using tumor xenograft assay. Results The ectopic overexpression of ZNF143 promoted the proliferation of GC cells, while its knockdown reduced the effect in vitro. The downregulation of ZNF143 facilitated cell apoptosis. ZNF143 decreased the ROS level in GC cells, resulting in the reduction of cell apoptosis. Transfection with p53 reversed the antiapoptotic effect of ZNF143, while pifithrin-α, a specific inhibitor of p53, reduced the apoptosis in ZNF143-knockdown GC cells. However, p53 had no influence on the ROS level in GC cells. p53 played a key role in inhibiting ROS generation in GC cells, thereby inhibiting apoptosis. The transplanted tumor weight and volume were higher in the ZNF143-overexpressed group than in the ZNF143-knockdown group in vivo was examined using tumor xenograft assay. Conclusion ZNF143, as a tumor oncogene, promoted the proliferation of GC cells both in vitro and in vivo, indicating that ZNF143 might function as a novel target for GC therapy.in vitro. The downregulation of ZNF143 facilitated cell apoptosis. ZNF143 decreased the ROS level in GC cells, resulting in the reduction of cell apoptosis. Transfection with p53 reversed the antiapoptotic effect of ZNF143, while pifithrin-in vivo was examined using tumor xenograft assay.
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12
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Wen Z, Huang ZT, Zhang R, Peng C. ZNF143 is a regulator of chromatin loop. Cell Biol Toxicol 2018; 34:471-478. [PMID: 30120652 DOI: 10.1007/s10565-018-9443-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/08/2018] [Indexed: 11/30/2022]
Abstract
It is known that transcription factor ZNF143 frequently co-binds with CTCF-Cohesin complex in the anchor regions of chromatin loops. However, there is currently no genome-wide experiment to explore the functional roles of ZNF143 in chromatin loops. In this work, we used both computational and experimental analyses to investigate the regulatory effect of ZNF143 on chromatin loops. By jointly analyzing the ZNF143 and CTCF motifs underlying the isolated ZNF143-binding sites, ZNF143-CTCF co-binding sites and ZNF143-CTCF-RAD21 co-binding sites, our result shows that the ZNF143-CTCF-RAD21 co-binding sites are enriched with CTCF motifs but depleted of Znf143 motifs, implying that the CTCF but not ZNF143 may directly binds to the genome and thus ZNF143 may act as a cofactor instead of pioneer factor of ZNF143-CTCF-Cohesin complex. To explore the regulatory effect of ZNF143 on chromatin loops, we conducted siRNA experiment to knock down the expression level of ZNF143 in HEK293T cell line, and then performed in situ Hi-C on the negative control and ZNF143-silenced HEK293T cells. Comparison shows that the majority of chromatin loops are lost or at least weakened in the ZNF143-silenced HEK293T cells. However, a small proportion of chromatin loops are gained or strengthened, indicating the complicated roles of ZNF143 reduction in regulating chromatin loops. To further validate the loop analyses, we thoroughly investigated the chromatin loop changes between negative control and ZNF143-silenced cells by using aggregate peak analysis. The calculation shows that the lost and gained chromatin loops do undergo loop strength changes after ZNF143 silencing. Altogether, our work shows that ZNF143 can regulate chromatin loops by acting as a cofactor of CTCF-Cohesin complex, and knocking down ZNF143 expression level mainly eliminates or destabilizes chromatin loops.
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Affiliation(s)
- Zi Wen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhi-Tao Huang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ran Zhang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Cheng Peng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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Aziz HA, Abdel-Salam ASG, Al-Obaide MAI, Alobydi HW, Al-Humaish S. Kynurenine 3-Monooxygenase Gene Associated With Nicotine Initiation and Addiction: Analysis of Novel Regulatory Features at 5' and 3'-Regions. Front Genet 2018; 9:198. [PMID: 29951083 PMCID: PMC6008986 DOI: 10.3389/fgene.2018.00198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/17/2018] [Indexed: 11/13/2022] Open
Abstract
Tobacco smoking is widespread behavior in Qatar and worldwide and is considered one of the major preventable causes of ill health and death. Nicotine is part of tobacco smoke that causes numerous health risks and is incredibly addictive; it binds to the α7 nicotinic acetylcholine receptor (α7nAChR) in the brain. Recent studies showed α7nAChR involvement in the initiation and addiction of smoking. Kynurenic acid (KA), a significant tryptophan metabolite, is an antagonist of α7nAChR. Inhibition of kynurenine 3-monooxygenase enzyme encoded by KMO enhances the KA levels. Modulating KMO gene expression could be a useful tactic for the treatment of tobacco initiation and dependence. Since KMO regulation is still poorly understood, we aimed to investigate the 5' and 3'-regulatory factors of KMO gene to advance our knowledge to modulate KMO gene expression. In this study, bioinformatics methods were used to identify the regulatory sequences associated with expression of KMO. The displayed differential expression of KMO mRNA in the same tissue and different tissues suggested the specific usage of the KMO multiple alternative promoters. Eleven KMO alternative promoters identified at 5'-regulatory region contain TATA-Box, lack CpG Island (CGI) and showed dinucleotide base-stacking energy values specific to transcription factor binding sites (TFBSs). The structural features of regulatory sequences can influence the transcription process and cell type-specific expression. The uncharacterized LOC105373233 locus coding for non-coding RNA (ncRNA) located on the reverse strand in a convergent manner at the 3'-side of KMO locus. The two genes likely expressed by a promoter that lacks TATA-Box harbor CGI and two TFBSs linked to the bidirectional transcription, the NRF1, and ZNF14 motifs. We identified two types of microRNA (miR) in the uncharacterized LOC105373233 ncRNA, which are like hsa-miR-5096 and hsa-miR-1285-3p and can target the miR recognition element (MRE) in the KMO mRNA. Pairwise sequence alignment identified 52 nucleotides sequence hosting MRE in the KMO 3' UTR untranslated region complementary to the ncRNA LOC105373233 sequence. We speculate that the identified miRs can modulate the KMO expression and together with alternative promoters at the 5'-regulatory region of KMO might contribute to the development of novel diagnostic and therapeutic algorithm for tobacco smoking.
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Affiliation(s)
- Hassan A Aziz
- College of Arts and Sciences, Qatar University, Doha, Qatar
| | | | - Mohammed A I Al-Obaide
- School of Medicine, Texas Tech University Health Sciences Center, Amarillo, TX, United States
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14
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Sniezewski L, Janik S, Laszkiewicz A, Majkowski M, Kisielow P, Cebrat M. The evolutionary conservation of the bidirectional activity of the NWC gene promoter in jawed vertebrates and the domestication of the RAG transposon. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 81:105-115. [PMID: 29175053 DOI: 10.1016/j.dci.2017.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 06/07/2023]
Abstract
The RAG-1 and RAG-2 genes form a recombinase complex that is indispensable for V(D)J recombination, which generates the diversity of immunoglobulins and T-cell receptors. It is widely accepted that the presence of RAGs in the genomes of jawed vertebrates and other lineages is a result of the horizontal transfer of a mobile genetic element. While a substantial amount of evidence has been gathered that clarifies the nature of the RAG transposon, far less attention has been paid to the genomic site of its integration in various host organisms. In all genomes of the jawed vertebrates that have been studied to date, the RAG genes are located in close proximity to the NWC gene. We have previously shown that the promoter of the murine NWC genes exhibits a bidirectional activity, which may have facilitated the integration and survival of the RAG transposon in the host genome. In this study, we characterise the promoters of the NWC homologues that are present in the representatives of other jawed vertebrates (H. sapiens, X. tropicalis and D. rerio). We show that the features that are characteristic for promoters as the hosts of a successful transposon integration (in terms of the arrangement, bidirectional and constitutive activity and the involvement of the Zfp143 transcription factor in the promoter regulation) are evolutionarily conserved, which indicates that the presence of RAG genes in jawed vertebrates is a direct result of a successful transposon integration into the NWC locus.
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Affiliation(s)
- Lukasz Sniezewski
- Laboratory of Molecular and Cellular Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Sylwia Janik
- Laboratory of Molecular and Cellular Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Agnieszka Laszkiewicz
- Laboratory of Molecular and Cellular Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Michal Majkowski
- Laboratory of Molecular and Cellular Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Pawel Kisielow
- Laboratory of Molecular and Cellular Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland; Laboratory of Tumor Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Malgorzata Cebrat
- Laboratory of Molecular and Cellular Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland.
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15
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Cabezas OR, Flanagan SE, Stanescu H, García-Martínez E, Caswell R, Lango-Allen H, Antón-Gamero M, Argente J, Bussell AM, Brandli A, Cheshire C, Crowne E, Dumitriu S, Drynda R, Hamilton-Shield JP, Hayes W, Hofherr A, Iancu D, Issler N, Jefferies C, Jones P, Johnson M, Kesselheim A, Klootwijk E, Koettgen M, Lewis W, Martos JM, Mozere M, Norman J, Patel V, Parrish A, Pérez-Cerdá C, Pozo J, Rahman SA, Sebire N, Tekman M, Turnpenny PD, Hoff WV, Viering DHHM, Weedon MN, Wilson P, Guay-Woodford L, Kleta R, Hussain K, Ellard S, Bockenhauer D. Polycystic Kidney Disease with Hyperinsulinemic Hypoglycemia Caused by a Promoter Mutation in Phosphomannomutase 2. J Am Soc Nephrol 2017; 28:2529-2539. [PMID: 28373276 DOI: 10.1681/asn.2016121312] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/22/2017] [Indexed: 01/10/2023] Open
Abstract
Hyperinsulinemic hypoglycemia (HI) and congenital polycystic kidney disease (PKD) are rare, genetically heterogeneous disorders. The co-occurrence of these disorders (HIPKD) in 17 children from 11 unrelated families suggested an unrecognized genetic disorder. Whole-genome linkage analysis in five informative families identified a single significant locus on chromosome 16p13.2 (logarithm of odds score 6.5). Sequencing of the coding regions of all linked genes failed to identify biallelic mutations. Instead, we found in all patients a promoter mutation (c.-167G>T) in the phosphomannomutase 2 gene (PMM2), either homozygous or in trans with PMM2 coding mutations. PMM2 encodes a key enzyme in N-glycosylation. Abnormal glycosylation has been associated with PKD, and we found that deglycosylation in cultured pancreatic β cells altered insulin secretion. Recessive coding mutations in PMM2 cause congenital disorder of glycosylation type 1a (CDG1A), a devastating multisystem disorder with prominent neurologic involvement. Yet our patients did not exhibit the typical clinical or diagnostic features of CDG1A. In vitro, the PMM2 promoter mutation associated with decreased transcriptional activity in patient kidney cells and impaired binding of the transcription factor ZNF143. In silico analysis suggested an important role of ZNF143 for the formation of a chromatin loop including PMM2 We propose that the PMM2 promoter mutation alters tissue-specific chromatin loop formation, with consequent organ-specific deficiency of PMM2 leading to the restricted phenotype of HIPKD. Our findings extend the spectrum of genetic causes for both HI and PKD and provide insights into gene regulation and PMM2 pleiotropy.
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Affiliation(s)
- Oscar Rubio Cabezas
- Pediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Sarah E Flanagan
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Exeter, United Kingdom
| | - Horia Stanescu
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | | | - Richard Caswell
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Exeter, United Kingdom
| | - Hana Lango-Allen
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Exeter, United Kingdom
| | | | - Jesús Argente
- Pediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain.,Instituto de Investigación La Princesa, Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.,Madrid Institute for Advanced Studies on Food, Comité de Ética de la Investigación de la Universidad Autónoma de Madrid, and Centro Superior de Investigaciones Científicas, Carretera de Cantoblanco 8.28049, Madrid, Spain
| | - Anna-Marie Bussell
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Exeter, United Kingdom
| | - Andre Brandli
- Walter-Brendel-Center of Experimental Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Chris Cheshire
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Elizabeth Crowne
- University of Bristol and Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Simona Dumitriu
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Robert Drynda
- Diabetes Research Group, King's College, London, United Kingdom
| | | | - Wesley Hayes
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Alexis Hofherr
- Renal Division, Department of Medicine, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniela Iancu
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Naomi Issler
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Craig Jefferies
- Starship Children's Hospital, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Peter Jones
- Diabetes Research Group, King's College, London, United Kingdom
| | - Matthew Johnson
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Exeter, United Kingdom
| | - Anne Kesselheim
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Enriko Klootwijk
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Michael Koettgen
- Renal Division, Department of Medicine, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wendy Lewis
- East of Scotland Genetic Service, Dundee, United Kingdom
| | - José María Martos
- Pediatric Endocrinology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Monika Mozere
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Jill Norman
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Vaksha Patel
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Andrew Parrish
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Exeter, United Kingdom
| | - Celia Pérez-Cerdá
- Centro de Diagnóstico de Enfermedades Moleculares, Universidad Autónoma de Madrid, Center for Biomedical Research in Rare diseases, Instituto de Investigacion Hospital Universitario La Paz, Madrid, Spain
| | - Jesús Pozo
- Pediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Sofia A Rahman
- University College London Institute of Child Health, London, United Kingdom
| | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.,University College London Institute of Child Health, London, United Kingdom
| | - Mehmet Tekman
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Peter D Turnpenny
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - William Van't Hoff
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Daan H H M Viering
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | - Michael N Weedon
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Exeter, United Kingdom
| | - Patricia Wilson
- University College London Centre for Nephrology, University College London, London, United Kingdom
| | | | - Robert Kleta
- University College London Centre for Nephrology, University College London, London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.,University College London Institute of Child Health, London, United Kingdom
| | - Khalid Hussain
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.,Department of Pediatric Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Sian Ellard
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Exeter, United Kingdom
| | - Detlef Bockenhauer
- University College London Centre for Nephrology, University College London, London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.,University College London Institute of Child Health, London, United Kingdom
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16
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Genomic Determinants of THAP11/ZNF143/HCFC1 Complex Recruitment to Chromatin. Mol Cell Biol 2015; 35:4135-46. [PMID: 26416877 DOI: 10.1128/mcb.00477-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023] Open
Abstract
The THAP11 and ZNF143 transcription factors recognize overlapping DNA sequences and are reported to exhibit signs of both competitive and cooperative binding. HCFC1 serves as a scaffold protein, bridging interactions between transcription factors, including THAP11 and ZNF143, and transcriptional coregulators. The exact mechanism of how DNA sequences guide the recruitment of the THAP11/ZNF143/HCFC1 complex to chromatin is still controversial. In this study, we use chromosomally integrated synthetic constructs and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9-mediated approaches in intact cells to elucidate the role of the DNA sequence in the recruitment of this complex and to establish its biological relevance. We show that the ACTACA submotif, shared by both THAP11 and ZNF143, directs the recruitment of THAP11 and HCFC1 to ZNF143-occupied loci. Importantly, its position, spacing, and orientation relative to the ZNF143 core motif are critical for this action. CRISPR-Cas9-mediated alterations of the ACTACA submotif at endogenous promoters recapitulated results obtained with synthetic constructs and resulted in altered gene transcription and histone modifications at targeted promoters. Our in vivo approaches provide strong evidence for the molecular role of the ACTACA submotif in THAP11, ZNF143, and HCFC1 cooperative recruitment to chromatin and its biological role in target gene expression.
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17
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Orekhova AS, Rubtsov PM. Bidirectional promoters in the transcription of mammalian genomes. BIOCHEMISTRY (MOSCOW) 2014; 78:335-41. [PMID: 23590436 DOI: 10.1134/s0006297913040020] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the genomes of humans and other mammals a large number of closely spaced pairs of genes that are transcribed in opposite directions were revealed. Their transcription is directed by so-called bidirectional promoters. This review is devoted to the characteristics of bidirectional promoters and features of their structure. The composition of "core" promoter elements in conventional unidirectional and bidirectional promoters is compared. Data on binding sites of transcription factors that are primarily specific for bidirectional promoters are discussed. The examples of promoters that share protein-coding genes transcribed by RNA polymerase II and the non-coding RNA genes transcribed by RNA polymerase III are described. Data obtained from global transcriptome analysis about the existence of short noncoding antisense RNA associated with the promoters in the context of the hypothesis of bidirectional transcription initiation as an inherent property of eukaryotic promoters are discussed.
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Affiliation(s)
- A S Orekhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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18
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Yang G, Lu X, Yuan L. LncRNA: a link between RNA and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1097-109. [PMID: 25159663 DOI: 10.1016/j.bbagrm.2014.08.012] [Citation(s) in RCA: 789] [Impact Index Per Article: 78.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/04/2014] [Accepted: 08/18/2014] [Indexed: 12/19/2022]
Abstract
Unraveling the gene expression networks governing cancer initiation and development is essential while remains largely uncompleted. With the innovations in RNA-seq technologies and computational biology, long noncoding RNAs (lncRNAs) are being identified and characterized at a rapid pace. Recent findings reveal that lncRNAs are implicated in serial steps of cancer development. These lncRNAs interact with DNA, RNA, protein molecules and/or their combinations, acting as an essential regulator in chromatin organization, and transcriptional and post-transcriptional regulation. Their misexpression confers the cancer cell capacities for tumor initiation, growth, and metastasis. The review here will emphasize their aberrant expression and function in cancer, and the roles in cancer diagnosis and therapy will be also discussed.
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Affiliation(s)
- Guodong Yang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an 710032, PR China.
| | - Xiaozhao Lu
- Department of Nephrology, 323 Hospital of PLA, Xi'an 710054, PR China
| | - Lijun Yuan
- Department of Ultrasound, Tangdu Hospital, The Fourth Military Medical University, Xi'an 710038, PR China.
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19
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Liu S, Yan B, Lai W, Chen L, Xiao D, Xi S, Jiang Y, Dong X, An J, Chen X, Cao Y, Tao Y. As a novel p53 direct target, bidirectional gene HspB2/αB-crystallin regulates the ROS level and Warburg effect. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:592-603. [PMID: 24859470 DOI: 10.1016/j.bbagrm.2014.05.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 05/13/2014] [Accepted: 05/15/2014] [Indexed: 02/02/2023]
Abstract
Many mammalian genes are composed of bidirectional gene pairs with the two genes separated by less than 1.0kb. The transcriptional regulation and function of these bidirectional genes remain largely unclear. Here, we report that bidirectional gene pair HspB2/αB-crystallin, both of which are members of the small heat shock protein gene family, is a novel direct target gene of p53. Two potential binding sites of p53 are present in the intergenic region of HspB2/αB-crystallin. p53 up-regulated the bidirectional promoter activities of HspB2/αB-crystallin. Actinomycin D (ActD), an activator of p53, induces the promoter and protein activities of HspB2/αB-crystallin. p53 binds to two p53 binding sites in the intergenic region of HspB2/αB-crystallin in vitro and in vivo. Moreover, the products of bidirectional gene pair HspB2/αB-crystallin regulate glucose metabolism, intracellular reactive oxygen species (ROS) level and the Warburg effect by affecting metabolic genes, including the synthesis of cytochrome c oxidase 2 (SCO2), hexokinase II (HK2), and TP53-induced glycolysis and apoptosis regulator (TIGAR). The ROS level and the Warburg effect are affected after the depletion of p53, HspB2 and αB-crystallin respectively. Finally, we show that both HspB2 and αB-crystallin are linked with human renal carcinogenesis. These findings provide novel insights into the role of p53 as a regulator of bidirectional gene pair HspB2/αB-crystallin-mediated ROS and the Warburg effect.
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Affiliation(s)
- Shuang Liu
- Center for Medicine Research, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Cancer Research Institute, Central South University, Changsha, Hunan 410078, China; Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bin Yan
- Cancer Research Institute, Central South University, Changsha, Hunan 410078, China; Center for Molecular Imaging, Central South University, Changsha, Hunan 410078, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan 410078, China; Key Laboratory of Carcinogenesis, Ministry of Health, Hunan 410078, China
| | - Weiwei Lai
- Cancer Research Institute, Central South University, Changsha, Hunan 410078, China; Center for Molecular Imaging, Central South University, Changsha, Hunan 410078, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan 410078, China; Key Laboratory of Carcinogenesis, Ministry of Health, Hunan 410078, China
| | - Ling Chen
- Cancer Research Institute, Central South University, Changsha, Hunan 410078, China; Center for Molecular Imaging, Central South University, Changsha, Hunan 410078, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan 410078, China; Key Laboratory of Carcinogenesis, Ministry of Health, Hunan 410078, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China
| | - Sichuan Xi
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892 USA
| | - Yiqun Jiang
- Cancer Research Institute, Central South University, Changsha, Hunan 410078, China; Center for Molecular Imaging, Central South University, Changsha, Hunan 410078, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan 410078, China; Key Laboratory of Carcinogenesis, Ministry of Health, Hunan 410078, China
| | - Xin Dong
- Cancer Research Institute, Central South University, Changsha, Hunan 410078, China; Center for Molecular Imaging, Central South University, Changsha, Hunan 410078, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan 410078, China; Key Laboratory of Carcinogenesis, Ministry of Health, Hunan 410078, China
| | - Jing An
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 4010078, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ya Cao
- Cancer Research Institute, Central South University, Changsha, Hunan 410078, China; Center for Molecular Imaging, Central South University, Changsha, Hunan 410078, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan 410078, China; Key Laboratory of Carcinogenesis, Ministry of Health, Hunan 410078, China
| | - Yongguang Tao
- Cancer Research Institute, Central South University, Changsha, Hunan 410078, China; Center for Molecular Imaging, Central South University, Changsha, Hunan 410078, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan 410078, China; Key Laboratory of Carcinogenesis, Ministry of Health, Hunan 410078, China.
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Ngondo RP, Carbon P. Transcription factor abundance controlled by an auto-regulatory mechanism involving a transcription start site switch. Nucleic Acids Res 2014; 42:2171-84. [PMID: 24234445 PMCID: PMC3936768 DOI: 10.1093/nar/gkt1136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/09/2013] [Accepted: 10/24/2013] [Indexed: 02/01/2023] Open
Abstract
A transcriptional feedback loop is the simplest and most direct means for a transcription factor to provide an increased stability of gene expression. In this work performed in human cells, we reveal a new negative auto-regulatory mechanism involving an alternative transcription start site (TSS) usage. Using the activating transcription factor ZNF143 as a model, we show that the ZNF143 low-affinity binding sites, located downstream of its canonical TSS, play the role of protein sensors to induce the up- or down-regulation of ZNF143 gene expression. We uncovered that the TSS switch that mediates this regulation implies the differential expression of two transcripts with an opposite protein production ability due to their different 5' untranslated regions. Moreover, our analysis of the ENCODE data suggests that this mechanism could be used by other transcription factors to rapidly respond to their own aberrant expression level.
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Affiliation(s)
- Richard Patryk Ngondo
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Philippe Carbon
- Architecture et Réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 Rue René Descartes, 67084 Strasbourg, France
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21
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Dhadi SR, Deshpande A, Driscoll K, Ramakrishna W. Major cis-regulatory elements for rice bidirectional promoter activity reside in the 5'-untranslated regions. Gene 2013; 526:400-10. [PMID: 23756196 DOI: 10.1016/j.gene.2013.05.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
Abstract
Bidirectional promoters are defined as those that regulate adjacent genes organized in a divergent fashion (head to head orientation) and separated by <1 kb. In order to dissect bidirectional promoter activity in a model plant, deletion analysis was performed for seven rice promoters using promoter-reporter gene constructs, which identified three promoters to be bidirectional. Regulatory elements located in or close to the 5'-untranslated regions (UTR) of one of the genes (divergent gene pair) were found to be responsible for their bidirectional activity. DNA footprinting analysis identified unique protein binding sites in these promoters. Deletion/alteration of these motifs resulted in significant loss of expression of the reporter genes on either side of the promoter. Changes in the motifs at both the positions resulted in a remarkable decrease in bidirectional activity of the reporter genes flanking the promoter. Based on our results, we propose a novel mechanism for the bidirectionality of rice bidirectional promoters.
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Affiliation(s)
- Surendar Reddy Dhadi
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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22
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Ding J, Chen FY, Ren SY, Qiao K, Chen B, Wang KJ. Molecular characterization and promoter analysis of crustacean heat shock protein 10 in Scylla paramemosain. Genome 2013; 56:273-81. [PMID: 23789995 DOI: 10.1139/gen-2013-0002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Heat shock proteins (Hsps) are an evolutionarily conserved group of molecules present in all eukaryotic and prokaryotic organisms. Hsp10 and Hsp60 were originally described as the essential mitochondrial proteins involved in protein folding. Recent studies demonstrate that Hsp10 has additional roles including immune modulation. In our study, an homologous Hsp10 (Sp-Hsp10) was identified in the mud crab Scylla paramemosain, and its genomic DNA organization was determined. The cDNA sequence of Sp-Hsp10 contains an open reading frame of 309 bp, encoding a putative protein of 102 amino acid residues with approximately 10 kDa. The Sp-Hsp10 gene is located next to the Sp-Hsp60 gene and shares a 1916-bp intergenic region. The promoter activity of the Sp-Hsp10 flanking gene was analyzed using luciferase reporter assays in transfected endothelial progenitor cells. The upregulation of Sp-Hsp10 expression was detected after exposure of hemocytes to a heat shock of 1 h at 37 °C compared with unstressed hemocytes raised at 20 °C. To our knowledge, this is the first report characterizing the genomic organization of a new Hsp10 in a crustacean.
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Affiliation(s)
- Jian Ding
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, P.R. China
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23
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Michaud J, Praz V, James Faresse N, Jnbaptiste CK, Tyagi S, Schütz F, Herr W. HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy. Genome Res 2013; 23:907-16. [PMID: 23539139 PMCID: PMC3668359 DOI: 10.1101/gr.150078.112] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In human transcriptional regulation, DNA-sequence-specific factors can associate with intermediaries that orchestrate interactions with a diverse set of chromatin-modifying enzymes. One such intermediary is HCFC1 (also known as HCF-1). HCFC1, first identified in herpes simplex virus transcription, has a poorly defined role in cellular transcriptional regulation. We show here that, in HeLa cells, HCFC1 is observed bound to 5400 generally active CpG-island promoters. Examination of the DNA sequences underlying the HCFC1-binding sites revealed three sequence motifs associated with the binding of (1) ZNF143 and THAP11 (also known as Ronin), (2) GABP, and (3) YY1 sequence-specific transcription factors. Subsequent analysis revealed colocalization of HCFC1 with these four transcription factors at ∼90% of the 5400 HCFC1-bound promoters. These studies suggest that a relatively small number of transcription factors play a major role in HeLa-cell transcriptional regulation in association with HCFC1.
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Affiliation(s)
- Joëlle Michaud
- Center for Integrative Genomics, University of Lausanne, Génopode, 1015 Lausanne, Switzerland
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24
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Bidirectional promoters as important drivers for the emergence of species-specific transcripts. PLoS One 2013; 8:e57323. [PMID: 23460838 PMCID: PMC3583895 DOI: 10.1371/journal.pone.0057323] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 01/21/2013] [Indexed: 11/23/2022] Open
Abstract
The diversification of gene functions has been largely attributed to the process of gene duplication. Novel examples of genes originating from previously untranscribed regions have been recently described without regard to a unifying functional mechanism for their emergence. Here we propose a model mechanism that could generate a large number of lineage-specific novel transcripts in vertebrates through the activation of bidirectional transcription from unidirectional promoters. We examined this model in silico using human transcriptomic and genomic data and identified evidence consistent with the emergence of more than 1,000 primate-specific transcripts. These are transcripts with low coding potential and virtually no functional annotation. They initiate at less than 1 kb upstream of an oppositely transcribed conserved protein coding gene, in agreement with the generally accepted definition of bidirectional promoters. We found that the genomic regions upstream of ancestral promoters, where the novel transcripts in our dataset reside, are characterized by preferential accumulation of transposable elements. This enhances the sequence diversity of regions located upstream of ancestral promoters, further highlighting their evolutionary importance for the emergence of transcriptional novelties. By applying a newly developed test for positive selection to transposable element-derived fragments in our set of novel transcripts, we found evidence of adaptive evolution in the human lineage in nearly 3% of the novel transcripts in our dataset. These findings indicate that at least some novel transcripts could become functionally relevant, and thus highlight the evolutionary importance of promoters, through their capacity for bidirectional transcription, for the emergence of novel genes.
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25
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Ngondo-Mbongo RP, Myslinski E, Aster JC, Carbon P. Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11. Nucleic Acids Res 2013; 41:4000-14. [PMID: 23408857 PMCID: PMC3627581 DOI: 10.1093/nar/gkt088] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
ZNF143 is a zinc-finger protein involved in the transcriptional regulation of both coding and non-coding genes from polymerase II and III promoters. Our study deciphers the genome-wide regulatory role of ZNF143 in relation with the two previously unrelated transcription factors Notch1/ICN1 and thanatos-associated protein 11 (THAP11) in several human and murine cells. We show that two distinct motifs, SBS1 and SBS2, are associated to ZNF143-binding events in promoters of >3000 genes. Without co-occupation, these sites are also bound by Notch1/ICN1 in T-lymphoblastic leukaemia cells as well as by THAP11, a factor involved in self-renewal of embryonic stem cells. We present evidence that ICN1 binding overlaps with ZNF143 binding events at the SBS1 and SBS2 motifs, whereas the overlap occurs only at SBS2 for THAP11. We demonstrate that the three factors modulate expression of common target genes through the mutually exclusive occupation of overlapping binding sites. The model we propose predicts that the binding competition between the three factors controls biological processes such as rapid cell growth of both neoplastic and stem cells. Overall, our study establishes a novel relationship between ZNF143, THAP11 and ICN1 and reveals important insights into ZNF143-mediated gene regulation.
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Affiliation(s)
- Richard Patryk Ngondo-Mbongo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg, France
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26
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Uchiumi F, Fujikawa M, Miyazaki S, Tanuma SI. Implication of bidirectional promoters containing duplicated GGAA motifs of mitochondrial function-associated genes. AIMS MOLECULAR SCIENCE 2013. [DOI: 10.3934/molsci.2013.1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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27
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Didych DA, Shamsutdinov MF, Smirnov NA, Akopov SB, Monastyrskaya GS, Uspenskaya NY, Nikolaev LG, Sverdlov ED. Human PSENEN and U2AF1L4 genes are concertedly regulated by a genuine bidirectional promoter. Gene 2012; 515:34-41. [PMID: 23246698 DOI: 10.1016/j.gene.2012.11.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/31/2012] [Accepted: 11/29/2012] [Indexed: 11/16/2022]
Abstract
Head-to-head genes with a short distance between their transcription start sites may constitute up to 10% of all genes in the genomes of various species. It was hypothesized that this intergenic space may represent bidirectional promoters which are able to initiate transcription of both genes, but the true bidirectionality was proved only for a few of them. We present experimental evidence that, according to several criteria, a 269 bp region located between the PSENEN and U2AF1L4 human genes is a genuine bidirectional promoter regulating a concerted divergent transcription of these genes. Concerted transcription of PSENEN and U2AF1L4 can be necessary for regulation of T-cell activity.
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Affiliation(s)
- D A Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
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28
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James Faresse N, Canella D, Praz V, Michaud J, Romascano D, Hernandez N. Genomic study of RNA polymerase II and III SNAPc-bound promoters reveals a gene transcribed by both enzymes and a broad use of common activators. PLoS Genet 2012; 8:e1003028. [PMID: 23166507 PMCID: PMC3499247 DOI: 10.1371/journal.pgen.1003028] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 08/24/2012] [Indexed: 12/23/2022] Open
Abstract
SNAPc is one of a few basal transcription factors used by both RNA polymerase (pol) II and pol III. To define the set of active SNAPc-dependent promoters in human cells, we have localized genome-wide four SNAPc subunits, GTF2B (TFIIB), BRF2, pol II, and pol III. Among some seventy loci occupied by SNAPc and other factors, including pol II snRNA genes, pol III genes with type 3 promoters, and a few un-annotated loci, most are primarily occupied by either pol II and GTF2B, or pol III and BRF2. A notable exception is the RPPH1 gene, which is occupied by significant amounts of both polymerases. We show that the large majority of SNAPc-dependent promoters recruit POU2F1 and/or ZNF143 on their enhancer region, and a subset also recruits GABP, a factor newly implicated in SNAPc-dependent transcription. These activators associate with pol II and III promoters in G1 slightly before the polymerase, and ZNF143 is required for efficient transcription initiation complex assembly. The results characterize a set of genes with unique properties and establish that polymerase specificity is not absolute in vivo. SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other, even though some of them recruit RNA polymerase II and others RNA polymerase III. We have examined all SNAPc-bound promoters present in the human genome. We find a surprisingly small number of them, some 70 promoters. Among these, the large majority is bound by either RNA polymerase II or RNA polymerase III, as expected, but one gene hitherto considered an RNA polymerase III gene is also occupied by significant levels of RNA polymerase II. Both RNA polymerase II and RNA polymerase III SNAPc-dependent promoters use a largely overlapping set of a few transcription activators, including GABP, a novel factor implicated in snRNA gene transcription.
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Affiliation(s)
- Nicole James Faresse
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Donatella Canella
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Viviane Praz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joëlle Michaud
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - David Romascano
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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29
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Laszkiewicz A, Sniezewski L, Kasztura M, Bzdzion L, Cebrat M, Kisielow P. Bidirectional activity of the NWC promoter is responsible for RAG-2 transcription in non-lymphoid cells. PLoS One 2012; 7:e44807. [PMID: 22984564 PMCID: PMC3439442 DOI: 10.1371/journal.pone.0044807] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 08/14/2012] [Indexed: 11/18/2022] Open
Abstract
The recombination-activating genes (RAG-1 and RAG-2) encode a V(D)J recombinase responsible for rearrangements of antigen-receptor genes during T and B cell development, and RAG expression is known to correlate strictly with the process of rearrangement. In contrast to RAG-1, the expression of RAG-2 was not previously detected during any other stage of lymphopoiesis or in any other normal tissue. Here we report that the CpG island-associated promoter of the NWC gene (the third evolutionarily conserved gene in the RAG locus), which is located in the second intron of RAG-2, has bidirectional activity and is responsible for the detectable transcription of RAG-2 in some non-lymphoid tissues. We also identify evolutionarily conserved promoter fragments responsible for this bidirectional activity, and show that it is activated by transcription factor ZFP143. The possible implications of our findings are briefly discussed.
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Affiliation(s)
- Agnieszka Laszkiewicz
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Lukasz Sniezewski
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Monika Kasztura
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Lukasz Bzdzion
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Malgorzata Cebrat
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
- * E-mail:
| | - Pawel Kisielow
- Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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30
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Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci 2012; 13:528-41. [PMID: 22814587 DOI: 10.1038/nrn3234] [Citation(s) in RCA: 420] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel classes of small and long non-coding RNAs (ncRNAs) are being characterized at a rapid pace, driven by recent paradigm shifts in our understanding of genomic architecture, regulation and transcriptional output, as well as by innovations in sequencing technologies and computational and systems biology. These ncRNAs can interact with DNA, RNA and protein molecules; engage in diverse structural, functional and regulatory activities; and have roles in nuclear organization and transcriptional, post-transcriptional and epigenetic processes. This expanding inventory of ncRNAs is implicated in mediating a broad spectrum of processes including brain evolution, development, synaptic plasticity and disease pathogenesis.
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31
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Wakano C, Byun JS, Di LJ, Gardner K. The dual lives of bidirectional promoters. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1819:688-93. [PMID: 22366276 PMCID: PMC3371153 DOI: 10.1016/j.bbagrm.2012.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 02/06/2012] [Accepted: 02/09/2012] [Indexed: 12/12/2022]
Abstract
The sequencing of the human genome led to many insights into gene organization and structure. One interesting observation was the high frequency of bidirectional promoters characterized by two protein encoding genes whose promoters are arranged in a divergent or "head-to-head" configuration with less than 2000 base pairs of intervening sequence. Computational estimates published by various groups indicate that nearly 10% of the coding gene promoters are arranged in such a manner and the extent of this bias is a unique feature of mammalian genomes. Moreover, as a class, head-to-head promoters appear to be enriched in specific categories of gene function. Here we review the structure, composition, genomic properties and functional classifications of genes controlled by bidirectional promoters and explore the biological implication of these features. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Clay Wakano
- Genetics Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Jung S. Byun
- Genetics Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Li-Jun Di
- Genetics Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Kevin Gardner
- Genetics Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland 20892, USA
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32
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Lalevée S, Anno YN, Chatagnon A, Samarut E, Poch O, Laudet V, Benoit G, Lecompte O, Rochette-Egly C. Genome-wide in silico identification of new conserved and functional retinoic acid receptor response elements (direct repeats separated by 5 bp). J Biol Chem 2011; 286:33322-34. [PMID: 21803772 PMCID: PMC3190930 DOI: 10.1074/jbc.m111.263681] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Revised: 07/28/2011] [Indexed: 11/06/2022] Open
Abstract
The nuclear retinoic acid receptors interact with specific retinoic acid (RA) response elements (RAREs) located in the promoters of target genes to orchestrate transcriptional networks involved in cell growth and differentiation. Here we describe a genome-wide in silico analysis of consensus DR5 RAREs based on the recurrent RGKTSA motifs. More than 15,000 DR5 RAREs were identified and analyzed for their localization and conservation in vertebrates. We selected 138 elements located ±10 kb from transcription start sites and gene ends and conserved across more than 6 species. We also validated the functionality of these RAREs by analyzing their ability to bind retinoic acid receptors (ChIP sequencing experiments) as well as the RA regulation of the corresponding genes (RNA sequencing and quantitative real time PCR experiments). Such a strategy provided a global set of high confidence RAREs expanding the known experimentally validated RAREs repertoire associated to a series of new genes involved in cell signaling, development, and tumor suppression. Finally, the present work provides a valuable knowledge base for the analysis of a wider range of RA-target genes in different species.
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Affiliation(s)
- Sébastien Lalevée
- From the Department of Functional Genomics and Cancer and
- CNRS UMR5534, F-69622 Villeurbanne
| | - Yannick N. Anno
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596 and CNRS UMR7104, Université de Strasbourg, F_67404 Illkirch Cedex
| | - Amandine Chatagnon
- CNRS UMR5534, F-69622 Villeurbanne
- Université Lyon 1, UMR5534, F-69622 Villeurbanne, and
| | - Eric Samarut
- From the Department of Functional Genomics and Cancer and
| | - Olivier Poch
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596 and CNRS UMR7104, Université de Strasbourg, F_67404 Illkirch Cedex
| | - Vincent Laudet
- Institut de Génomique Fonctionelle de Lyon, UMR 5242, Institut National de la Recherche Agronomique, Université de Lyon, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France
| | - Gerard Benoit
- CNRS UMR5534, F-69622 Villeurbanne
- Université Lyon 1, UMR5534, F-69622 Villeurbanne, and
| | - Odile Lecompte
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U596 and CNRS UMR7104, Université de Strasbourg, F_67404 Illkirch Cedex
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33
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Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proc Natl Acad Sci U S A 2011; 108:14908-13. [PMID: 21737748 DOI: 10.1073/pnas.1109023108] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Notch1 regulates gene expression by associating with the DNA-binding factor RBPJ and is oncogenic in murine and human T-cell progenitors. Using ChIP-Seq, we find that in human and murine T-lymphoblastic leukemia (TLL) genomes Notch1 binds preferentially to promoters, to RBPJ binding sites, and near imputed ZNF143, ETS, and RUNX sites. ChIP-Seq confirmed that ZNF143 binds to ∼40% of Notch1 sites. Notch1/ZNF143 sites are characterized by high Notch1 and ZNF143 signals, frequent cobinding of RBPJ (generally through sites embedded within ZNF143 motifs), strong promoter bias, and relatively low mean levels of activating chromatin marks. RBPJ and ZNF143 binding to DNA is mutually exclusive in vitro, suggesting RBPJ/Notch1 and ZNF143 complexes exchange on these sites in cells. K-means clustering of Notch1 binding sites and associated motifs identified conserved Notch1-RUNX, Notch1-ETS, Notch1-RBPJ, Notch1-ZNF143, and Notch1-ZNF143-ETS clusters with different genomic distributions and levels of chromatin marks. Although Notch1 binds mainly to gene promoters, ∼75% of direct target genes lack promoter binding and are presumably regulated by enhancers, which were identified near MYC, DTX1, IGF1R, IL7R, and the GIMAP cluster. Human and murine TLL genomes also have many sites that bind only RBPJ. Murine RBPJ-only sites are highly enriched for imputed REST (a DNA-binding transcriptional repressor) sites, whereas human RPBJ-only sites lack REST motifs and are more highly enriched for imputed CREB sites. Thus, there is a conserved network of cis-regulatory factors that interacts with Notch1 to regulate gene expression in TLL cells, as well as unique classes of divergent RBPJ-only sites that also likely regulate transcription.
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