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Karagiannis D, Wu W, Li A, Hayashi M, Chen X, Yip M, Mangipudy V, Xu X, Sánchez-Rivera FJ, Soto-Feliciano YM, Ye J, Papagiannakopoulos T, Lu C. Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors. Cell Rep 2024; 43:113629. [PMID: 38165806 PMCID: PMC10853943 DOI: 10.1016/j.celrep.2023.113629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/27/2023] [Accepted: 12/12/2023] [Indexed: 01/04/2024] Open
Abstract
The interplay between metabolism and chromatin signaling is implicated in cancer progression. However, whether and how metabolic reprogramming in tumors generates chromatin vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor aberrant activation of the NRF2 antioxidant pathway, which drives aggressive and chemo-resistant disease. Using a chromatin-focused CRISPR screen, we report that NRF2 activation sensitizes LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDACs). This association is observed across cultured cells, mouse models, and patient-derived xenografts. Integrative epigenomic, transcriptomic, and metabolomic analysis demonstrates that HDAC inhibition causes widespread redistribution of H4ac and its reader protein, which transcriptionally downregulates metabolic enzymes. This results in reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest NRF2 activation as a potential biomarker for effective repurposing of HDAC inhibitors to treat solid tumors.
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Affiliation(s)
- Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Warren Wu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Albert Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Makiko Hayashi
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michaela Yip
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vaibhav Mangipudy
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xinjing Xu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Francisco J Sánchez-Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Yadira M Soto-Feliciano
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thales Papagiannakopoulos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Karagiannis D, Wu W, Li A, Hayashi M, Chen X, Yip M, Mangipudy V, Xu X, Sánchez-Rivera FJ, Soto-Feliciano YM, Ye J, Papagiannakopoulos T, Lu C. Metabolic Reprogramming by Histone Deacetylase Inhibition Selectively Targets NRF2-activated tumors. bioRxiv 2023:2023.04.24.538118. [PMID: 37162970 PMCID: PMC10168258 DOI: 10.1101/2023.04.24.538118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Interplay between metabolism and chromatin signaling have been implicated in cancer initiation and progression. However, whether and how metabolic reprogramming in tumors generates specific epigenetic vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor mutations that cause aberrant activation of the NRF2 antioxidant pathway and drive aggressive and chemo-resistant disease. We performed a chromatin-focused CRISPR screen and report that NRF2 activation sensitized LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDAC). This association was consistently observed across cultured cells, syngeneic mouse models and patient-derived xenografts. HDAC inhibition causes widespread increases in histone H4 acetylation (H4ac) at intergenic regions, but also drives re-targeting of H4ac reader protein BRD4 away from promoters with high H4ac levels and transcriptional downregulation of corresponding genes. Integrative epigenomic, transcriptomic and metabolomic analysis demonstrates that these chromatin changes are associated with reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest that metabolic alterations such as NRF2 activation could serve as biomarkers for effective repurposing of HDAC inhibitors to treat solid tumors.
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Jiang H, Greathouse RL, Tiche SJ, Zhao M, He B, Li Y, Li AM, Forgo B, Yip M, Li A, Shih M, Banuelos S, Zhou MN, Gruber JJ, Rankin EB, Hu Z, Shimada H, Chiu B, Ye J. Mitochondrial Uncoupling Induces Epigenome Remodeling and Promotes Differentiation in Neuroblastoma. Cancer Res 2023; 83:181-194. [PMID: 36318118 PMCID: PMC9851961 DOI: 10.1158/0008-5472.can-22-1029] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/23/2022] [Accepted: 10/28/2022] [Indexed: 11/22/2022]
Abstract
The Warburg effect is the major metabolic hallmark of cancer. According to Warburg himself, the consequence of the Warburg effect is cell dedifferentiation. Therefore, reversing the Warburg effect might be an approach to restore cell differentiation in cancer. In this study, we used a mitochondrial uncoupler, niclosamide ethanolamine (NEN), to activate mitochondrial respiration, which induced neural differentiation in neuroblastoma cells. NEN treatment increased the NAD+/NADH and pyruvate/lactate ratios and also the α-ketoglutarate/2-hydroxyglutarate (2-HG) ratio. Consequently, NEN treatment induced promoter CpG island demethylation and epigenetic landscape remodeling, activating the neural differentiation program. In addition, NEN treatment upregulated p53 but downregulated N-Myc and β-catenin signaling in neuroblastoma cells. Importantly, even under hypoxia, NEN treatment remained effective in inhibiting 2-HG generation, promoting DNA demethylation, and suppressing hypoxia-inducible factor signaling. Dietary NEN intervention reduced tumor growth rate, 2-HG levels, and expression of N-Myc and β-catenin in tumors in an orthotopic neuroblastoma mouse model. Integrative analysis indicated that NEN treatment upregulated favorable prognosis genes and downregulated unfavorable prognosis genes, which were defined using multiple neuroblastoma patient datasets. Altogether, these results suggest that mitochondrial uncoupling is an effective metabolic and epigenetic therapy for reversing the Warburg effect and inducing differentiation in neuroblastoma. SIGNIFICANCE Targeting cancer metabolism using the mitochondrial uncoupler niclosamide ethanolamine leads to methylome reprogramming and differentiation in neuroblastoma, providing a therapeutic opportunity to reverse the Warburg effect and suppress tumor growth. See related commentary by Byrne and Bell, p.167.
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Affiliation(s)
- Haowen Jiang
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Rachel L. Greathouse
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah Jane Tiche
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Man Zhao
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Bo He
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Yang Li
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Albert M. Li
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA,Cancer Biology Program, Stanford University School of Medicine
| | - Balint Forgo
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michaela Yip
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Allison Li
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Moriah Shih
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Selene Banuelos
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Meng-Ning Zhou
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Joshua J. Gruber
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center. Dallas, TX 75235, USA
| | - Erinn B. Rankin
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA
| | - Zhen Hu
- Olivia Consulting Service, Redwood City, CA 94063, USA
| | - Hiroyuki Shimada
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Bill Chiu
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA,Stanford Cancer Institute, Stanford University School of Medicine. Stanford, CA 94305, US
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine. Stanford, CA 94305, USA,Cancer Biology Program, Stanford University School of Medicine,Stanford Cancer Institute, Stanford University School of Medicine. Stanford, CA 94305, US,Correspondence to: Jiangbin Ye (), CCSR-S, Rm.1245, 269 Campus Drive, Stanford, CA 94305, Tel: 650-724-7459
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Jiang H, Greathouse RL, Tiche SJ, Zhao M, He B, Li Y, Li AM, Forgo B, Yip M, Li A, Shih M, Banuelos S, Zhou MN, Gruber JJ, Rankin EB, Hu Z, Shimada H, Chiu B, Ye J. Correction: Mitochondrial Uncoupling Induces Epigenome Remodeling and Promotes Differentiation in Neuroblastoma. Cancer Res 2023; 83:346. [PMID: 36651077 DOI: 10.1158/0008-5472.can-22-3873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Li Y, Gruber JJ, Litzenburger UM, Zhou Y, Miao YR, LaGory EL, Li AM, Hu Z, Yip M, Hart LS, Maris JM, Chang HY, Giaccia AJ, Ye J. Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia. Cell Death Dis 2020; 11:102. [PMID: 32029721 PMCID: PMC7005271 DOI: 10.1038/s41419-020-2303-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
Abstract
Despite the fact that Otto H. Warburg discovered the Warburg effect almost one hundred years ago, why cancer cells waste most of the glucose carbon as lactate remains an enigma. Warburg proposed a connection between the Warburg effect and cell dedifferentiation. Hypoxia is a common tumor microenvironmental stress that induces the Warburg effect and blocks tumor cell differentiation. The underlying mechanism by which this occurs is poorly understood, and no effective therapeutic strategy has been developed to overcome this resistance to differentiation. Using a neuroblastoma differentiation model, we discovered that hypoxia repressed cell differentiation through reducing cellular acetyl-CoA levels, leading to reduction of global histone acetylation and chromatin accessibility. The metabolic switch triggering this global histone hypoacetylation was the induction of pyruvate dehydrogenase kinases (PDK1 and PDK3). Inhibition of PDKs using dichloroacetate (DCA) restored acetyl-CoA generation and histone acetylation under hypoxia. Knocking down PDK1 induced neuroblastoma cell differentiation, highlighting the critical role of PDK1 in cell fate control. Importantly, acetate or glycerol triacetate (GTA) supplementation restored differentiation markers expression and neuron differentiation under hypoxia. Moreover, ATAC-Seq analysis demonstrated that hypoxia treatment significantly reduced chromatin accessibility at RAR/RXR binding sites, which can be restored by acetate supplementation. In addition, hypoxia-induced histone hypermethylation by increasing 2-hydroxyglutarate (2HG) and reducing α-ketoglutarate (αKG). αKG supplementation reduced histone hypermethylation upon hypoxia, but did not restore histone acetylation or differentiation markers expression. Together, these findings suggest that diverting pyruvate flux away from acetyl-CoA generation to lactate production is the key mechanism that Warburg effect drives dedifferentiation and tumorigenesis. We propose that combining differentiation therapy with acetate/GTA supplementation might represent an effective therapy against neuroblastoma.
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Affiliation(s)
- Yang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joshua J Gruber
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ulrike M Litzenburger
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yiren Zhou
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yu Rebecca Miao
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Edward L LaGory
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Albert M Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhen Hu
- Olivia Consulting Service, Redwood City, CA, 94063, USA
| | - Michaela Yip
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lori S Hart
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA
| | - Amato J Giaccia
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Sadak T, Gaster B, Hirsh A, Ishado E, Yip M, Borson S. POTENTIALLY UN-AVOIDABLE HOSPITALIZATIONS IN DEMENTIA: AN INSIDE STORY. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- T Sadak
- University of Washington School of Nursing, Lynnwood, Washington, United States
| | - B Gaster
- University of Washington School of Medicine, Seattle, WA
| | - A Hirsh
- University of Washington School of Nursing, Seattle, WA
| | - E Ishado
- University of Washington School of Nursing, Seattle, WA
| | - M Yip
- University of Washington School of Nursing, Seattle, WA
| | - S Borson
- University of Washington School of Medicine, Seattle, WA
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Zhou Y, Sadak T, Ishado E, Yip M, Borson S. OPERATIONALIZING THE CONCEPT OF RESILIENCE FOR DEMENTIA CAREGIVING. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Y Zhou
- School of Social Work, University of Washington, Seattle, Washington, United States
| | - T Sadak
- University of Washington School of Nursing, Seattle, WA
| | - E Ishado
- University of Washington School of Nursing, Seattle, WA
| | - M Yip
- University of Washington School of Nursing, Seattle, WA
| | - S Borson
- University of Washington School of Medicine, Seattle, WA
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Littauer R, Sather J, Rothenberg C, Finn E, Yip M, Matouk C, Pham L, Sheth K, Ulrich A, Parwani Y, Venkatesh A. 57 Improving the Safety and Quality of Inter-Hospital Transfer for Nontraumatic Intracerebral and Subarachnoid Hemorrhage. Ann Emerg Med 2018. [DOI: 10.1016/j.annemergmed.2018.08.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abuzeid O, Yip M, Hebert J, Abuzeid M. Laparoscopy Is the Gold Standard for the Diagnosis of Subtle Fimbrial Pathology, Peritubal and Periovarian Adhesions. J Minim Invasive Gynecol 2016. [DOI: 10.1016/j.jmig.2016.08.780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Turner S, Yip M, Smith D, Weibel S, van Seggelen W, Foster A, Morey T, Barbati Z, Branch A, Fierer D. O22.2 Detection of hepatitis c virus (hcv) in semen from hiv-infected men who have sex with men (msm) during acute hcv infection. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Turner S, Yip M, Smith D, Weibel S, van Seggelen W, Foster A, Morey T, Barbati Z, Branch A, Fierer D. 007.3 Detection of hepatitis c virus (hcv) in semen from hiv-infected men who have sex with men (msm) during acute hcv infection. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Rashidnasab A, Elangovan P, Yip M, Diaz O, Dance DR, Young KC, Wells K. Simulation and assessment of realistic breast lesions using fractal growth models. Phys Med Biol 2013; 58:5613-27. [DOI: 10.1088/0031-9155/58/16/5613] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Yip M, Mackenzie A, Lewis E, Dance DR, Young KC, Christmas W, Wells K. Image resampling effects in mammographic image simulation. Phys Med Biol 2011; 56:N275-86. [DOI: 10.1088/0031-9155/56/22/n02] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Mestel R, Yip M, Holland JP, Wang E, Kang J, Holland MJ. Sequences within the spacer region of yeast rRNA cistrons that stimulate 35S rRNA synthesis in vivo mediate RNA polymerase I-dependent promoter and terminator activities. Mol Cell Biol 1989; 9:1243-54. [PMID: 2657388 PMCID: PMC362715 DOI: 10.1128/mcb.9.3.1243-1254.1989] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Sequences within the spacer region of yeast rRNA cistrons stimulate synthesis of the major 35S rRNA precursor in vivo 10- to 30-fold (E. A. Elion and J. R. Warner, Cell 39:663-673, 1984). Spacer sequences that mediate this stimulatory activity are located approximately 2.2 kilobases upstream from sequences that encode the 5' terminus of the 35S rRNA precursor. By utilizing a centromere-containing plasmid carrying a 35S rRNA minigene, a 160-base-pair region of spacer rDNA was identified by deletion mapping that is required for efficient stimulation of 35S rRNA synthesis in vivo. A 22-base-pair sequence, previously shown to support RNA polymerase I-dependent selective initiation of transcription in vitro, was located 15 base pairs upstream from the 3' boundary of the stimulatory region. A 77-base pair region of spacer DNA that mediates transcriptional terminator activity in vivo was identified immediately downstream from the 5' boundary of the stimulatory region. Deletion mutations extending downstream from the 5' boundary of the 160-base-pair stimulatory region simultaneously interfere with terminator activity and stimulation of 35S rRNA synthesis from the minigene. The terminator region supported termination of transcripts initiated by RNA polymerase I in vivo. The organization of sequences that support terminator and promoter activities within the 160-base-pair stimulatory region is similar to the organization of rDNA gene promoters in higher organisms. Possible mechanisms for spacer-sequence-dependent stimulation of yeast 35S rRNA synthesis in vivo are discussed.
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Affiliation(s)
- R Mestel
- Department of Biological Chemistry, School of Medicine, University of California, Davis 95616
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Swanson ME, Yip M, Holland MJ. Characterization of an RNA polymerase I-dependent promoter within the spacer region of yeast ribosomal cistrons. J Biol Chem 1985; 260:9905-15. [PMID: 2991269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nucleotide sequences which are required for RNA polymerase I-dependent selective initiation of transcription in vitro from a site within the spacer region of cloned yeast ribosomal DNA have been identified. Yeast rDNA templates containing deletion mutations extending from restriction endonuclease cleavage sites located upstream and downstream from the transcriptional initiation site were constructed. The ability of these mutant templates to support selective transcription in vitro was determined using a yeast whole cell extract. Nucleotide sequences which are required for selective transcription in vitro are within a 22-base pair region which is located immediately adjacent to the transcriptional initiation site. The 3' boundary of this 22-base pair sequence was mapped within a single base pair and resides within the transcribed portion of the rDNA. Nucleotide sequences upstream and downstream from the 22-base pair region are not required for selective transcription and do not appear to affect the efficiency of transcription in vitro. A hybrid plasmid containing only 32 base pairs of yeast rDNA, which includes the 22-base pair region, supports efficient and accurate RNA polymerase I-dependent transcription in vitro. These data demonstrate that the 22-base pair region of yeast rDNA is sufficient for accurate initiation of transcription in vitro. The transcriptional properties of several cloned rDNA templates isolated from two haploid yeast strains and a strain of bakers' yeast were examined. Four cistrons were identified which differ in nucleotide sequence. Three cistrons contain the 22-base pair promoter region and they support selective transcription in vitro. The fourth cistron does not support selective transcription in vitro and contains a single base pair substitution within the 22-base pair promoter sequence.
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Lee S, Yip M, Sacks HJ. Factor IX deficiency in liver disease. JAMA 1972; 221:1410 passim. [PMID: 5068563 DOI: 10.1001/jama.221.12.1410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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