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Nichols RV, O’Connell BL, Mulqueen RM, Thomas J, Woodfin AR, Acharya S, Mandel G, Pokholok D, Steemers FJ, Adey AC. High-throughput robust single-cell DNA methylation profiling with sciMETv2. Nat Commun 2022; 13:7627. [PMID: 36494343 PMCID: PMC9734657 DOI: 10.1038/s41467-022-35374-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a key epigenetic property that drives gene regulatory programs in development and disease. Current single-cell methods that produce high quality methylomes are expensive and low throughput without the aid of extensive automation. We previously described a proof-of-principle technique that enabled high cell throughput; however, it produced only low-coverage profiles and was a difficult protocol that required custom sequencing primers and recipes and frequently produced libraries with excessive adapter contamination. Here, we describe a greatly improved version that generates high-coverage profiles (~15-fold increase) using a robust protocol that does not require custom sequencing capabilities, includes multiple stopping points, and exhibits minimal adapter contamination. We demonstrate two versions of sciMETv2 on primary human cortex, a high coverage and rapid version, identifying distinct cell types using CH methylation patterns. These datasets are able to be directly integrated with one another as well as with existing snmC-seq2 datasets with little discernible bias. Finally, we demonstrate the ability to determine cell types using CG methylation alone, which is the dominant context for DNA methylation in most cell types other than neurons and the most applicable analysis outside of brain tissue.
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Affiliation(s)
- Ruth V. Nichols
- grid.5288.70000 0000 9758 5690Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Brendan L. O’Connell
- grid.5288.70000 0000 9758 5690Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Institute, Oregon Health & Science University, Portland, OR USA
| | - Ryan M. Mulqueen
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Institute, Oregon Health & Science University, Portland, OR USA
| | | | | | - Sonia Acharya
- grid.5288.70000 0000 9758 5690Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Gail Mandel
- grid.5288.70000 0000 9758 5690Vollum Institute for Neuroscience, Oregon Health & Science University, Portland, OR USA
| | | | | | - Andrew C. Adey
- grid.5288.70000 0000 9758 5690Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Institute, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR USA
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2
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Aoi Y, Smith ER, Shah AP, Rendleman EJ, Marshall SA, Woodfin AR, Chen FX, Shiekhattar R, Shilatifard A. NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release. Mol Cell 2020; 78:261-274.e5. [PMID: 32155413 PMCID: PMC7402197 DOI: 10.1016/j.molcel.2020.02.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [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: 05/02/2019] [Revised: 12/17/2019] [Accepted: 02/18/2020] [Indexed: 02/08/2023]
Abstract
RNA polymerase II (RNA Pol II) is generally paused at promoter-proximal regions in most metazoans, and based on in vitro studies, this function has been attributed to the negative elongation factor (NELF). Here, we show that upon rapid depletion of NELF, RNA Pol II fails to be released into gene bodies, stopping instead around the +1 nucleosomal dyad-associated region. The transition to the 2nd pause region is independent of positive transcription elongation factor P-TEFb. During the heat shock response, RNA Pol II is rapidly released from pausing at heat shock-induced genes, while most genes are paused and transcriptionally downregulated. Both of these aspects of the heat shock response remain intact upon NELF loss. We find that NELF depletion results in global loss of cap-binding complex from chromatin without global reduction of nascent transcript 5' cap stability. Thus, our studies implicate NELF functioning in early elongation complexes distinct from RNA Pol II pause-release.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Edwin R Smith
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Avani P Shah
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stacy A Marshall
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ashley R Woodfin
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Fei X Chen
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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3
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Liang K, Smith ER, Aoi Y, Stoltz KL, Katagi H, Woodfin AR, Rendleman EJ, Marshall SA, Murray DC, Wang L, Ozark PA, Mishra RK, Hashizume R, Schiltz GE, Shilatifard A. Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy. Cell 2018; 175:766-779.e17. [PMID: 30340042 PMCID: PMC6422358 DOI: 10.1016/j.cell.2018.09.027] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/02/2018] [Accepted: 09/13/2018] [Indexed: 11/15/2022]
Abstract
The super elongation complex (SEC) is required for robust and productive transcription through release of RNA polymerase II (Pol II) with its P-TEFb module and promoting transcriptional processivity with its ELL2 subunit. Malfunction of SEC contributes to multiple human diseases including cancer. Here, we identify peptidomimetic lead compounds, KL-1 and its structural homolog KL-2, which disrupt the interaction between the SEC scaffolding protein AFF4 and P-TEFb, resulting in impaired release of Pol II from promoter-proximal pause sites and a reduced average rate of processive transcription elongation. SEC is required for induction of heat-shock genes and treating cells with KL-1 and KL-2 attenuates the heat-shock response from Drosophila to human. SEC inhibition downregulates MYC and MYC-dependent transcriptional programs in mammalian cells and delays tumor progression in a mouse xenograft model of MYC-driven cancer, indicating that small-molecule disruptors of SEC could be used for targeted therapy of MYC-induced cancer.
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Affiliation(s)
- Kaiwei Liang
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Edwin R. Smith
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Yuki Aoi
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kristen L. Stoltz
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Hiroaki Katagi
- Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Ashley R. Woodfin
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Emily J. Rendleman
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stacy A. Marshall
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - David C. Murray
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lu Wang
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Patrick A. Ozark
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rama K. Mishra
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA,Department of Pharmacology, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Rintaro Hashizume
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Gary E. Schiltz
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA,Department of Pharmacology, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg, School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA.
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4
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Haddad JF, Yang Y, Takahashi YH, Joshi M, Chaudhary N, Woodfin AR, Benyoucef A, Yeung S, Brunzelle JS, Skiniotis G, Brand M, Shilatifard A, Couture JF. Structural Analysis of the Ash2L/Dpy-30 Complex Reveals a Heterogeneity in H3K4 Methylation. Structure 2018; 26:1594-1603.e4. [PMID: 30270175 DOI: 10.1016/j.str.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/28/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023]
Abstract
Dpy-30 is a regulatory subunit controlling the histone methyltransferase activity of the KMT2 enzymes in vivo. Paradoxically, in vitro methyltransferase assays revealed that Dpy-30 only modestly participates in the positive heterotypic allosteric regulation of these methyltransferases. Detailed genome-wide, molecular and structural studies reveal that an extensive network of interactions taking place at the interface between Dpy-30 and Ash2L are critical for the correct placement, genome-wide, of H3K4me2 and H3K4me3 but marginally contribute to the methyltransferase activity of KMT2 enzymes in vitro. Moreover, we show that H3K4me2 peaks persisting following the loss of Dpy-30 are found in regions of highly transcribed genes, highlighting an interplay between Complex of Proteins Associated with SET1 (COMPASS) kinetics and the cycling of RNA polymerase to control H3K4 methylation. Overall, our data suggest that Dpy-30 couples its modest positive heterotypic allosteric regulation of KMT2 methyltransferase activity with its ability to help the positioning of SET1/COMPASS to control epigenetic signaling.
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Affiliation(s)
- John Faissal Haddad
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Yidai Yang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Monika Joshi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Nidhi Chaudhary
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Aissa Benyoucef
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Sylvain Yeung
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, IL, USA
| | - Georgios Skiniotis
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marjorie Brand
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada.
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5
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Arnold CD, Nemčko F, Woodfin AR, Wienerroither S, Vlasova A, Schleiffer A, Pagani M, Rath M, Stark A. A high-throughput method to identify trans-activation domains within transcription factor sequences. EMBO J 2018; 37:embj.201798896. [PMID: 30006452 PMCID: PMC6092621 DOI: 10.15252/embj.201798896] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 11/09/2022] Open
Abstract
Even though transcription factors (TFs) are central players of gene regulation and have been extensively studied, their regulatory trans-activation domains (tADs) often remain unknown and a systematic functional characterization of tADs is lacking. Here, we present a novel high-throughput approach tAD-seq to functionally test thousands of candidate tADs from different TFs in parallel. The tADs we identify by pooled screening validate in individual luciferase assays, whereas neutral regions do not. Interestingly, the tADs are found at arbitrary positions within the TF sequences and can contain amino acid (e.g., glutamine) repeat regions or overlap structured domains, including helix-loop-helix domains that are typically annotated as DNA-binding. We also identified tADs in the non-native reading frames, confirming that random sequences can function as tADs, albeit weakly. The identification of tADs as short protein sequences sufficient for transcription activation will enable the systematic study of TF function, which-particularly for TFs of different transcription activating functionalities-is still poorly understood.
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Affiliation(s)
- Cosmas D Arnold
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Filip Nemčko
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Ashley R Woodfin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | | | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Martina Rath
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria .,Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
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6
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Muerdter F, Boryń ŁM, Woodfin AR, Neumayr C, Rath M, Zabidi MA, Pagani M, Haberle V, Kazmar T, Catarino RR, Schernhuber K, Arnold CD, Stark A. Resolving systematic errors in widely used enhancer activity assays in human cells. Nat Methods 2018; 15:141-149. [PMID: 29256496 PMCID: PMC5793997 DOI: 10.1038/nmeth.4534] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022]
Abstract
The identification of transcriptional enhancers in the human genome is a prime goal in biology. Enhancers are typically predicted via chromatin marks, yet their function is primarily assessed with plasmid-based reporter assays. Here, we show that such assays are rendered unreliable by two previously reported phenomena relating to plasmid transfection into human cells: (i) the bacterial plasmid origin of replication (ORI) functions as a conflicting core promoter and (ii) a type I interferon (IFN-I) response is activated. These cause confounding false positives and negatives in luciferase assays and STARR-seq screens. We overcome both problems by employing the ORI as core promoter and by inhibiting two IFN-I-inducing kinases, enabling genome-wide STARR-seq screens in human cells. In HeLa-S3 cells, we uncover strong enhancers, IFN-I-induced enhancers, and enhancers endogenously silenced at the chromatin level. Our findings apply to all episomal enhancer activity assays in mammalian cells and are key to the characterization of human enhancers.
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Affiliation(s)
- Felix Muerdter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Łukasz M Boryń
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Ashley R Woodfin
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Christoph Neumayr
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Martina Rath
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Muhammad A Zabidi
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Vanja Haberle
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Tomáš Kazmar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Rui R Catarino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Katharina Schernhuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Cosmas D Arnold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
- Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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7
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Liang K, Volk AG, Haug JS, Marshall SA, Woodfin AR, Bartom ET, Gilmore JM, Florens L, Washburn MP, Sullivan KD, Espinosa JM, Cannova J, Zhang J, Smith ER, Crispino JD, Shilatifard A. Therapeutic Targeting of MLL Degradation Pathways in MLL-Rearranged Leukemia. Cell 2017; 168:59-72.e13. [PMID: 28065413 DOI: 10.1016/j.cell.2016.12.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/26/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
Abstract
Chromosomal translocations of the mixed-lineage leukemia (MLL) gene with various partner genes result in aggressive leukemia with dismal outcomes. Despite similar expression at the mRNA level from the wild-type and chimeric MLL alleles, the chimeric protein is more stable. We report that UBE2O functions in regulating the stability of wild-type MLL in response to interleukin-1 signaling. Targeting wild-type MLL degradation impedes MLL leukemia cell proliferation, and it downregulates a specific group of target genes of the MLL chimeras and their oncogenic cofactor, the super elongation complex. Pharmacologically inhibiting this pathway substantially delays progression, and it improves survival of murine leukemia through stabilizing wild-type MLL protein, which displaces the MLL chimera from some of its target genes and, therefore, relieves the cellular oncogenic addiction to MLL chimeras. Stabilization of MLL provides us with a paradigm in the development of therapies for aggressive MLL leukemia and perhaps for other cancers caused by translocations.
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Affiliation(s)
- Kaiwei Liang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA
| | - Andrew G Volk
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA; Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Jeffrey S Haug
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA
| | - Joshua M Gilmore
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66150, USA
| | - Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome & Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome & Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joseph Cannova
- Oncology Institute, Loyola University Chicago, Maywood, IL 60153, USA; Department of Pathology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Jiwang Zhang
- Oncology Institute, Loyola University Chicago, Maywood, IL 60153, USA; Department of Pathology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Edwin R Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA
| | - John D Crispino
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA; Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, Il 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, Il 60611, USA.
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8
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Abstract
In this study, Luo et al. find that the AFF family protein AFF3 can specifically bind both gametic differentially DNA-methylated regions (gDMRs) and enhancers within imprinted loci in an allele-specific manner. These results provide the mechanistic details of the control of dosage-critical imprinted gene expression through the regulated binding of the transcription elongation factor AFF3 between a DMR and an enhancer. Genomic imprinting is a critical developmental process characteristic of parent of origin-specific gene expression. It is well accepted that differentially DNA-methylated regions (DMRs) and enhancers are two major classes of cis-elements determining parent of origin-specific gene expression, with each recruiting different sets of transcription factors. Previously, we identified the AF4/FMR2 (AFF) family protein AFF3 within the transcription elongation complex SEC-L3. Here, we report that AFF3 can specifically bind both gametic DMRs (gDMRs) and enhancers within imprinted loci in an allele-specific manner. We identify the molecular regulators involved in the recruitment of AFF3 to gDMRs and provide mechanistic insight into the requirement of AFF3 at an enhancer for the expression of an ∼200-kb polycistronic transcript within the imprinted Dlk1-Dio3 locus. Our data suggest that the heterochromatic environment at the gDMR reinforces silencing of its related enhancer by controlling the binding and activity of AFF3 in an allele-specific manner. In summary, this study provides molecular details about the regulation of dosage-critical imprinted gene expression through the regulated binding of the transcription elongation factor AFF3 between a DMR and an enhancer.
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Affiliation(s)
- Zhuojuan Luo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA; Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Chengqi Lin
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Xin Gao
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Edwin R Smith
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA; Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Robert H. Lurie National Cancer Institute Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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9
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Liang K, Woodfin AR, Slaughter BD, Unruh JR, Box AC, Rickels RA, Gao X, Haug JS, Jaspersen SL, Shilatifard A. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis. Mol Cell 2016; 60:435-45. [PMID: 26527278 DOI: 10.1016/j.molcel.2015.09.021] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/04/2015] [Accepted: 09/22/2015] [Indexed: 12/14/2022]
Abstract
Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division.
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Affiliation(s)
- Kaiwei Liang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Andrew C Box
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jeffrey S Haug
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
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10
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Chen FX, Woodfin AR, Gardini A, Rickels RA, Marshall SA, Smith ER, Shiekhattar R, Shilatifard A. PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II. Cell 2015; 162:1003-15. [PMID: 26279188 DOI: 10.1016/j.cell.2015.07.042] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 05/16/2015] [Accepted: 07/02/2015] [Indexed: 10/25/2022]
Abstract
The control of promoter-proximal pausing and the release of RNA polymerase II (Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify that Pol-II-associated factor 1 (PAF1) possesses an evolutionarily conserved function in metazoans in the regulation of promoter-proximal pausing. Reduction in PAF1 levels leads to an increased release of paused Pol II into gene bodies at thousands of genes. PAF1 depletion results in increased nascent and mature transcripts and increased levels of phosphorylation of Pol II's C-terminal domain on serine 2 (Ser2P). These changes can be explained by the recruitment of the Ser2P kinase super elongation complex (SEC) effecting increased release of paused Pol II into productive elongation, thus establishing PAF1 as a regulator of promoter-proximal pausing by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Alessandro Gardini
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1501 NW 10(th) Avenue, Miami, FL 33136, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Edwin R Smith
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1501 NW 10(th) Avenue, Miami, FL 33136, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
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11
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Thornton JL, Westfield GH, Takahashi YH, Cook M, Gao X, Woodfin AR, Lee JS, Morgan MA, Jackson J, Smith ER, Couture JF, Skiniotis G, Shilatifard A. Context dependency of Set1/COMPASS-mediated histone H3 Lys4 trimethylation. Genes Dev 2014; 28:115-20. [PMID: 24402317 PMCID: PMC3909785 DOI: 10.1101/gad.232215.113] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The stimulation of H3K4 trimethylation (H3K4me3) by H2B monoubiquitination (H2Bub) has been widely studied, and multiple mechanisms have been proposed for this form of histone cross-talk. Thornton et al. combine biochemical, structural, and in vivo approaches to provide a novel mechanism for the role of H2B ubiquitination machinery in the regulation of histone H3K4 methylation by COMPASS. This study demonstrates that the H2Bub machinery and Cps35/Swd2 function to focus the H3K4me3 activity of COMPASS at promoter-proximal regions in a context-dependent manner. The stimulation of trimethylation of histone H3 Lys4 (H3K4) by H2B monoubiquitination (H2Bub) has been widely studied, with multiple mechanisms having been proposed for this form of histone cross-talk. Cps35/Swd2 within COMPASS (complex of proteins associated with Set1) is considered to bridge these different processes. However, a truncated form of Set1 (762-Set1) is reported to function in H3K4 trimethylation (H3K4me3) without interacting with Cps35/Swd2, and such cross-talk is attributed to the n-SET domain of Set1 and its interaction with the Cps40/Spp1 subunit of COMPASS. Here, we used biochemical, structural, in vivo, and chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq) approaches to demonstrate that Cps40/Spp1 and the n-SET domain of Set1 are required for the stability of Set1 and not the cross-talk. Furthermore, the apparent wild-type levels of H3K4me3 in the 762-Set1 strain are due to the rogue methylase activity of this mutant, resulting in the mislocalization of H3K4me3 from the promoter-proximal regions to the gene bodies and intergenic regions. We also performed detailed screens and identified yeast strains lacking H2Bub but containing intact H2Bub enzymes that have normal levels of H3K4me3, suggesting that monoubiquitination may not directly stimulate COMPASS but rather works in the context of the PAF and Rad6/Bre1 complexes. Our study demonstrates that the monoubiquitination machinery and Cps35/Swd2 function to focus COMPASS's H3K4me3 activity at promoter-proximal regions in a context-dependent manner.
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Affiliation(s)
- Janet L Thornton
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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