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Su Y, Wu J, Chen W, Shan J, Chen D, Zhu G, Ge S, Liu Y. Spliceosomal snRNAs, the Essential Players in pre-mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics. Adv Biol (Weinh) 2024:e2400006. [PMID: 38797893 DOI: 10.1002/adbi.202400006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Spliceosomal small nuclear RNAs (snRNAs) are a fundamental class of non-coding small RNAs abundant in the nucleoplasm of eukaryotic cells, playing a crucial role in splicing precursor messenger RNAs (pre-mRNAs). They are transcribed by DNA-dependent RNA polymerase II (Pol II) or III (Pol III), and undergo subsequent processing and 3' end cleavage to become mature snRNAs. Numerous protein factors are involved in the transcription initiation, elongation, termination, splicing, cellular localization, and terminal modification processes of snRNAs. The transcription and processing of snRNAs are regulated spatiotemporally by various mechanisms, and the homeostatic balance of snRNAs within cells is of great significance for the growth and development of organisms. snRNAs assemble with specific accessory proteins to form small nuclear ribonucleoprotein particles (snRNPs) that are the basal components of spliceosomes responsible for pre-mRNA maturation. This article provides an overview of the biological functions, biosynthesis, terminal structure, and tissue-specific regulation of snRNAs.
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Affiliation(s)
- Yuan Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jiaming Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Junling Shan
- Department of basic medicine, Guangxi Medical University of Nursing College, Nanning, Guangxi, 530021, China
| | - Dan Chen
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, Guangxi, 530011, China
| | - Guangyu Zhu
- Guangxi Medical University Hospital of Stomatology, Nanning, Guangxi, 530021, China
| | - Shengchao Ge
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
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2
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Benyoucef A, Haigh JJ, Brand M. Unveiling the complexity of transcription factor networks in hematopoietic stem cells: implications for cell therapy and hematological malignancies. Front Oncol 2023; 13:1151343. [PMID: 37441426 PMCID: PMC10333584 DOI: 10.3389/fonc.2023.1151343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The functionality and longevity of hematopoietic tissue is ensured by a tightly controlled balance between self-renewal, quiescence, and differentiation of hematopoietic stem cells (HSCs) into the many different blood lineages. Cell fate determination in HSCs is influenced by signals from extrinsic factors (e.g., cytokines, irradiation, reactive oxygen species, O2 concentration) that are translated and integrated by intrinsic factors such as Transcription Factors (TFs) to establish specific gene regulatory programs. TFs also play a central role in the establishment and/or maintenance of hematological malignancies, highlighting the need to understand their functions in multiple contexts. TFs bind to specific DNA sequences and interact with each other to form transcriptional complexes that directly or indirectly control the expression of multiple genes. Over the past decades, significant research efforts have unraveled molecular programs that control HSC function. This, in turn, led to the identification of more than 50 TF proteins that influence HSC fate. However, much remains to be learned about how these proteins interact to form molecular networks in combination with cofactors (e.g. epigenetics factors) and how they control differentiation, expansion, and maintenance of cellular identity. Understanding these processes is critical for future applications particularly in the field of cell therapy, as this would allow for manipulation of cell fate and induction of expansion, differentiation, or reprogramming of HSCs using specific cocktails of TFs. Here, we review recent findings that have unraveled the complexity of molecular networks controlled by TFs in HSCs and point towards possible applications to obtain functional HSCs ex vivo for therapeutic purposes including hematological malignancies. Furthermore, we discuss the challenges and prospects for the derivation and expansion of functional adult HSCs in the near future.
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Affiliation(s)
- Aissa Benyoucef
- Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Jody J. Haigh
- Department of Pharmacology and Therapeutics, Rady Faulty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
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3
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Thieme E, Bruss N, Sun D, Dominguez EC, Coleman D, Liu T, Roleder C, Martinez M, Garcia-Mansfield K, Ball B, Pirrotte P, Wang L, Xia Z, Danilov AV. CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma. Mol Cancer 2023; 22:64. [PMID: 36998071 PMCID: PMC10061728 DOI: 10.1186/s12943-023-01762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) exhibits significant genetic heterogeneity which contributes to drug resistance, necessitating development of novel therapeutic approaches. Pharmacological inhibitors of cyclin-dependent kinases (CDK) demonstrated pre-clinical activity in DLBCL, however many stalled in clinical development. Here we show that AZD4573, a selective inhibitor of CDK9, restricted growth of DLBCL cells. CDK9 inhibition (CDK9i) resulted in rapid changes in the transcriptome and proteome, with downmodulation of multiple oncoproteins (eg, MYC, Mcl-1, JunB, PIM3) and deregulation of phosphoinotiside-3 kinase (PI3K) and senescence pathways. Following initial transcriptional repression due to RNAPII pausing, we observed transcriptional recovery of several oncogenes, including MYC and PIM3. ATAC-Seq and ChIP-Seq experiments revealed that CDK9i induced epigenetic remodeling with bi-directional changes in chromatin accessibility, suppressed promoter activation and led to sustained reprograming of the super-enhancer landscape. A CRISPR library screen suggested that SE-associated genes in the Mediator complex, as well as AKT1, confer resistance to CDK9i. Consistent with this, sgRNA-mediated knockout of MED12 sensitized cells to CDK9i. Informed by our mechanistic findings, we combined AZD4573 with either PIM kinase or PI3K inhibitors. Both combinations decreased proliferation and induced apoptosis in DLBCL and primary lymphoma cells in vitro as well as resulted in delayed tumor progression and extended survival of mice xenografted with DLBCL in vivo. Thus, CDK9i induces reprogramming of the epigenetic landscape, and super-enhancer driven recovery of select oncogenes may contribute to resistance to CDK9i. PIM and PI3K represent potential targets to circumvent resistance to CDK9i in the heterogeneous landscape of DLBCL.
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Affiliation(s)
- Elana Thieme
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Nur Bruss
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Duanchen Sun
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- grid.5288.70000 0000 9758 5690Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA
- grid.27255.370000 0004 1761 1174Present address: School of Mathematics, Shandong University, Jinan, 250100 Shandong China
| | - Edward C. Dominguez
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Daniel Coleman
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
| | - Tingting Liu
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Carly Roleder
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Melissa Martinez
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Krystine Garcia-Mansfield
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Brian Ball
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Patrick Pirrotte
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Lili Wang
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Zheng Xia
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- grid.5288.70000 0000 9758 5690Biomedical Engineering Department, Oregon Health & Science University, Portland, OR USA
| | - Alexey V. Danilov
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
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Guiro J, Fagbemi M, Tellier M, Zaborowska J, Barker S, Fournier M, Murphy S. CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors. Biomolecules 2022; 12:704. [PMID: 35625631 PMCID: PMC9138887 DOI: 10.3390/biom12050704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/29/2022] [Accepted: 05/12/2022] [Indexed: 11/29/2022] Open
Abstract
In order to identify factors involved in transcription of human snRNA genes and 3' end processing of the transcripts, we have carried out CRISPR affinity purification in situ of regulatory elements (CAPTURE), which is deadCas9-mediated pull-down, of the tandemly repeated U2 snRNA genes in human cells. CAPTURE enriched many factors expected to be associated with these human snRNA genes including RNA polymerase II (pol II), Cyclin-Dependent Kinase 7 (CDK7), Negative Elongation Factor (NELF), Suppressor of Ty 5 (SPT5), Mediator 23 (MED23) and several subunits of the Integrator Complex. Suppressor of Ty 6 (SPT6); Cyclin K, the partner of Cyclin-Dependent Kinase 12 (CDK12) and Cyclin-Dependent Kinase 13 (CDK13); and SWI/SNF chromatin remodelling complex-associated SWI/SNF-related, Matrix-associated, Regulator of Chromatin (SMRC) factors were also enriched. Several polyadenylation factors, including Cleavage and Polyadenylation Specificity Factor 1 (CPSF1), Cleavage Stimulation Factors 1 and 2 (CSTF1,and CSTF2) were enriched by U2 gene CAPTURE. We have already shown by chromatin immunoprecipitation (ChIP) that CSTF2-and Pcf11 and Ssu72, which are also polyadenylation factors-are associated with the human U1 and U2 genes. ChIP-seq and ChIP-qPCR confirm the association of SPT6, Cyclin K, and CDK12 with the U2 genes. In addition, knockdown of SPT6 causes loss of subunit 3 of the Integrator Complex (INTS3) from the U2 genes, indicating a functional role in snRNA gene expression. CAPTURE has therefore expanded the repertoire of transcription and RNA processing factors associated with these genes and helped to identify a functional role for SPT6.
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Affiliation(s)
- Joana Guiro
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Mathias Fagbemi
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Justyna Zaborowska
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Stephanie Barker
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
| | - Marjorie Fournier
- Advanced Proteomics Facility, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK;
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (J.G.); (M.F.); (M.T.); (J.Z.); (S.B.)
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5
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Bellefroid M, Rodari A, Galais M, Krijger PHL, Tjalsma SJD, Nestola L, Plant E, Vos ESM, Cristinelli S, Van Driessche B, Vanhulle C, Ait-Ammar A, Burny A, Ciuffi A, de Laat W, Van Lint C. Role of the cellular factor CTCF in the regulation of bovine leukemia virus latency and three-dimensional chromatin organization. Nucleic Acids Res 2022; 50:3190-3202. [PMID: 35234910 PMCID: PMC8989512 DOI: 10.1093/nar/gkac107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 01/12/2023] Open
Abstract
Bovine leukemia virus (BLV)-induced tumoral development is a multifactorial phenomenon that remains incompletely understood. Here, we highlight the critical role of the cellular CCCTC-binding factor (CTCF) both in the regulation of BLV transcriptional activities and in the deregulation of the three-dimensional (3D) chromatin architecture surrounding the BLV integration site. We demonstrated the in vivo recruitment of CTCF to three conserved CTCF binding motifs along the provirus. Next, we showed that CTCF localized to regions of transitions in the histone modifications profile along the BLV genome and that it is implicated in the repression of the 5′Long Terminal Repeat (LTR) promoter activity, thereby contributing to viral latency, while favoring the 3′LTR promoter activity. Finally, we demonstrated that BLV integration deregulated the host cellular 3D chromatin organization through the formation of viral/host chromatin loops. Altogether, our results highlight CTCF as a new critical effector of BLV transcriptional regulation and BLV-induced physiopathology.
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Affiliation(s)
- Maxime Bellefroid
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Anthony Rodari
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Mathilde Galais
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Sjoerd J D Tjalsma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Lorena Nestola
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Erica S M Vos
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne 1011, Switzerland
| | - Benoit Van Driessche
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Caroline Vanhulle
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Amina Ait-Ammar
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Arsène Burny
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne 1011, Switzerland
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
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6
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Alharbi AB, Schmitz U, Bailey CG, Rasko JEJ. CTCF as a regulator of alternative splicing: new tricks for an old player. Nucleic Acids Res 2021; 49:7825-7838. [PMID: 34181707 PMCID: PMC8373115 DOI: 10.1093/nar/gkab520] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Three decades of research have established the CCCTC-binding factor (CTCF) as a ubiquitously expressed chromatin organizing factor and master regulator of gene expression. A new role for CTCF as a regulator of alternative splicing (AS) has now emerged. CTCF has been directly and indirectly linked to the modulation of AS at the individual transcript and at the transcriptome-wide level. The emerging role of CTCF-mediated regulation of AS involves diverse mechanisms; including transcriptional elongation, DNA methylation, chromatin architecture, histone modifications, and regulation of splicing factor expression and assembly. CTCF thereby appears to not only co-ordinate gene expression regulation but contributes to the modulation of transcriptomic complexity. In this review, we highlight previous discoveries regarding the role of CTCF in AS. In addition, we summarize detailed mechanisms by which CTCF mediates AS regulation. We propose opportunities for further research designed to examine the possible fate of CTCF-mediated alternatively spliced genes and associated biological consequences. CTCF has been widely acknowledged as the 'master weaver of the genome'. Given its multiple connections, further characterization of CTCF's emerging role in splicing regulation might extend its functional repertoire towards a 'conductor of the splicing orchestra'.
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Affiliation(s)
- Adel B Alharbi
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Ulf Schmitz
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
| | - Charles G Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E J Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
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Linzer N, Trumbull A, Nar R, Gibbons MD, Yu DT, Strouboulis J, Bungert J. Regulation of RNA Polymerase II Transcription Initiation and Elongation by Transcription Factor TFII-I. Front Mol Biosci 2021; 8:681550. [PMID: 34055891 PMCID: PMC8155576 DOI: 10.3389/fmolb.2021.681550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription by RNA polymerase II (Pol II) is regulated by different processes, including alterations in chromatin structure, interactions between distal regulatory elements and promoters, formation of transcription domains enriched for Pol II and co-regulators, and mechanisms involved in the initiation, elongation, and termination steps of transcription. Transcription factor TFII-I, originally identified as an initiator (INR)-binding protein, contains multiple protein–protein interaction domains and plays diverse roles in the regulation of transcription. Genome-wide analysis revealed that TFII-I associates with expressed as well as repressed genes. Consistently, TFII-I interacts with co-regulators that either positively or negatively regulate the transcription. Furthermore, TFII-I has been shown to regulate transcription pausing by interacting with proteins that promote or inhibit the elongation step of transcription. Changes in TFII-I expression in humans are associated with neurological and immunological diseases as well as cancer. Furthermore, TFII-I is essential for the development of mice and represents a barrier for the induction of pluripotency. Here, we review the known functions of TFII-I related to the regulation of Pol II transcription at the stages of initiation and elongation.
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Affiliation(s)
- Niko Linzer
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - Alexis Trumbull
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - Rukiye Nar
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - Matthew D Gibbons
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - David T Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
| | - John Strouboulis
- Comprehensive Cancer Center, School of Cancer and Pharmaceutical Sciences, King's College London, United Kingdom
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, Powell Gene Therapy Center, University of Florida, Gainesville, FL, United States
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8
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Luan J, Xiang G, Gómez-García PA, Tome JM, Zhang Z, Vermunt MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA. Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Cell Rep 2021; 34:108783. [PMID: 33626344 PMCID: PMC7999233 DOI: 10.1016/j.celrep.2021.108783] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/25/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
CCCTC-binding factor (CTCF) is a conserved zinc finger transcription factor implicated in a wide range of functions, including genome organization, transcription activation, and elongation. To explore the basis for CTCF functional diversity, we coupled an auxin-induced degron system with precision nuclear run-on. Unexpectedly, oriented CTCF motifs in gene bodies are associated with transcriptional stalling in a manner independent of bound CTCF. Moreover, CTCF at different binding sites (CBSs) displays highly variable resistance to degradation. Motif sequence does not significantly predict degradation behavior, but location at chromatin boundaries and chromatin loop anchors, as well as co-occupancy with cohesin, are associated with delayed degradation. Single-molecule tracking experiments link chromatin residence time to CTCF degradation kinetics, which has ramifications regarding architectural CTCF functions. Our study highlights the heterogeneity of CBSs, uncovers properties specific to architecturally important CBSs, and provides insights into the basic processes of genome organization and transcription regulation.
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Affiliation(s)
- Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guanjue Xiang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jacob M Tome
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Marit W Vermunt
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Haoyue Zhang
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yu Zhang
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Yemin Lan
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA.
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9
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Maß L, Holtmannspötter M, Zachgo S. Dual-color 3D-dSTORM colocalization and quantification of ROXY1 and RNAPII variants throughout the transcription cycle in root meristem nuclei. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1423-1436. [PMID: 32896918 DOI: 10.1111/tpj.14986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/04/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
To unravel the function of a protein of interest, it is crucial to asses to what extent it associates via direct interactions or by overlapping expression with other proteins. ROXY1, a land plant-specific glutaredoxin, exerts a function in Arabidopsis flower development and interacts with TGA transcription factors in the nucleus. We detected a novel ROXY1 function in the root meristem. Root cells that lack chlorophyll reducing plant-specific background problems that can hamper colocalization 3D microscopy. Thus far, a super-resolution three-dimensional stochastic optical reconstruction microscopy (3D-dSTORM) approach has mainly been applied in animal studies. We established 3D-dSTORM using the roxy1 mutant complemented with green fluorescence protein-ROXY1 and investigated its colocalization with three distinct RNAPII isoforms. To quantify the colocalization results, 3D-dSTORM was coupled with the coordinate-based colocalization method. Interestingly, ROXY1 proteins colocalize with different RNA polymerase II (RNAPII) isoforms that are active at distinct transcription cycle steps. Our colocalization data provide new insights on nuclear glutaredoxin activities suggesting that ROXY1 is not only required in early transcription initiation events via interaction with transcription factors but likely also participates throughout further transcription processes until late termination steps. Furthermore, we showed the applicability of the combined approaches to detect and quantify responses to altered growth conditions, exemplified by analysis of H2 O2 treatment, causing a dissociation of ROXY1 and RNAPII isoforms. We envisage that the powerful dual-color 3D-dSTORM/coordinate-based colocalization combination offers plant cell biologists the opportunity to colocalize and quantify root meristem proteins at an increased, unprecedented resolution level <50 nm, which will enable the detection of novel subcellular protein associations and functions.
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Affiliation(s)
- Lucia Maß
- Botany Department, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
| | - Michael Holtmannspötter
- Integrated Bioimaging Facility iBiOs, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
- Center of Cellular Nanoanalytics Osnabrück, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
| | - Sabine Zachgo
- Botany Department, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
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10
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Tellier M, Zaborowska J, Caizzi L, Mohammad E, Velychko T, Schwalb B, Ferrer-Vicens I, Blears D, Nojima T, Cramer P, Murphy S. CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation. Nucleic Acids Res 2020; 48:7712-7727. [PMID: 32805052 PMCID: PMC7641311 DOI: 10.1093/nar/gkaa514] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/12/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Justyna Zaborowska
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Livia Caizzi
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eusra Mohammad
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Björn Schwalb
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ivan Ferrer-Vicens
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Daniel Blears
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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11
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Tellier M, Hardy JG, Norbury CJ, Murphy S. Effect of CFIm68 knockdown on RNA polymerase II transcription. BMC Res Notes 2019; 12:554. [PMID: 31477156 PMCID: PMC6720987 DOI: 10.1186/s13104-019-4582-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/21/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Transcription of eukaryotic protein-coding genes by RNA polymerase II (pol II) is highly regulated at initiation, elongation and termination. Transcription is also coordinated with co-transcriptional processing of the emerging pre-mRNA by capping, splicing, and cleavage and polyadenylation. Polyadenylation (poly(A)) site recognition, which defines the end of the mRNA, relies on the cleavage and polyadenylation (CPA) complex. It was previously observed that knocking-down proteins of the CPA complex affects not only recognition of the poly(A) site but also results in increased pausing of pol II at the beginning of genes. This finding suggests that the CPA complex plays a role in regulating pol II turnover after transcription initiation. DATA DESCRIPTION To explore this possibility, we knocked-down a subunit of the cleavage factor I (CFIm), CFIm68, which is part of the CPA complex and involved in alternative polyadenylation, and performed pol II ChIP-seq in absence or presence of a transcription elongation inhibitor. In addition, we performed pol II ChIP-qPCR on a subset of protein coding genes after knocking down CFIm68.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE, UK.
| | - Jessica G Hardy
- Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE, UK
| | - Chris J Norbury
- Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE, UK
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12
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Tellier M, Chalmers R. Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome. Nucleic Acids Res 2019; 47:122-133. [PMID: 30329085 PMCID: PMC6326780 DOI: 10.1093/nar/gky937] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Transposons impart dynamism to the genomes they inhabit and their movements frequently rewire the control of nearby genes. Occasionally, their proteins are domesticated when they evolve a new function. SETMAR is a protein methylase with a sequence-specific DNA binding domain. It began to evolve about 50 million years ago when an Hsmar1 transposon integrated downstream of a SET-domain methylase gene. Here we show that the DNA-binding domain of the transposase targets the enzyme to transposon-end remnants and that this is capable of regulating gene expression, dependent on the methylase activity. When SETMAR was modestly overexpressed in human cells, almost 1500 genes changed expression by more than 2-fold (65% up- and 35% down-regulated). These genes were enriched for the KEGG Pathways in Cancer and include several transcription factors important for development and differentiation. Expression of a similar level of a methylase-deficient SETMAR changed the expression of many fewer genes, 77% of which were down-regulated with no significant enrichment of KEGG Pathways. Our data is consistent with a model in which SETMAR is part of an anthropoid primate-specific regulatory network centered on the subset of genes containing a transposon end.
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Affiliation(s)
- Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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Vorobyeva NE, Mazina MY. Functions of Insulators in the Context of Modern Whole-Genome Investigations. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419020170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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14
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Giraud G, Terrone S, Bourgeois CF. Functions of DEAD box RNA helicases DDX5 and DDX17 in chromatin organization and transcriptional regulation. BMB Rep 2019. [PMID: 30293550 PMCID: PMC6330936 DOI: 10.5483/bmbrep.2018.51.12.234] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA helicases DDX5 and DDX17 are multitasking proteins that regulate gene expression in different biological contexts through diverse activities. Special attention has long been paid to their function as coregulators of transcription factors, providing insight about their functional association with a number of chromatin modifiers and remodelers. However, to date, the variety of described mechanisms has made it difficult to understand precisely how these proteins work at the molecular level, and the contribution of their ATPase domain to these mechanisms remains unclear as well. In light of their association with long noncoding RNAs that are key epigenetic regulators, an emerging view is that DDX5 and DDX17 may act through modulating the activity of various ribonucleoprotein complexes that could ensure their targeting to specific chromatin loci. This review will comprehensively describe the current knowledge on these different mechanisms. We will also discuss the potential roles of DDX5 and DDX17 on the 3D chromatin organization and how these could impact gene expression at the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Guillaume Giraud
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Sophie Terrone
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Universite de Lyon, CNRS UMR 5239, INSERM U1210, Ecole Normale Superieure de Lyon, Universite Claude Bernard Lyon 1, F-69007 Lyon, France
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15
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Tellier M, Hardy JG, Norbury CJ, Murphy S. Effect of CFIm25 knockout on RNA polymerase II transcription. BMC Res Notes 2018; 11:894. [PMID: 30547832 PMCID: PMC6295108 DOI: 10.1186/s13104-018-4006-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/10/2018] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Transcription of eukaryotic protein-coding genes by RNA polymerase II (pol II) is a highly regulated process. Most human genes have multiple poly(A) sites, which define different possible mRNA ends, suggesting the existence of mechanisms that regulate which poly(A) site is used. Poly(A) site selection may be mediated by cleavage factor I (CFIm), which is part of the cleavage and polyadenylation (CPA) complex. CFIm comprises CFIm25, CFIm59 and CFim68 subunits. It has been documented that the CPA complex also regulates pol II transcription at the start of genes. We therefore investigated whether CFIm, in addition to its role in poly(A) site selection, is involved in the regulation of pol II transcription. DATA DESCRIPTION We provide genome-wide data of the effect of reducing by 90% expression of the CFIm25 constituent of CFIm, which is involved in pre-mRNA cleavage and polyadenylation, on pol II transcription in human cells. We performed pol II ChIP-seq in the presence or absence of CFIm25 and with or without an inhibitor of the cyclin-dependent kinase (CDK)9, which regulates the entry of pol II into productive elongation.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE UK
| | - Jessica G. Hardy
- Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE UK
| | - Chris J. Norbury
- Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE UK
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16
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Guiro J, Murphy S. Regulation of expression of human RNA polymerase II-transcribed snRNA genes. Open Biol 2018; 7:rsob.170073. [PMID: 28615474 PMCID: PMC5493778 DOI: 10.1098/rsob.170073] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3′ end formation of the transcripts.
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Affiliation(s)
- Joana Guiro
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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17
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CTCF interacts with the lytic HSV-1 genome to promote viral transcription. Sci Rep 2017; 7:39861. [PMID: 28045091 PMCID: PMC5206630 DOI: 10.1038/srep39861] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/28/2016] [Indexed: 12/29/2022] Open
Abstract
CTCF is an essential chromatin regulator implicated in important nuclear processes including in nuclear organization and transcription. Herpes Simplex Virus-1 (HSV-1) is a ubiquitous human pathogen, which enters productive infection in human epithelial and many other cell types. CTCF is known to bind several sites in the HSV-1 genome during latency and reactivation, but its function has not been defined. Here, we report that CTCF interacts extensively with the HSV-1 DNA during lytic infection by ChIP-seq, and its knockdown results in the reduction of viral transcription, viral genome copy number and virus yield. CTCF knockdown led to increased H3K9me3 and H3K27me3, and a reduction of RNA pol II occupancy on viral genes. Importantly, ChIP-seq analysis revealed that there is a higher level of CTD Ser2P modified RNA Pol II near CTCF peaks relative to the Ser5P form in the viral genome. Consistent with this, CTCF knockdown reduced the Ser2P but increased Ser5P modified forms of RNA Pol II on viral genes. These results suggest that CTCF promotes HSV-1 lytic transcription by facilitating the elongation of RNA Pol II and preventing silenced chromatin on the viral genome.
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18
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Sawyer IA, Sturgill D, Sung MH, Hager GL, Dundr M. Cajal body function in genome organization and transcriptome diversity. Bioessays 2016; 38:1197-1208. [PMID: 27767214 DOI: 10.1002/bies.201600144] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nuclear bodies contribute to non-random organization of the human genome and nuclear function. Using a major prototypical nuclear body, the Cajal body, as an example, we suggest that these structures assemble at specific gene loci located across the genome as a result of high transcriptional activity. Subsequently, target genes are physically clustered in close proximity in Cajal body-containing cells. However, Cajal bodies are observed in only a limited number of human cell types, including neuronal and cancer cells. Ultimately, Cajal body depletion perturbs splicing kinetics by reducing target small nuclear RNA (snRNA) transcription and limiting the levels of spliceosomal snRNPs, including their modification and turnover following each round of RNA splicing. As such, Cajal bodies are capable of shaping the chromatin interaction landscape and the transcriptome by influencing spliceosome kinetics. Future studies should concentrate on characterizing the direct influence of Cajal bodies upon snRNA gene transcriptional dynamics. Also see the video abstract here.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.,Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miroslav Dundr
- Department of Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
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