1
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Sibai DS, Tremblay MG, Lessard F, Tav C, Sabourin-Félix M, Robinson M, Moss T. TTF1 control of LncRNA synthesis delineates a tumor suppressor pathway directly regulating the ribosomal RNA genes. J Cell Physiol 2024; 239:e31303. [PMID: 38764354 DOI: 10.1002/jcp.31303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
The tumor suppressor p14/19ARF regulates ribosomal RNA (rRNA) synthesis by controlling the nucleolar localization of Transcription Termination Factor 1 (TTF1). However, the role played by TTF1 in regulating the rRNA genes and in potentially controlling growth has remained unclear. We now show that TTF1 expression regulates cell growth by determining the cellular complement of ribosomes. Unexpectedly, it achieves this by acting as a "roadblock" to synthesis of the noncoding LncRNA and pRNA that we show are generated from the "Spacer Promoter" duplications present upstream of the 47S pre-rRNA promoter on the mouse and human ribosomal RNA genes. Unexpectedly, the endogenous generation of these noncoding RNAs does not induce CpG methylation or gene silencing. Rather, it acts in cis to suppress 47S preinitiation complex formation and hence de novo pre-rRNA synthesis by a mechanism reminiscent of promoter interference or occlusion. Taken together, our data delineate a pathway from p19ARF to cell growth suppression via the regulation of ribosome biogenesis by noncoding RNAs and validate a key cellular growth law in mammalian cells.
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Affiliation(s)
- Dany S Sibai
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Michel G Tremblay
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Frédéric Lessard
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Christophe Tav
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Marianne Sabourin-Félix
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
| | - Mark Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tom Moss
- St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
- Cancer Research Centre, Laval University, Quebec City, Quebec, Canada
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2
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Kim JH, Nagaraja R, Ogurtsov AY, Noskov VN, Liskovykh M, Lee HS, Hori Y, Kobayashi T, Hunter K, Schlessinger D, Kouprina N, Shabalina SA, Larionov V. Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability. NAR Genom Bioinform 2024; 6:lqae070. [PMID: 38881577 PMCID: PMC11177557 DOI: 10.1093/nargab/lqae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/20/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35 to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5'ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.
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Affiliation(s)
- Jung-Hyun Kim
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Ramaiah Nagaraja
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Alexey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir N Noskov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Mikhail Liskovykh
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Hee-Sheung Lee
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Yutaro Hori
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Kent Hunter
- National Cancer Institute, Laboratory of Cancer Biology and Genetics, Bethesda, MD, USA
| | - David Schlessinger
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Natalay Kouprina
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir Larionov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
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3
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Braden AA, Xiao J, Hori R, Brown C, Khan MM. An Overview of UBTF Neuroregression Syndrome. Brain Sci 2024; 14:179. [PMID: 38391753 PMCID: PMC10886456 DOI: 10.3390/brainsci14020179] [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: 01/19/2024] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
Recently, a recurrent de novo dominant mutation in UBTF (c.628G>A, p.Glu210Lys; UBTF E210K) was identified as the cause of a neurological disorder which has been named UBTF Neuroregression Syndrome (UNS), or Childhood-Onset Neurodegeneration with Brain Atrophy (CONDBA). To date, only 17 cases have been reported worldwide. The molecular etiology is a pathogenic variant, E210K, within the HMG-box 2 of Upstream Binding Transcription Factor (UBTF). UBTF, a nucleolar protein, plays an important role in ribosomal RNA (rRNA) synthesis, nucleolar integrity, and cell survival. This variant causes unstable preinitiation complexes to form, resulting in altered rDNA chromatin structures, rRNA dysregulation, DNA damage, and ultimately, neurodegeneration. Defining clinical characteristics of the disorder include but are not limited to developmental regression beginning at approximately three years of age, progressive motor dysfunction, declining cognition, ambulatory loss, and behavioral problems. Histological and neuroimaging abnormalities include cortical atrophy, white matter deficits, and enlarged ventricles. Herein, we present a detailed overview of all published cases as well as the functional roles of UBTF to better understand the pathophysiology. Bringing undiagnosed cases to the attention of clinicians and researchers by making them aware of the clinical features will improve research and support the development of therapeutic interventions.
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Affiliation(s)
- Anneliesse A Braden
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38104, USA
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jianfeng Xiao
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38104, USA
| | - Roderick Hori
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Chester Brown
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38104, USA
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Division of Regenerative and Rehabilitation Sciences, Department of Physical Therapy, Center for Muscle, Metabolism and Neuropathology, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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4
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Barajas JM, Rasouli M, Umeda M, Hiltenbrand R, Abdelhamed S, Mohnani R, Arthur B, Westover T, Thomas ME, Ashtiani M, Janke LJ, Xu B, Chang TC, Rosikiewicz W, Xiong E, Rolle C, Low J, Krishan R, Song G, Walsh MP, Ma J, Rubnitz JE, Iacobucci I, Chen T, Krippner-Heidenreich A, Zwaan CM, Heidenreich O, Klco JM. Acute myeloid leukemias with UBTF tandem duplications are sensitive to menin inhibitors. Blood 2024; 143:619-630. [PMID: 37890156 PMCID: PMC10873536 DOI: 10.1182/blood.2023021359] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/29/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
ABSTRACT UBTF tandem duplications (UBTF-TDs) have recently emerged as a recurrent alteration in pediatric and adult acute myeloid leukemia (AML). UBTF-TD leukemias are characterized by a poor response to conventional chemotherapy and a transcriptional signature that mirrors NUP98-rearranged and NPM1-mutant AMLs, including HOX-gene dysregulation. However, the mechanism by which UBTF-TD drives leukemogenesis remains unknown. In this study, we investigated the genomic occupancy of UBTF-TD in transformed cord blood CD34+ cells and patient-derived xenograft models. We found that UBTF-TD protein maintained genomic occupancy at ribosomal DNA loci while also occupying genomic targets commonly dysregulated in UBTF-TD myeloid malignancies, such as the HOXA/HOXB gene clusters and MEIS1. These data suggest that UBTF-TD is a gain-of-function alteration that results in mislocalization to genomic loci dysregulated in UBTF-TD leukemias. UBTF-TD also co-occupies key genomic loci with KMT2A and menin, which are known to be key partners involved in HOX-dysregulated leukemias. Using a protein degradation system, we showed that stemness, proliferation, and transcriptional signatures are dependent on sustained UBTF-TD localization to chromatin. Finally, we demonstrate that primary cells from UBTF-TD leukemias are sensitive to the menin inhibitor SNDX-5613, resulting in markedly reduced in vitro and in vivo tumor growth, myeloid differentiation, and abrogation of the UBTF-TD leukemic expression signature. These findings provide a viable therapeutic strategy for patients with this high-risk AML subtype.
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Affiliation(s)
- Juan M. Barajas
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Milad Rasouli
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Hematology/Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Masayuki Umeda
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Rebecca Mohnani
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Bright Arthur
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Tamara Westover
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Melvin E. Thomas
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Minoo Ashtiani
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Laura J. Janke
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Emily Xiong
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Chandra Rolle
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jonathan Low
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN
| | - Reethu Krishan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Guangchun Song
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Michael P. Walsh
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jing Ma
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Jeffrey E. Rubnitz
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Christian M. Zwaan
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Hematology/Oncology, Erasmus MC-Sophia Children’s Hospital, Rotterdam, The Netherlands
| | - Olaf Heidenreich
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
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5
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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6
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Lu Y, Wang S, Jiao Y. The Effects of Deregulated Ribosomal Biogenesis in Cancer. Biomolecules 2023; 13:1593. [PMID: 38002277 PMCID: PMC10669593 DOI: 10.3390/biom13111593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/04/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Ribosomes are macromolecular ribonucleoprotein complexes assembled from RNA and proteins. Functional ribosomes arise from the nucleolus, require ribosomal RNA processing and the coordinated assembly of ribosomal proteins (RPs), and are frequently hyperactivated to support the requirement for protein synthesis during the self-biosynthetic and metabolic activities of cancer cells. Studies have provided relevant information on targeted anticancer molecules involved in ribosome biogenesis (RiBi), as increased RiBi is characteristic of many types of cancer. The association between unlimited cell proliferation and alterations in specific steps of RiBi has been highlighted as a possible critical driver of tumorigenesis and metastasis. Thus, alterations in numerous regulators and actors involved in RiBi, particularly in cancer, significantly affect the rate and quality of protein synthesis and, ultimately, the transcriptome to generate the associated proteome. Alterations in RiBi in cancer cells activate nucleolar stress response-related pathways that play important roles in cancer-targeted interventions and immunotherapies. In this review, we focus on the association between alterations in RiBi and cancer. Emphasis is placed on RiBi deregulation and its secondary consequences, including changes in protein synthesis, loss of RPs, adaptive transcription and translation, nucleolar stress regulation, metabolic changes, and the impaired ribosome biogenesis checkpoint.
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Affiliation(s)
| | - Shizhuo Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110055, China;
| | - Yisheng Jiao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110055, China;
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7
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Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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8
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Theophanous A, Christodoulou A, Mattheou C, Sibai DS, Moss T, Santama N. Transcription factor UBF depletion in mouse cells results in downregulation of both downstream and upstream elements of the rRNA transcription network. J Biol Chem 2023; 299:105203. [PMID: 37660911 PMCID: PMC10558777 DOI: 10.1016/j.jbc.2023.105203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Transcription/processing of the ribosomal RNA (rRNA) precursor, as part of ribosome biosynthesis, is intensively studied and characterized in eukaryotic cells. Here, we constructed shRNA-based mouse cell lines partially silenced for the Upstream Binding Factor UBF, the master regulator of rRNA transcription and organizer of open rDNA chromatin. Full Ubf silencing in vivo is not viable, and these new tools allow further characterization of rRNA transcription and its coordination with cellular signaling. shUBF cells display cell cycle G1 delay and reduced 47S rRNA precursor and 28S rRNA at baseline and serum-challenged conditions. Growth-related mTOR signaling is downregulated with the fractions of active phospho-S6 Kinase and pEIF4E translation initiation factor reduced, similar to phosphorylated cell cycle regulator retinoblastoma, pRB, positive regulator of UBF availability/rRNA transcription. Additionally, we find transcription-competent pUBF (Ser484) severely restricted and its interacting initiation factor RRN3 reduced and responsive to extracellular cues. Furthermore, fractional UBF occupancy on the rDNA unit is decreased in shUBF, and expression of major factors involved in different aspects of rRNA transcription is severely downregulated by UBF depletion. Finally, we observe reduced RNA Pol1 occupancy over rDNA promoter sequences and identified unexpected regulation of RNA Pol1 expression, relative to serum availability and under UBF silencing, suggesting that regulation of rRNA transcription may not be restricted to modulation of Pol1 promoter binding/elongation rate. Overall, this work reveals that UBF depletion has a critical downstream and upstream impact on the whole network orchestrating rRNA transcription in mammalian cells.
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Affiliation(s)
- Andria Theophanous
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | | | - Dany S Sibai
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Tom Moss
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada
| | - Niovi Santama
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
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9
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Moss T, LeDoux MS, Crane-Robinson C. HMG-boxes, ribosomopathies and neurodegenerative disease. Front Genet 2023; 14:1225832. [PMID: 37600660 PMCID: PMC10435976 DOI: 10.3389/fgene.2023.1225832] [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: 05/19/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
The UBTF E210K neuroregression syndrome is a predominantly neurological disorder caused by recurrent de novo dominant variants in Upstream Binding Factor, that is, essential for transcription of the ribosomal RNA genes. This unusual form of ribosomopathy is characterized by a slow decline in cognition, behavior, and sensorimotor functioning during the critical period of development. UBTF (or UBF) is a multi-HMGB-box protein that acts both as an epigenetic factor to establish "open" chromatin on the ribosomal genes and as a basal transcription factor in their RNA Polymerase I transcription. Here we review the possible mechanistic connections between the UBTF variants, ribosomal RNA gene transcription and the neuroregression syndrome, and suggest that DNA topology may play an important role.
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Affiliation(s)
- Tom Moss
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Mark S. LeDoux
- Department of Psychology, University of Memphis, Memphis, TN, United States
- Veracity Neuroscience LLC, Memphis, TN, United States
| | - Colyn Crane-Robinson
- Biophysics Laboratories, School of Biology, University of Portsmouth, Portsmouth, United Kingdom
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10
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Zhu G, Khalid F, Zhang D, Cao Z, Maity P, Kestler HA, Orioli D, Scharffetter-Kochanek K, Iben S. Ribosomal Dysfunction Is a Common Pathomechanism in Different Forms of Trichothiodystrophy. Cells 2023; 12:1877. [PMID: 37508541 PMCID: PMC10377840 DOI: 10.3390/cells12141877] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Mutations in a broad variety of genes can provoke the severe childhood disorder trichothiodystrophy (TTD) that is classified as a DNA repair disease or a transcription syndrome of RNA polymerase II. In an attempt to identify the common underlying pathomechanism of TTD we performed a knockout/knockdown of the two unrelated TTD factors TTDN1 and RNF113A and investigated the consequences on ribosomal biogenesis and performance. Interestingly, interference with these TTD factors created a nearly uniform impact on RNA polymerase I transcription with downregulation of UBF, disturbed rRNA processing and reduction of the backbone of the small ribosomal subunit rRNA 18S. This was accompanied by a reduced quality of decoding in protein translation and the accumulation of misfolded and carbonylated proteins, indicating a loss of protein homeostasis (proteostasis). As the loss of proteostasis by the ribosome has been identified in the other forms of TTD, here we postulate that ribosomal dysfunction is a common underlying pathomechanism of TTD.
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Affiliation(s)
- Gaojie Zhu
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Fatima Khalid
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Danhui Zhang
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Zhouli Cao
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Pallab Maity
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Hans A Kestler
- Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Donata Orioli
- Istituto di Genetica Molecolare L.L. Cavalli-Sforza CNR, 27100 Pavia, Italy
| | | | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
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11
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Georgi JA, Stasik S, Eckardt JN, Zukunft S, Hartwig M, Röllig C, Middeke JM, Oelschlägel U, Krug U, Sauer T, Scholl S, Hochhaus A, Brümmendorf TH, Naumann R, Steffen B, Einsele H, Schaich M, Burchert A, Neubauer A, Schäfer-Eckart K, Schliemann C, Krause SW, Hänel M, Noppeney R, Kaiser U, Baldus CD, Kaufmann M, Müller-Tidow C, Platzbecker U, Berdel WE, Serve H, Ehninger G, Bornhäuser M, Schetelig J, Kroschinsky F, Thiede C. UBTF tandem duplications are rare but recurrent alterations in adult AML and associated with younger age, myelodysplasia, and inferior outcome. Blood Cancer J 2023; 13:88. [PMID: 37236968 DOI: 10.1038/s41408-023-00858-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Tandem-duplication mutations of the UBTF gene (UBTF-TDs) coding for the upstream binding transcription factor have recently been described in pediatric patients with acute myeloid leukemia (AML) and were found to be associated with particular genetics (trisomy 8 (+8), FLT3-internal tandem duplications (FLT3-ITD), WT1-mutations) and inferior outcome. Due to limited knowledge on UBTF-TDs in adult AML, we screened 4247 newly diagnosed adult AML and higher-risk myelodysplastic syndrome (MDS) patients using high-resolution fragment analysis. UBTF-TDs were overall rare (n = 52/4247; 1.2%), but significantly enriched in younger patients (median age 41 years) and associated with MDS-related morphology as well as significantly lower hemoglobin and platelet levels. Patients with UBTF-TDs had significantly higher rates of +8 (34% vs. 9%), WT1 (52% vs. 7%) and FLT3-ITD (50% vs. 20.8%) co-mutations, whereas UBTF-TDs were mutually exclusive with several class-defining lesions such as mutant NPM1, in-frame CEBPAbZIP mutations as well as t(8;21). Based on the high-variant allele frequency found and the fact that all relapsed patients analyzed (n = 5) retained the UBTF-TD mutation, UBTF-TDs represent early clonal events and are stable over the disease course. In univariate analysis, UBTF-TDs did not represent a significant factor for overall or relapse-free survival in the entire cohort. However, in patients under 50 years of age, who represent the majority of UBTF-mutant patients, UBTF-TDs were an independent prognostic factor for inferior event-free (EFS), relapse-free (RFS) and overall survival (OS), which was confirmed by multivariable analyses including established risk factors such as age and ELN2022 genetic risk groups (EFS [HR: 2.20; 95% CI 1.52-3.17, p < 0.001], RFS [HR: 1.59; 95% CI 1.02-2.46, p = 0.039] and OS [HR: 1.64; 95% CI 1.08-2.49, p = 0.020]). In summary, UBTF-TDs appear to represent a novel class-defining lesion not only in pediatric AML but also younger adults and are associated with myelodysplasia and inferior outcome in these patients.
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Affiliation(s)
- Julia-Annabell Georgi
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Sebastian Stasik
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Jan-Niklas Eckardt
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Sven Zukunft
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Marita Hartwig
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Christoph Röllig
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Jan Moritz Middeke
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Uta Oelschlägel
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Utz Krug
- Medizinische Klinik 3, Klinikum Leverkusen, Leverkusen, Germany
| | - Tim Sauer
- Universität Heidelberg, Medizinische Klinik und Poliklinik, Abteilung Innere Medizin V, Heidelberg, Germany
| | - Sebastian Scholl
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Andreas Hochhaus
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | | | - Ralph Naumann
- Medizinische Klinik III, St. Marien-Krankenhaus Siegen, Siegen, Germany
| | - Björn Steffen
- Medizinische Klinik 2, Hämatologie/Onkologie, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Markus Schaich
- Klinik für Hämatologie, Onkologie und Palliativmedizin, Rems-Murr-Klinikum Winnenden, Winnenden, Germany
| | - Andreas Burchert
- Klinik für Innere Medizin, Schwerpunkt Hämatologie, Onkologie und Immunologie, Philipps Universität Marburg, Marburg, Germany
| | - Andreas Neubauer
- Klinik für Innere Medizin, Schwerpunkt Hämatologie, Onkologie und Immunologie, Philipps Universität Marburg, Marburg, Germany
| | - Kerstin Schäfer-Eckart
- Klinikum Nürnberg, Paracelsus Medizinische Privatuniversität, Medizinische Klinik 5, Nürnberg, Germany
| | | | - Stefan W Krause
- Medizinische Klinik 5, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Mathias Hänel
- Klinik für Innere Medizin III, Klinikum Chemnitz, Chemnitz, Germany
| | - Richard Noppeney
- Klinik für Hämatologie, Universitätsklinikum Essen, Essen, Germany
| | - Ulrich Kaiser
- Medizinische Klinik II, St. Bernward Krankenhaus, Hildesheim, Germany
| | - Claudia D Baldus
- Klinik für Innere Medizin II, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Martin Kaufmann
- Abteilung für Hämatologie, Onkologie und Palliativmedizin, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - Carsten Müller-Tidow
- Universität Heidelberg, Medizinische Klinik und Poliklinik, Abteilung Innere Medizin V, Heidelberg, Germany
| | - Uwe Platzbecker
- Klinik und Poliklinik für Hämatologie, Zelltherapie und Hämostaseologie, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Wolfgang E Berdel
- Medizinische Klinik A, Universitätsklinikum Münster, Münster, Germany
| | - Hubert Serve
- Medizinische Klinik 2, Hämatologie/Onkologie, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
| | | | - Martin Bornhäuser
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
- National Center for Tumor Diseases NCT, Dresden, Germany
| | - Johannes Schetelig
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
- DKMS Clinical Trials Unit, Dresden, Germany
| | - Frank Kroschinsky
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Christian Thiede
- Medizinische Klinik und Poliklinik 1, Universitätsklinikum Carl Gustav Carus, Dresden, Germany.
- AgenDix GmbH, Dresden, Germany.
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12
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Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tlučková K, Mars JC, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Sci Alliance 2022; 5:5/11/e202201568. [PMID: 36271492 PMCID: PMC9438803 DOI: 10.26508/lsa.202201568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/20/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022] Open
Abstract
We characterize the human RNA polymerase I by evolutionary biochemistry and cryo-EM revealing a built-in structural domain that apparently serves as transcription factor–binding platform in metazoans. Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Pilsl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Andrea Bleckmann
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Höcherl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Florian B Heiss
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Guillermo Abascal-Palacios
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Biofisika Institute (CSIC, UPV/EHU), Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Ewan P Ramsay
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Fondazione Human Technopole, Structural Biology Research Centre, Milan, Italy
| | | | - Jean-Clement Mars
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
- Borden Laboratory, IRIC, Université de Montréal, Montréal, Québec, Canada
| | - Torben Fürtges
- Protein Crystallography, Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Till Rudack
- Protein Crystallography, Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Carrie Bernecky
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Valérie Lamour
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Integrated Structural Biology, Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Konstantin Panov
- School of Biological Sciences and PGJCCR, Queen’s University Belfast, Belfast, UK
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Fondazione Human Technopole, Structural Biology Research Centre, Milan, Italy
| | - Tom Moss
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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13
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Hori RT, Moshahid Khan M, Xiao J, Hargrove PW, Moss T, LeDoux MS. Behavioral and molecular effects of Ubtf knockout and knockdown in mice. Brain Res 2022; 1793:148053. [PMID: 35973608 PMCID: PMC10908547 DOI: 10.1016/j.brainres.2022.148053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/10/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022]
Abstract
The UBTF E210K neuroregression syndrome is caused by de novo dominant mutations in UBTF (NM_014233.3:c.628G > A, p.Glu210Lys). In humans, onset is typically at 2.5 to 3 years and characterized by slow progression of global motor, cognitive and behavioral dysfunction. Other potentially pathogenic UBTF variants have been reported in humans with severe neurological disease and it remains undetermined if the UBTF E210K mutation operates via gain- and/or loss-of-function. Here we examine the behavioral, cognitive, motor, and molecular effects of Ubtf knockout and knockdown in mice as a means of gauging the role of loss-of-function in humans. Ubtf+/- mice show progression of behavioral (dominance tube), cognitive (cross maze), and mild motor abnormalities from 3 to 18 months. At 18 months, Ubtf+/- mice had more slips on a raised 9-mm round beam task, shorter latencies to fall on the accelerated rotarod, reduced open field vertical and jump counts, and significant deficits in spatial learning and memory. Via crosses to Nestin-Cre (NesCre) mice we found that homozygous Ubtf deletion limited to the central nervous system was embryonic lethal. Tamoxifen-induced homozygous knockdown of Ubtf in adult mice with the Cre-ERT2 system was associated with precipitous deterioration in neurological functioning. At the molecular level, 18-month-old Ubtf+/- mice showed mild increases in cerebellar 53BP1 immunoreactivity. These findings show that UBTF is essential for embryogenesis and survival in adults, and the deleterious effects of UBTF haploinsufficiency progress with age. Loss-of-function mechanisms may contribute, in part, to the human UBTF E210K neuroregression syndrome.
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Affiliation(s)
- Roderick T Hori
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Physical Therapy, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Jianfeng Xiao
- Department of Neurology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Phillip W Hargrove
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Tom Moss
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada
| | - Mark S LeDoux
- Department of Psychology, University of Memphis, Memphis, TN 38152, USA; Veracity Neuroscience, Memphis, TN, 38157, USA.
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