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Battista S, Fedele M, Secco L, Ingo AMD, Sgarra R, Manfioletti G. Binding to the Other Side: The AT-Hook DNA-Binding Domain Allows Nuclear Factors to Exploit the DNA Minor Groove. Int J Mol Sci 2024; 25:8863. [PMID: 39201549 DOI: 10.3390/ijms25168863] [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: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
The "AT-hook" is a peculiar DNA-binding domain that interacts with DNA in the minor groove in correspondence to AT-rich sequences. This domain has been first described in the HMGA protein family of architectural factors and later in various transcription factors and chromatin proteins, often in association with major groove DNA-binding domains. In this review, using a literature search, we identified about one hundred AT-hook-containing proteins, mainly chromatin proteins and transcription factors. After considering the prototypes of AT-hook-containing proteins, the HMGA family, we review those that have been studied in more detail and that have been involved in various pathologies with a particular focus on cancer. This review shows that the AT-hook is a domain that gives proteins not only the ability to interact with DNA but also with RNA and proteins. This domain can have enzymatic activity and can influence the activity of the major groove DNA-binding domain and chromatin docking modules when present, and its activity can be modulated by post-translational modifications. Future research on the function of AT-hook-containing proteins will allow us to better decipher their function and contribution to the different pathologies and to eventually uncover their mutual influences.
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Affiliation(s)
- Sabrina Battista
- Institute of Experimental Endocrinology and Oncology "G. Salvatore" (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Monica Fedele
- Institute of Experimental Endocrinology and Oncology "G. Salvatore" (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Luca Secco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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2
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Saha D, Animireddy S, Bartholomew B. The SWI/SNF ATP-dependent chromatin remodeling complex in cell lineage priming and early development. Biochem Soc Trans 2024; 52:603-616. [PMID: 38572912 PMCID: PMC11088921 DOI: 10.1042/bst20230416] [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: 12/19/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
ATP dependent chromatin remodelers have pivotal roles in transcription, DNA replication and repair, and maintaining genome integrity. SWI/SNF remodelers were first discovered in yeast genetic screens for factors involved in mating type switching or for using alternative energy sources therefore termed SWI/SNF complex (short for SWItch/Sucrose NonFermentable). The SWI/SNF complexes utilize energy from ATP hydrolysis to disrupt histone-DNA interactions and shift, eject, or reposition nucleosomes making the underlying DNA more accessible to specific transcription factors and other regulatory proteins. In development, SWI/SNF orchestrates the precise activation and repression of genes at different stages, safe guards the formation of specific cell lineages and tissues. Dysregulation of SWI/SNF have been implicated in diseases such as cancer, where they can drive uncontrolled cell proliferation and tumor metastasis. Additionally, SWI/SNF defects are associated with neurodevelopmental disorders, leading to disruption of neural development and function. This review offers insights into recent developments regarding the roles of the SWI/SNF complex in pluripotency and cell lineage primining and the approaches that have helped delineate its importance. Understanding these molecular mechanisms is crucial for unraveling the intricate processes governing embryonic stem cell biology and developmental transitions and may potentially apply to human diseases linked to mutations in the SWI/SNF complex.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77054, U.S.A
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3
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Breindl M, Spitzer D, Gerasimaitė R, Kairys V, Schubert T, Henfling R, Schwartz U, Lukinavičius G, Manelytė L. Biochemical and cellular insights into the Baz2B protein, a non-catalytic subunit of the chromatin remodeling complex. Nucleic Acids Res 2024; 52:337-354. [PMID: 38000389 PMCID: PMC10783490 DOI: 10.1093/nar/gkad1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Baz2B is a regulatory subunit of the ATP-dependent chromatin remodeling complexes BRF1 and BRF5, which control access to DNA during DNA-templated processes. Baz2B has been implicated in several diseases and also in unhealthy ageing, however limited information is available on the domains and cellular roles of Baz2B. To gain more insight into the Baz2B function, we biochemically characterized the TAM (Tip5/ARBP/MBD) domain with the auxiliary AT-hook motifs and the bromodomain (BRD). We observed alterations in histone code recognition in bromodomains carrying cancer-associated point mutations, suggesting their potential involvement in disease. Furthermore, the depletion of Baz2B in the Hap1 cell line resulted in altered cell morphology, reduced colony formation and perturbed transcriptional profiles. Despite that, super-resolution microscopy images revealed no changes in the overall chromatin structure in the absence of Baz2B. These findings provide insights into the biological function of Baz2B.
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Affiliation(s)
- Matthias Breindl
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Dominika Spitzer
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Visvaldas Kairys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | | | - Ramona Henfling
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
| | - Uwe Schwartz
- NGS Analysis Center, University of Regensburg, Regensburg DE-93053, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, DE-37077 Göttingen, Germany
| | - Laura Manelytė
- Biochemistry III, University of Regensburg, Regensburg DE-93053, Germany
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Corbeski I, Horn V, van der Valk RA, le Paige U, Dame RT, van Ingen H. Microscale Thermophoresis Analysis of Chromatin Interactions. Methods Mol Biol 2024; 2819:357-379. [PMID: 39028515 DOI: 10.1007/978-1-0716-3930-6_17] [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] [Indexed: 07/20/2024]
Abstract
Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. The activity of architectural proteins is often subject to further modulation and regulation through the interaction with a diverse array of other protein factors. Detailed knowledge on the binding modes involved is crucial for our understanding of how these protein-protein and protein-DNA interactions shape the functional landscape of chromatin in all kingdoms of life: bacteria, archaea, and eukarya.Microscale thermophoresis (MST) is a biophysical technique for the study of biomolecular interactions. It has seen increasing application in recent years thanks to its solution-based nature, rapid application, modest sample demand, and the sensitivity of the thermophoresis effect to binding events.Here, we describe the use of MST in the study of chromatin interactions. The emphasis lies on the wide range of ways in which these experiments are set up and the diverse types of information they reveal. These aspects are illustrated with four very different systems: the sequence-dependent DNA compaction by architectural protein HMfB, the sequential binding of core histone complexes to histone chaperone APLF, the impact of the nucleosomal context on the recognition of histone modifications, and the binding of a viral peptide to the nucleosome. Special emphasis is given to the key steps in the design, execution, and analysis of MST experiments in the context of the provided examples.
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Affiliation(s)
- Ivan Corbeski
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Velten Horn
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- CSL Behring, Hattersheim, Germany
| | - Ramon A van der Valk
- Kavli Institute of NanoScience, Department of Bionanoscience, Faculty of Applied Sciences, TU Delft, Delft, The Netherlands
| | - Ulric le Paige
- Structure and Dynamics of Biomolecules, Department of Chemistry, Ecole Normale Supérieure - Paris Sciences et Lettres, Paris, France
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Hugo van Ingen
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
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5
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Saha D, Hailu S, Hada A, Lee J, Luo J, Ranish JA, Lin YC, Feola K, Persinger J, Jain A, Liu B, Lu Y, Sen P, Bartholomew B. The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming. Nat Commun 2023; 14:4682. [PMID: 37542049 PMCID: PMC10403523 DOI: 10.1038/s41467-023-40386-8] [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: 12/30/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit's AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Solomon Hailu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- Illumina, 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Arjan Hada
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jeff A Ranish
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Yuan-Chi Lin
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- BioAgilytix, Durham, NC, 27713, USA
| | - Kyle Feola
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- Department of Internal Medicine (Nephrology) and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jim Persinger
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Abhinav Jain
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA.
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA.
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6
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In vivo CRISPR screening identifies BAZ2 chromatin remodelers as druggable regulators of mammalian liver regeneration. Cell Stem Cell 2022; 29:372-385.e8. [PMID: 35090595 PMCID: PMC8897233 DOI: 10.1016/j.stem.2022.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 09/17/2021] [Accepted: 12/30/2021] [Indexed: 12/17/2022]
Abstract
Identifying new pathways that regulate mammalian regeneration is challenging due to the paucity of in vivo screening approaches. We employed pooled CRISPR knockout and activation screening in the regenerating liver to evaluate 165 chromatin regulatory proteins. Both screens identified the imitation-SWI chromatin remodeling components Baz2a and Baz2b, not previously implicated in regeneration. In vivo sgRNA, siRNA, and knockout strategies against either paralog confirmed increased regeneration. Distinct BAZ2-specific bromodomain inhibitors, GSK2801 and BAZ2-ICR, resulted in accelerated liver healing after diverse injuries. Inhibitor-treated mice also exhibited improved healing in an inflammatory bowel disease model, suggesting multi-tissue applicability. Transcriptomics on regenerating livers showed increases in ribosomal and cell cycle mRNAs. Surprisingly, CRISPRa screening to define mechanisms showed that overproducing Rpl10a or Rpl24 was sufficient to drive regeneration, whereas Rpl24 haploinsufficiency was rate limiting for BAZ2 inhibition-mediated regeneration. The discovery of regenerative roles for imitation-SWI components provides immediate strategies to enhance tissue repair.
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7
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Chen S, Zhou M, Dong A, Loppnau P, Wang M, Min J, Liu K. Structural basis of the TAM domain of BAZ2A in binding to DNA or RNA independent of methylation status. J Biol Chem 2021; 297:101351. [PMID: 34715126 PMCID: PMC8600091 DOI: 10.1016/j.jbc.2021.101351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/26/2022] Open
Abstract
Bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) (also called transcription termination factor-1 interacting protein 5), a key component of the nucleolar remodeling complex, recruits the nucleolar remodeling complex to ribosomal RNA genes, leading to their transcriptional repression. In addition to its tandem plant homeodomain-bromodomain that is involved in binding to acetylated histone H4, BAZ2A also contains a methyl-CpG-binding domain (MBD)-like Tip5/ARBP/MBD (TAM) domain that shares sequence homology with the MBD. In contrast with the methyl-CpG-binding ability of the canonical MBD, the BAZ2A TAM domain has been shown to bind to promoter-associated RNAs of ribosomal RNA genes and promoter DNAs of other genes independent of DNA methylation. Nevertheless, how the TAM domain binds to RNA/DNA mechanistically remains elusive. Here, we characterized the DNA-/RNA-binding basis of the BAZ2A TAM domain by EMSAs, isothermal titration calorimetry binding assays, mutagenesis analysis, and X-ray crystallography. Our results showed that the TAM domain of BAZ2A selectively binds to dsDNA and dsRNA and that it binds to the backbone of dsDNA in a sequence nonspecific manner, which is distinct from the base-specific binding of the canonical MBD. Thus, our results explain why the TAM domain of BAZ2A does not specifically bind to mCG or TG dsDNA like the canonical MBD and also provide insights for further biological study of BAZ2A acting as a transcription factor in the future.
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Affiliation(s)
- Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Min Wang
- Testing & Analysis Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China; Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, PR China.
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Smirnov E, Chmúrčiaková N, Liška F, Bažantová P, Cmarko D. Variability of Human rDNA. Cells 2021; 10:cells10020196. [PMID: 33498263 PMCID: PMC7909238 DOI: 10.3390/cells10020196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.
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9
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Rolicka A, Guo Y, Gañez Zapater A, Tariq K, Quin J, Vintermist A, Sadeghifar F, Arsenian-Henriksson M, Östlund Farrants AK. The chromatin-remodeling complexes B-WICH and NuRD regulate ribosomal transcription in response to glucose. FASEB J 2020; 34:10818-10834. [PMID: 32598531 DOI: 10.1096/fj.202000411r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022]
Abstract
Regulation of ribosomal transcription is under tight control from environmental stimuli, and this control involves changes in the chromatin structure. The underlying mechanism of how chromatin changes in response to nutrient and energy supply in the cell is still unclear. The chromatin-remodeling complex B-WICH is involved in activating the ribosomal transcription, and we show here that knock down of the B-WICH component WSTF results in cells that do not respond to glucose. The promoter is less accessible, and RNA pol I and its transcription factors SL1/TIF-1B and RRN3/TIF-1A, as well as the proto-oncogene c-MYC and the activating deacetylase SIRT7 do not bind upon glucose stimulation. In contrast, the repressive chromatin state that forms after glucose deprivation is reversible, and RNA pol I factors are recruited. WSTF knock down results in an accumulation of the ATPase CHD4, a component of the NuRD chromatin remodeling complex, which is responsible for establishing a repressive poised state at the promoter. The TTF-1, which binds and affect the binding of the chromatin complexes, is important to control the association of activating chromatin component UBF. We suggest that B-WICH is required to allow for a shift to an active chromatin state upon environmental stimulation, by counteracting the repressive state induced by the NuRD complex.
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Affiliation(s)
- Anna Rolicka
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Antoni Gañez Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Kanwal Tariq
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Jaclyn Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Anna Vintermist
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Fatemeh Sadeghifar
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum B7, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
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10
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Gao JH, Wang TY, Zhang MY, Shi F, Gu SZ. Identification of consensus sequence from matrix attachment regions and functional analysis of its activity in stably transfected Chinese hamster ovary cells. J Cell Biochem 2019; 120:13985-13993. [PMID: 30957285 DOI: 10.1002/jcb.28673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/30/2018] [Accepted: 01/09/2019] [Indexed: 01/01/2023]
Abstract
Matrix attachment regions (MARs) can enhance transgene expression levels and maintain stability. However, the consensus sequence from MARs and its functional analysis remains to be examined. Here, we assessed a possible consensus sequence from MARs and assessed its activity in stably transfected Chinese hamster ovary (CHO) cells. First, we analyzed the effects of 10 MARs on transfected CHO cells and then analyzed the consensus motifs from these MARs using a bioinformatics method. The consensus sequence was synthesized and cloned upstream or downstream of the eukaryotic vector. The constructs were transfected into CHO cells and the expression levels and stability of enhanced green fluorescent protein were detected by flow cytometry. The results indicated that eight of the ten MARs increased transgene expression in transfected CHO cells. Three consensus motifs were found after bioinformatics analyses. The consensus sequence tandemly enhanced transgene expression when it was inserted into the eukaryotic expression vector; the effect of the addition upstream was stronger than that downstream. Thus, we found a MAR consensus sequence that may regulate the MAR-mediated increase in transgene expression.
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Affiliation(s)
- Jian-Hui Gao
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Mao-Ying Zhang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Fang Shi
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan, China
| | - Shan-Zhi Gu
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
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11
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A novel DNA-binding motif in prostate tumor overexpressed-1 (PTOV1) required for the expression of ALDH1A1 and CCNG2 in cancer cells. Cancer Lett 2019; 452:158-167. [PMID: 30922918 DOI: 10.1016/j.canlet.2019.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/01/2019] [Accepted: 03/08/2019] [Indexed: 12/26/2022]
Abstract
PTOV1 is a transcription and translation regulator and a promoter of cancer progression. Its overexpression in prostate cancer induces transcription of drug resistance and self-renewal genes, and docetaxel resistance. Here we studied PTOV1 ability to directly activate the transcription of ALDH1A1 and CCNG2 by binding to specific promoter sequences. Chromatin immunoprecipitation and electrophoretic mobility shift assays identified a DNA-binding motif inside the PTOV-A domain with similarities to known AT-hooks that specifically interacts with ALDH1A1 and CCNG2 promoters. Mutation of this AT-hook-like sequence significantly decreased the expression of ALDH1A1 and CCNG2 promoted by PTOV1. Immunohistochemistry revealed the association of PTOV1 with mitotic chromosomes in high grade prostate, colon, bladder, and breast carcinomas. Overexpression of PTOV1, ALDH1A1, and CCNG2 significantly correlated with poor prognosis in prostate carcinomas and with shorter relapse-free survival in colon carcinoma. The previously described interaction with translation complexes and its direct binding to ALDH1A1 and CCNG2 promoters found here reveal the PTOV1 capacity to modulate the expression of critical genes at multiple levels in aggressive cancers. Remarkably, the AT-hook motifs in PTOV1 open possibilities for selective targeting its nuclear and/or cytoplasmic activities.
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12
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Diesch J, Bywater MJ, Sanij E, Cameron DP, Schierding W, Brajanovski N, Son J, Sornkom J, Hein N, Evers M, Pearson RB, McArthur GA, Ganley ARD, O’Sullivan JM, Hannan RD, Poortinga G. Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation. Commun Biol 2019; 2:39. [PMID: 30701204 PMCID: PMC6349880 DOI: 10.1038/s42003-019-0284-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 12/28/2018] [Indexed: 12/15/2022] Open
Abstract
The three-dimensional organization of the genome contributes to its maintenance and regulation. While chromosomal regions associate with nucleolar ribosomal RNA genes (rDNA), the biological significance of rDNA-genome interactions and whether they are dynamically regulated during disease remain unclear. rDNA chromatin exists in multiple inactive and active states and their transition is regulated by the RNA polymerase I transcription factor UBTF. Here, using a MYC-driven lymphoma model, we demonstrate that during malignant progression the rDNA chromatin converts to the open state, which is required for tumor cell survival. Moreover, this rDNA transition co-occurs with a reorganization of rDNA-genome contacts which correlate with gene expression changes at associated loci, impacting gene ontologies including B-cell differentiation, cell growth and metabolism. We propose that UBTF-mediated conversion to open rDNA chromatin during malignant transformation contributes to the regulation of specific gene pathways that regulate growth and differentiation through reformed long-range physical interactions with the rDNA.
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Affiliation(s)
- Jeannine Diesch
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- Present Address: Josep Carreras Leukaemia Research Institute, Barcelona, 08021 Spain
| | - Megan J. Bywater
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- Present Address: QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029 Australia
| | - Elaine Sanij
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- Department of Pathology, University of Melbourne, Parkville, VIC 3010 Australia
| | - Donald P. Cameron
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010 Australia
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, 1023 New Zealand
| | - Natalie Brajanovski
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
| | - Jinbae Son
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010 Australia
| | - Jirawas Sornkom
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010 Australia
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
| | - Maurits Evers
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
| | - Richard B. Pearson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010 Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800 VIC Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010 Australia
| | - Grant A. McArthur
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010 Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC 3065 Australia
| | - Austen R. D. Ganley
- School of Biological Sciences, The University of Auckland, Auckland, 1010 New Zealand
| | | | - Ross D. Hannan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010 Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800 VIC Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010 Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Gretchen Poortinga
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3010 Australia
- Department of Medicine, St Vincent’s Hospital, University of Melbourne, Fitzroy, VIC 3065 Australia
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13
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Abstract
The nucleolus as site of ribosome biogenesis holds a pivotal role in cell metabolism. It is composed of ribosomal DNA (rDNA), which is present as tandem arrays located in nucleolus organizer regions (NORs). In interphase cells, rDNA can be found inside and adjacent to nucleoli and the location is indicative for transcriptional activity of ribosomal genes-inactive rDNA (outside) versus active one (inside). Moreover, the nucleolus itself acts as a spatial organizer of non-nucleolar chromatin. Microscopy-based approaches offer the possibility to explore the spatially distinct localization of the different DNA populations in relation to the nucleolar structure. Recent technical developments in microscopy and preparatory methods may further our understanding of the functional architecture of nucleoli. This review will attempt to summarize the current understanding of mammalian nucleolar chromatin organization as seen from a microscopist's perspective.
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Affiliation(s)
- Christian Schöfer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
| | - Klara Weipoltshammer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
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14
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Asmari M, Ratih R, Alhazmi HA, El Deeb S. Thermophoresis for characterizing biomolecular interaction. Methods 2018; 146:107-119. [PMID: 29438829 DOI: 10.1016/j.ymeth.2018.02.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/06/2018] [Accepted: 02/09/2018] [Indexed: 12/20/2022] Open
Abstract
The study of biomolecular interactions is crucial to get more insight into the biological system. The interactions of protein-protein, protein-nucleic acids, protein-sugars, nucleic acid-nucleic acids and protein-small molecules are supporting therapeutics and technological developments. Recently, the development in a large number of analytical techniques for characterizing biomolecular interactions reflect the promising research investments in this field. In this review, microscale thermophoresis technology (MST) is presented as an analytical technique for characterizing biomolecular interactions. Recent years have seen much progress and several applications established. MST is a powerful technique in quantitation of binding events based on the movement of molecules in microscopic temperature gradient. Simplicity, free solutions analysis, low sample volume, short analysis time, and immobilization free are the MST advantages over other competitive techniques. A wide range of studies in biomolecular interactions have been successfully carried out using MST, which tend to the versatility of the technique to use in screening binding events in order to save time, cost and obtained high data quality.
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Affiliation(s)
- Mufarreh Asmari
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany
| | - Ratih Ratih
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany
| | - Hassan A Alhazmi
- College of Pharmacy, Jazan University, P.O. Box 114, 45142 Jazan, Saudi Arabia
| | - Sami El Deeb
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany.
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15
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Corbeski I, Horn V, van der Valk RA, le Paige UB, Dame RT, van Ingen H. Microscale Thermophoresis Analysis of Chromatin Interactions. Methods Mol Biol 2018; 1837:177-197. [PMID: 30109612 DOI: 10.1007/978-1-4939-8675-0_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. The activity of architectural proteins is often subject to further modulation and regulation through the interaction with a diverse array of other protein factors. Detailed knowledge on the binding modes involved is crucial for our understanding of how these protein-protein and protein-DNA interactions shape the functional landscape of chromatin in all kingdoms of life: bacteria, archaea, and eukarya.Microscale thermophoresis (MST) is a biophysical technique that has seen increasing application in the study of biomolecular interactions thanks to its solution-based nature, its rapid application, modest sample demand, and the sensitivity of the thermophoresis effect to binding events. Here, we describe the use of MST in the study of chromatin interactions, with emphasis on the wide range of ways in which these experiments are set up and the diverse types of information they reveal. These aspects are illustrated with four very different systems: the sequence-dependent DNA compaction by architectural protein HMfB; the sequential binding of core histone complexes to histone chaperone APLF; the impact of the nucleosomal context on the recognition of histone modifications; and the binding of a LANA-derived peptide to nucleosome core. Special emphasis is given to the key steps in the design, execution, and analysis of MST experiments in the context of the provided examples.
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Affiliation(s)
- Ivan Corbeski
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Velten Horn
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Ulric B le Paige
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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16
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Rajarajacholan UK, Thalappilly S, Riabowol K. ING1 regulates rRNA levels by altering nucleolar chromatin structure and mTOR localization. Nucleic Acids Res 2017; 45:1776-1792. [PMID: 27903908 PMCID: PMC5389678 DOI: 10.1093/nar/gkw1161] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 11/10/2016] [Indexed: 01/31/2023] Open
Abstract
Epigenetic, transcriptional and signaling processes in the nucleolus regulate rRNA transcription and cell growth. We report here that the tumor suppressor ING1b binds rDNA, regulates rDNA chromatin modifications and affects nucleolar localization of mTOR to modulate rRNA levels. ING1 represses rDNA transcription by recruiting HDAC1 to rDNA loci, increasing its association with the NoRC complex and deacetylating the histone H3K9 and H3K27 marks of active transcription. Loss of ING1 enhances nucleolar localization of phospho-mTOR and its association with Raptor and GβL, even during rapamycin treatment. ING1 inhibits rDNA transcription by inhibiting UBF activity and its interaction with mTOR. Regulation of rDNA heterochromatin and rRNA synthesis by ING1 is also apparent during normal cell growth and during cell stress. Moreover, this function was also important during PMA induced differentiation of THP1 cells, since knocking down ING1 affected the process by inhibiting rRNA transcriptional repression. These observations show that ING1 regulates the nucleolar epigenome and rDNA transcription suggesting that regulation of protein synthesis might serve as the basis for ING1 function as a type II tumor suppressor.
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Affiliation(s)
- Uma Karthika Rajarajacholan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Subhash Thalappilly
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Karl Riabowol
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Oncology, Faculty of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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17
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Hoang TT, Raines RT. Molecular basis for the autonomous promotion of cell proliferation by angiogenin. Nucleic Acids Res 2017; 45:818-831. [PMID: 27915233 PMCID: PMC5314776 DOI: 10.1093/nar/gkw1192] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/13/2016] [Accepted: 11/20/2016] [Indexed: 12/13/2022] Open
Abstract
Canonical growth factors act indirectly via receptor-mediated signal transduction pathways. Here, we report on an autonomous pathway in which a growth factor is internalized, has its localization regulated by phosphorylation, and ultimately uses intrinsic catalytic activity to effect epigenetic change. Angiogenin (ANG), a secreted vertebrate ribonuclease, is known to promote cell proliferation, leading to neovascularization as well as neuroprotection in mammals. Upon entering cells, ANG encounters the cytosolic ribonuclease inhibitor protein, which binds with femtomolar affinity. We find that protein kinase C and cyclin-dependent kinase phosphorylate ANG, enabling ANG to evade its inhibitor and enter the nucleus. After migrating to the nucleolus, ANG cleaves promoter-associated RNA, which prevents the recruitment of the nucleolar remodeling complex to the ribosomal DNA promoter. The ensuing derepression of rDNA transcription promotes cell proliferation. The biochemical basis for this unprecedented mechanism of signal transduction suggests new modalities for the treatment of cancers and neurological disorders.
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Affiliation(s)
- Trish T Hoang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ronald T Raines
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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18
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Filarsky M, Zillner K, Araya I, Villar-Garea A, Merkl R, Längst G, Németh A. The extended AT-hook is a novel RNA binding motif. RNA Biol 2016; 12:864-76. [PMID: 26156556 PMCID: PMC4615771 DOI: 10.1080/15476286.2015.1060394] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The AT-hook has been defined as a DNA binding peptide motif that contains a glycine-arginine-proline (G-R-P) tripeptide core flanked by basic amino acids. Recent reports documented variations in the sequence of AT-hooks and revealed RNA binding activity of some canonical AT-hooks, suggesting a higher structural and functional variability of this protein domain than previously anticipated. Here we describe the discovery and characterization of the extended AT-hook peptide motif (eAT-hook), in which basic amino acids appear symmetrical mainly at a distance of 12-15 amino acids from the G-R-P core. We identified 80 human and 60 mouse eAT-hook proteins and biochemically characterized the eAT-hooks of Tip5/BAZ2A, PTOV1 and GPBP1. Microscale thermophoresis and electrophoretic mobility shift assays reveal the nucleic acid binding features of this peptide motif, and show that eAT-hooks bind RNA with one order of magnitude higher affinity than DNA. In addition, cellular localization studies suggest a role for the N-terminal eAT-hook of PTOV1 in nucleocytoplasmic shuttling. In summary, our findings classify the eAT-hook as a novel nucleic acid binding motif, which potentially mediates various RNA-dependent cellular processes.
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Affiliation(s)
- Michael Filarsky
- a Biochemistry Center Regensburg ; University of Regensburg ; Regensburg , Germany
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19
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Abstract
Nucleoli are formed on the basis of ribosomal genes coding for RNAs of ribosomal particles, but also include a great variety of other DNA regions. In this article, we discuss the characteristics of ribosomal DNA: the structure of the rDNA locus, complex organization and functions of the intergenic spacer, multiplicity of gene copies in one cell, selective silencing of genes and whole gene clusters, relation to components of nucleolar ultrastructure, specific problems associated with replication. We also review current data on the role of non-ribosomal DNA in the organization and function of nucleoli. Finally, we discuss probable causes preventing efficient visualization of DNA in nucleoli.
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20
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Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015; 34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.
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Affiliation(s)
- Maïwen Caudron-Herger
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Teresa Pankert
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Jeanette Seiler
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Attila Németh
- Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
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21
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Tallant C, Valentini E, Fedorov O, Overvoorde L, Ferguson FM, Filippakopoulos P, Svergun DI, Knapp S, Ciulli A. Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC. Structure 2014; 23:80-92. [PMID: 25533489 PMCID: PMC4291147 DOI: 10.1016/j.str.2014.10.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/24/2014] [Accepted: 10/13/2014] [Indexed: 12/22/2022]
Abstract
Binding of the chromatin remodeling complex NoRC to RNA complementary to the rDNA promoter mediates transcriptional repression. TIP5, the largest subunit of NoRC, is involved in recruitment to rDNA by interactions with promoter-bound TTF-I, pRNA, and acetylation of H4K16. TIP5 domains that recognize posttranslational modifications on histones are essential for recruitment of NoRC to chromatin, but how these reader modules recognize site-specific histone tails has remained elusive. Here, we report crystal structures of PHD zinc finger and bromodomains from human TIP5 and BAZ2B in free form and bound to H3 and/or H4 histones. PHD finger functions as an independent structural module in recognizing unmodified H3 histone tails, and the bromodomain prefers H3 and H4 acetylation marks followed by a key basic residue, KacXXR. Further low-resolution analyses of PHD-bromodomain modules provide molecular insights into their trans histone tail recognition, required for nucleosome recruitment and transcriptional repression of the NoRC complex. TIP5 and BAZ2B PHD zinc fingers recognize unmodified H3K4 TIP5 and BAZ2B bromodomain recognize H4K16ac and H3K14ac with specific motif KacXXR Cocrystal structures of individual domains define the basis for histone recognition SAXS data for BAZ2B suggest independent PTM recognition
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Affiliation(s)
- Cynthia Tallant
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Erica Valentini
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Lois Overvoorde
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Fleur M Ferguson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK; Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Alessio Ciulli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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22
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Jerabek-Willemsen M, André T, Wanner R, Roth HM, Duhr S, Baaske P, Breitsprecher D. MicroScale Thermophoresis: Interaction analysis and beyond. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.03.009] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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23
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Manelyte L, Strohner R, Gross T, Längst G. Chromatin targeting signals, nucleosome positioning mechanism and non-coding RNA-mediated regulation of the chromatin remodeling complex NoRC. PLoS Genet 2014; 10:e1004157. [PMID: 24651573 PMCID: PMC3961174 DOI: 10.1371/journal.pgen.1004157] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 12/17/2013] [Indexed: 11/21/2022] Open
Abstract
Active and repressed ribosomal RNA (rRNA) genes are characterised by specific epigenetic marks and differentially positioned nucleosomes at their promoters. Repression of the rRNA genes requires a non-coding RNA (pRNA) and the presence of the nucleolar remodeling complex (NoRC). ATP-dependent chromatin remodeling enzymes are essential regulators of DNA-dependent processes, and this regulation occurs via the modulation of DNA accessibility in chromatin. We have studied the targeting of NoRC to the rRNA gene promoter; its mechanism of nucleosome positioning, in which a nucleosome is placed over the transcription initiation site; and the functional role of the pRNA. We demonstrate that NoRC is capable of recognising and binding to the nucleosomal rRNA gene promoter on its own and binds with higher affinity the nucleosomes positioned at non-repressive positions. NoRC recognises the promoter nucleosome within a chromatin array and positions the nucleosomes, as observed in vivo. NoRC uses the release mechanism of positioning, which is characterised by a reduced affinity for the remodeled substrate. The pRNA specifically binds to NoRC and regulates the enzyme by switching off its ATPase activity. Given the known role of pRNA in tethering NoRC to the rDNA, we propose that pRNA is a key factor that links the chromatin modification activity and scaffolding function of NoRC. Tumour cells overexpress ribosomal RNA (rRNA), which is required for ribosome assembly and cell growth. rRNA gene repression is mediated by the chromatin remodeling complex (NoRC) and a non-coding RNA that binds to this enzyme. This study addresses the mechanism of nucleosome positioning by NoRC and the functional role of the non-coding RNA, which is termed pRNA because it corresponds to the promoter sequence. NoRC recognises the promoter nucleosome in a chromatin array with high affinity and uses a release mechanism to position the nucleosome over the transcription initiation site. The pRNA binds specifically to NoRC and inhibits its ATPase activity. We suggest that the RNA retains NoRC at the gene promoter after remodeling, linking its chromatin modification and scaffolding activity to inactive rDNA copies.
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Affiliation(s)
- Laura Manelyte
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Ralf Strohner
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Thomas Gross
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Gernot Längst
- Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
- * E-mail:
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24
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Shiue CN, Nematollahi-Mahani A, Wright APH. Myc-induced anchorage of the rDNA IGS region to nucleolar matrix modulates growth-stimulated changes in higher-order rDNA architecture. Nucleic Acids Res 2014; 42:5505-17. [PMID: 24609384 PMCID: PMC4027186 DOI: 10.1093/nar/gku183] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Chromatin domain organization and the compartmentalized distribution of chromosomal regions are essential for packaging of deoxyribonucleic acid (DNA) in the eukaryotic nucleus as well as regulated gene expression. Nucleoli are the most prominent morphological structures of cell nuclei and nucleolar organization is coupled to cell growth. It has been shown that nuclear scaffold/matrix attachment regions often define the base of looped chromosomal domains in vivo and that they are thereby critical for correct chromosome architecture and gene expression. Here, we show regulated organization of mammalian ribosomal ribonucleic acid genes into distinct chromatin loops by tethering to nucleolar matrix via the non-transcribed inter-genic spacer region of the ribosomal DNA (rDNA). The rDNA gene loop structures are induced specifically upon growth stimulation and are dependent on the activity of the c-Myc protein. Matrix-attached rDNA genes are hypomethylated at the promoter and are thus available for transcriptional activation. rDNA genes silenced by methylation are not recruited to the matrix. c-Myc, which has been shown to induce rDNA transcription directly, is physically associated with rDNA gene looping structures and the intergenic spacer sequence in growing cells. Such a role of Myc proteins in gene activation has not been reported previously.
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Affiliation(s)
- Chiou-Nan Shiue
- Clinical Research Center (KFC), Department of Laboratory Medicine and Center for Biosciences, Karolinska Institute, SE-141 86 Huddinge, Sweden
| | - Amir Nematollahi-Mahani
- Clinical Research Center (KFC), Department of Laboratory Medicine and Center for Biosciences, Karolinska Institute, SE-141 86 Huddinge, Sweden
| | - Anthony P H Wright
- Clinical Research Center (KFC), Department of Laboratory Medicine and Center for Biosciences, Karolinska Institute, SE-141 86 Huddinge, Sweden
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25
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Gallenkamp D, Gelato KA, Haendler B, Weinmann H. Bromodomains and their pharmacological inhibitors. ChemMedChem 2014; 9:438-64. [PMID: 24497428 DOI: 10.1002/cmdc.201300434] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/23/2013] [Indexed: 12/15/2022]
Abstract
Over 60 bromodomains belonging to proteins with very different functions have been identified in humans. Several of them interact with acetylated lysine residues, leading to the recruitment and stabilization of protein complexes. The bromodomain and extra-terminal domain (BET) proteins contain tandem bromodomains which bind to acetylated histones and are thereby implicated in a number of DNA-centered processes, including the regulation of gene expression. The recent identification of inhibitors of BET and non-BET bromodomains is one of the few examples in which effective blockade of a protein-protein interaction can be achieved with a small molecule. This has led to major strides in the understanding of the function of bromodomain-containing proteins and their involvement in diseases such as cancer and inflammation. Indeed, BET bromodomain inhibitors are now being clinically evaluated for the treatment of hematological tumors and have also been tested in clinical trials for the relatively rare BRD-NUT midline carcinoma. This review gives an overview of the newest developments in the field, with a focus on the biology of selected bromodomain proteins on the one hand, and on reported pharmacological inhibitors on the other, including recent examples from the patent literature.
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