1
|
Sun Q, Jin C. Cell signaling and epigenetic regulation of nicotine-induced carcinogenesis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123426. [PMID: 38295934 PMCID: PMC10939829 DOI: 10.1016/j.envpol.2024.123426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/22/2023] [Accepted: 01/21/2024] [Indexed: 02/05/2024]
Abstract
Nicotine, a naturally occurring tobacco alkaloid responsible for tobacco addiction, has long been considered non-carcinogenic. However, emerging evidence suggests that nicotine may possess carcinogenic properties in mice and could be a potential carcinogen in humans. This review aims to summarize the potential molecular mechanisms underlying nicotine-induced carcinogenesis, with a specific focus on epigenetic regulation and the activation of nicotinic acetylcholine receptors (nAChRs) in addition to genotoxicity and excess reactive oxygen species (ROS). Additionally, we explore a novel hypothesis regarding nicotine's carcinogenicity involving the downregulation of stem-loop binding protein (SLBP), a critical regulator of canonical histone mRNA, and the polyadenylation of canonical histone mRNA. By shedding light on these mechanisms, this review underscores the need for further research to elucidate the carcinogenic potential of nicotine and its implications for human health.
Collapse
Affiliation(s)
- Qi Sun
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10010, USA; Department of Child and Adolescent Health, School of Public Health, China Medical University, Shenyang, Liaoning, 110013, China; Key Laboratory of Environmental Stress and Chronic Disease Control and Prevention, Ministry of Education, China Medical University, Shenyang, Liaoning, 110122, China
| | - Chunyuan Jin
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10010, USA; Perlmutter Cancer Center, NYU Langone Health, New York, NY, 10016, USA.
| |
Collapse
|
2
|
Mendiratta S, Ray-Gallet D, Lemaire S, Gatto A, Forest A, Kerlin MA, Almouzni G. Regulation of replicative histone RNA metabolism by the histone chaperone ASF1. Mol Cell 2024; 84:791-801.e6. [PMID: 38262410 DOI: 10.1016/j.molcel.2023.12.038] [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: 12/05/2022] [Revised: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]
Abstract
In S phase, duplicating and assembling the whole genome into chromatin requires upregulation of replicative histone gene expression. Here, we explored how histone chaperones control histone production in human cells to ensure a proper link with chromatin assembly. Depletion of the ASF1 chaperone specifically decreases the pool of replicative histones both at the protein and RNA levels. The decrease in their overall expression, revealed by total RNA sequencing (RNA-seq), contrasted with the increase in nascent/newly synthesized RNAs observed by 4sU-labeled RNA-seq. Further inspection of replicative histone RNAs showed a 3' end processing defect with an increase of pre-mRNAs/unprocessed transcripts likely targeted to degradation. Collectively, these data argue for a production defect of replicative histone RNAs in ASF1-depleted cells. We discuss how this regulation of replicative histone RNA metabolism by ASF1 as a "chaperone checkpoint" fine-tunes the histone dosage to avoid unbalanced situations deleterious for cell survival.
Collapse
Affiliation(s)
- Shweta Mendiratta
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, Equipe Labellisée Ligue contre le Cancer, 75005 Paris, France
| | - Dominique Ray-Gallet
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, Equipe Labellisée Ligue contre le Cancer, 75005 Paris, France
| | - Sébastien Lemaire
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, Equipe Labellisée Ligue contre le Cancer, 75005 Paris, France
| | - Alberto Gatto
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, Equipe Labellisée Ligue contre le Cancer, 75005 Paris, France
| | - Audrey Forest
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, Equipe Labellisée Ligue contre le Cancer, 75005 Paris, France
| | - Maciej A Kerlin
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, 75005 Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Laboratoire Dynamique du Noyau, Equipe Labellisée Ligue contre le Cancer, 75005 Paris, France.
| |
Collapse
|
3
|
Geisler MS, Kemp JP, Duronio RJ. Histone locus bodies: a paradigm for how nuclear biomolecular condensates control cell cycle regulated gene expression. Nucleus 2023; 14:2293604. [PMID: 38095604 PMCID: PMC10730174 DOI: 10.1080/19491034.2023.2293604] [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: 09/29/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Histone locus bodies (HLBs) are biomolecular condensates that assemble at replication-dependent (RD) histone genes in animal cells. These genes produce unique mRNAs that are not polyadenylated and instead end in a conserved 3' stem loop critical for coordinated production of histone proteins during S phase of the cell cycle. Several evolutionarily conserved factors necessary for synthesis of RD histone mRNAs concentrate only in the HLB. Moreover, because HLBs are present throughout the cell cycle even though RD histone genes are only expressed during S phase, changes in HLB composition during cell cycle progression drive much of the cell cycle regulation of RD histone gene expression. Thus, HLBs provide a powerful opportunity to determine the cause-and-effect relationships between nuclear body formation and cell cycle regulated gene expression. In this review, we focus on progress during the last five years that has advanced our understanding of HLB biology.
Collapse
Affiliation(s)
- Mark S. Geisler
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - James P. Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J. Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
4
|
Chaubal A, Waldern JM, Taylor C, Laederach A, Marzluff WF, Duronio RJ. Coordinated expression of replication-dependent histone genes from multiple loci promotes histone homeostasis in Drosophila. Mol Biol Cell 2023; 34:ar118. [PMID: 37647143 PMCID: PMC10846616 DOI: 10.1091/mbc.e22-11-0532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 08/07/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Production of large amounts of histone proteins during S phase is critical for proper chromatin formation and genome integrity. This process is achieved in part by the presence of multiple copies of replication dependent (RD) histone genes that occur in one or more clusters in metazoan genomes. In addition, RD histone gene clusters are associated with a specialized nuclear body, the histone locus body (HLB), which facilitates efficient transcription and 3' end-processing of RD histone mRNA. How all five RD histone genes within these clusters are coordinately regulated such that neither too few nor too many histones are produced, a process referred to as histone homeostasis, is not fully understood. Here, we explored the mechanisms of coordinate regulation between multiple RD histone loci in Drosophila melanogaster and Drosophila virilis. We provide evidence for functional competition between endogenous and ectopic transgenic histone arrays located at different chromosomal locations in D. melanogaster that helps maintain proper histone mRNA levels. Consistent with this model, in both species we found that individual histone gene arrays can independently assemble an HLB that results in active histone transcription. Our findings suggest a role for HLB assembly in coordinating RD histone gene expression to maintain histone homeostasis.
Collapse
Affiliation(s)
- Ashlesha Chaubal
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Justin M. Waldern
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Colin Taylor
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - William F. Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J. Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| |
Collapse
|
5
|
McPherson JME, Grossmann LC, Salzler HR, Armstrong RL, Kwon E, Matera AG, McKay DJ, Duronio RJ. Reduced histone gene copy number disrupts Drosophila Polycomb function. Genetics 2023; 224:iyad106. [PMID: 37279945 PMCID: PMC10411577 DOI: 10.1093/genetics/iyad106] [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: 03/27/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/08/2023] Open
Abstract
The chromatin of animal cells contains two types of histones: canonical histones that are expressed during S phase of the cell cycle to package the newly replicated genome, and variant histones with specialized functions that are expressed throughout the cell cycle and in non-proliferating cells. Determining whether and how canonical and variant histones cooperate to regulate genome function is integral to understanding how chromatin-based processes affect normal and pathological development. Here, we demonstrate that variant histone H3.3 is essential for Drosophila development only when canonical histone gene copy number is reduced, suggesting that coordination between canonical H3.2 and variant H3.3 expression is necessary to provide sufficient H3 protein for normal genome function. To identify genes that depend upon, or are involved in, this coordinate regulation we screened for heterozygous chromosome 3 deficiencies that impair development of flies bearing reduced H3.2 and H3.3 gene copy number. We identified two regions of chromosome 3 that conferred this phenotype, one of which contains the Polycomb gene, which is necessary for establishing domains of facultative chromatin that repress master regulator genes during development. We further found that reduction in Polycomb dosage decreases viability of animals with no H3.3 gene copies. Moreover, heterozygous Polycomb mutations result in de-repression of the Polycomb target gene Ubx and cause ectopic sex combs when either canonical or variant H3 gene copy number is reduced. We conclude that Polycomb-mediated facultative heterochromatin function is compromised when canonical and variant H3 gene copy number falls below a critical threshold.
Collapse
Affiliation(s)
- Jeanne-Marie E McPherson
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lucy C Grossmann
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Harmony R Salzler
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Robin L Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Esther Kwon
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| |
Collapse
|
6
|
McPherson JME, Grossmann LC, Armstrong RL, Kwon E, Salzler HR, Matera AG, McKay DJ, Duronio RJ. Reduced histone gene copy number disrupts Drosophila Polycomb function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534544. [PMID: 37034607 PMCID: PMC10081267 DOI: 10.1101/2023.03.28.534544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The chromatin of animal cells contains two types of histones: canonical histones that are expressed during S phase of the cell cycle to package the newly replicated genome, and variant histones with specialized functions that are expressed throughout the cell cycle and in non-proliferating cells. Determining whether and how canonical and variant histones cooperate to regulate genome function is integral to understanding how chromatin-based processes affect normal and pathological development. Here, we demonstrate that variant histone H3.3 is essential for Drosophila development only when canonical histone gene copy number is reduced, suggesting that coordination between canonical H3.2 and variant H3.3 expression is necessary to provide sufficient H3 protein for normal genome function. To identify genes that depend upon, or are involved in, this coordinate regulation we screened for heterozygous chromosome 3 deficiencies that impair development of flies bearing reduced H3.2 and H3.3 gene copy number. We identified two regions of chromosome 3 that conferred this phenotype, one of which contains the Polycomb gene, which is necessary for establishing domains of facultative chromatin that repress master regulator genes during development. We further found that reduction in Polycomb dosage decreases viability of animals with no H3.3 gene copies. Moreover, heterozygous Polycomb mutations result in de-repression of the Polycomb target gene Ubx and cause ectopic sex combs when either canonical or variant H3 gene copy number is also reduced. We conclude that Polycomb-mediated facultative heterochromatin function is compromised when canonical and variant H3 gene copy number falls below a critical threshold.
Collapse
Affiliation(s)
- Jeanne-Marie E. McPherson
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lucy C. Grossmann
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Robin L. Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Esther Kwon
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Harmony R. Salzler
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - A. Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel J. McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Robert J. Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| |
Collapse
|
7
|
Shine M, Harris SE, Pellegrene KA, Kensinger AH, Mihailescu MR, Evanseck JD, Lackey PE. Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3'hExo. RNA Biol 2023; 20:469-481. [PMID: 37516934 PMCID: PMC10388802 DOI: 10.1080/15476286.2023.2171760] [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: 07/08/2022] [Revised: 12/03/2022] [Accepted: 01/19/2023] [Indexed: 07/31/2023] Open
Abstract
Histone mRNA degradation is controlled by the unique 3' stem-loop of histone mRNA and the stem-loop binding protein (SLBP). As part of this process, the 3' stem-loop is trimmed by the histone-specific 3' exonuclease (3'hExo) and uridylated by the terminal uridylyl transferase 7 (TUT7), creating partially degraded intermediates with short uridylations. The role of these uridylations in degradation is not fully understood. Our work examines changes in the stability of the ternary complex created by trimming and uridylation of the stem-loop to better understand the role of this process in the histone mRNA life cycle. In this study, we used fluorescence polarization and electrophoretic mobility shift assays to demonstrate that both SLBP and 3'hExo can bind to uridylated and partially degraded stem-loop intermediates, although with lower affinity. We further characterized this complex by performing 1-µs molecular dynamics simulations using the AMBER force field and Nanoscale Molecular Dynamics (NAMD). These simulations show that while uridylation helps maintain the overall shape of the stem-loop, the combination of uridylation and dephosphorylation of the TPNK motif in SLBP disrupts key RNA-protein interactions. They also demonstrate that uridylation allows 3'hExo to maintain contact with the stem-loop after partial degradation and plays a role in disrupting key base pairs in partially degraded histone mRNA intermediates. Together, these experiments and simulations suggest that trimming by 3'hExo, uridylation, and SLBP dephosphorylation weakens both RNA-protein interactions and the stem-loop itself. Our results further elucidate the role of uridylation and SLBP dephosphorylation in the early stages of histone mRNA degradation.
Collapse
Affiliation(s)
- Morgan Shine
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, PA, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Sarah E Harris
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, PA, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendy A Pellegrene
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Adam H Kensinger
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Jeffrey D Evanseck
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Patrick E Lackey
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, PA, USA
| |
Collapse
|
8
|
Veerappan A, Stavrou A, Costa M. Polyadenylation of canonical histone H3.1 in carcinogenesis. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2023; 96:267-282. [PMID: 36858776 DOI: 10.1016/bs.apha.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Canonical histone messenger RNAs (mRNAs) are transcribed during S phase and do not terminate with a poly(A) tail at the 3' end. Instead, the histone mRNAs display a stem-loop structure at their 3-end. Stem-loop-binding protein (SLBP) binds the stem-loop and regulates canonical histone mRNA metabolism. We previously demonstrated that exposure to arsenic, an environmental carcinogen, induces polyadenylation of canonical histone H3.1 mRNA, causing transformation of human cells in vitro. Arsenic decreased cellular levels of SLBP by inducing its proteasomal degradation and inhibiting SLBP transcription via epigenetic mechanisms. Similarly, we also reported that nickel and arsenic have similar effects on canonical histone mRNA transcription and translation. Most recently, we further demonstrated that bisphenols' exposure increased polyadenylation of canonical histone H3.1 mRNA possibly through down-regulation of SLBP expression. This facilitates the abnormal stability of at least one canonical histone isoform (H3.1), and also increases H3 protein levels. Excess expression of canonical histones have been shown to increase sensitivity to DNA damage as well as increase the frequency of missing chromosomes and induce genomic instability. Thus, polyadenylation of canonical histone mRNA following arsenic, nickel and bisphenols exposure may contribute to metal and bisphenol-induced carcinogenesis.
Collapse
Affiliation(s)
- Arul Veerappan
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Aikaterini Stavrou
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States
| | - Max Costa
- Division of Environmental Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY, United States.
| |
Collapse
|
9
|
Sun Q, Chen D, Raja A, Grunig G, Zelikoff J, Jin C. Downregulation of Stem-Loop Binding Protein by Nicotine via α7-Nicotinic Acetylcholine Receptor and Its Role in Nicotine-Induced Cell Transformation. Toxicol Sci 2022; 189:186-202. [PMID: 35929799 PMCID: PMC9801712 DOI: 10.1093/toxsci/kfac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The use of electronic-cigarettes (e-cigs) has increased substantially in recent years, particularly among the younger generations. Liquid nicotine is the main component of e-cigs. Previous studies have shown that mice exposed to e-cig aerosols developed lung adenocarcinoma and bladder hyperplasia. These findings implicated a potential role for e-cig aerosols and nicotine in cancer development, although the underlying mechanisms are not fully understood. Here we report that exposure to liquid nicotine or nicotine aerosol generated from e-cig induces downregulation of Stem-loop binding protein (SLBP) and polyadenylation of canonical histone mRNAs in human bronchial epithelial cells and in mice lungs. Canonical histone mRNAs typically do not end in a poly(A) tail and the acquisition of such a tail via depletion of SLBP has been shown to causes chromosome instability. We show that nicotine-induced SLBP depletion is reversed by an inhibitor of α7-nicotinic acetylcholine receptors (α7-nAChR) or siRNA specific for α7-nAChR, indicating a nAChR-dependent reduction of SLBP by nicotine. Moreover, PI3K/AKT pathway is activated by nicotine exposure and CK2 and probably CDK1, 2 kinases well known for their function for SLBP phosphorylation and degradation, are shown to be involved, α7-nAChR-dependently, in nicotine-induced SLBP depletion. Importantly, nicotine-induced anchorage-independent cell growth is attenuated by inhibition of α7-nAChR and is rescued by overexpression of SLBP. We propose that the SLBP depletion and polyadenylation of canonical histone mRNAs via activation of α7-nAChR and a series of downstream signal transduction pathways are critical for nicotine-induced cell transformation and potential carcinogenesis.
Collapse
Affiliation(s)
- Qi Sun
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA,Department of Child and Adolescent Health, School of Public Health, China Medical University, Shenyang, Liaoning 110013, China
| | - Danqi Chen
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA
| | - Amna Raja
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA
| | - Gabriele Grunig
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA,Department of Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA
| | - Judith Zelikoff
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, New York 10010, USA
| | - Chunyuan Jin
- To whom correspondence should be addressed at Department of Environmental Medicine, New York University Grossman School of Medicine, 341E 25th Street, New York, NY 10010, USA. E-mail:
| |
Collapse
|
10
|
Bradford BR, Jin C. Stem-loop binding protein and metal carcinogenesis. Semin Cancer Biol 2021; 76:38-44. [PMID: 34416372 PMCID: PMC8627438 DOI: 10.1016/j.semcancer.2021.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 11/21/2022]
Abstract
Pre-mRNA processing of the replication-dependent canonical histone mRNAs requires an endonucleolytic cleavage immediately after a conserved stem loop structure which occurs before RNA Pol II encounters any poly(A) signal. Thus, in contrast to all other eukaryotic mRNAs, the canonical histone mRNAs are not polyadenylated in their 3' ends. The binding of stem-loop binding protein (SLBP) to the stem loop structure of the histone mRNAs is required for this process. SLBP is also involved in regulation of histone mRNA nuclear export, degradation, and translation. Depletion of SLBP has been shown to induce polyadenylation of histone mRNAs and alteration of histone protein levels, which are considered to contribute to the observed aberrant cell cycle progress and genomic instability resulting from the loss of SLBP function. Recent studies have demonstrated that some heavy metal carcinogens, including arsenic and nickel, can induce the loss of SLBP and the gain of polyadenylation of canonical histone mRNAs. Polyadenylated canonical histone H3 can result in abnormal transcription, cell cycle arrest, genomic instability, and cell transformation, which links SLBP depletion and subsequent histone mRNA misprocessing to cancer. This review seeks to briefly summarize what is known about regulation of SLBP expression, consequences of SLBP depletion, its roles in cancer-related end points, with particular focus on metal-induced SLBP depletion and the potential of SLBP depletion as a new mechanism for metal-induced carcinogenesis.
Collapse
Affiliation(s)
- Beatrix R Bradford
- Department of Environmental Medicine, New York University Grossman School of Medicine, 341 East 25th Street, New York, NY, 10010, USA
| | - Chunyuan Jin
- Department of Environmental Medicine, New York University Grossman School of Medicine, 341 East 25th Street, New York, NY, 10010, USA.
| |
Collapse
|
11
|
Zhao R, Wang B, Guo Y, Zhang J, Chen D, He WM, Zhao YJ, Ding Y, Jin C, Li C, Zhao Y, Ren W, Fang L. Quantitative proteomics reveals arsenic attenuates stem-loop binding protein stability via a chaperone complex containing heat shock proteins and ERp44. Proteomics 2021; 21:e2100035. [PMID: 34132035 DOI: 10.1002/pmic.202100035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022]
Abstract
Arsenic pollution impacts health of millions of people in the world. Inorganic arsenic is a carcinogenic agent in skin and lung cancers. The stem-loop binding protein (SLBP) binds to the stem-loop of the canonical histone mRNA and regulates its metabolism during cell cycle. Our previous work has shown arsenic induces ubiquitin-proteasome dependent degradation of SLBP and contributes to lung cancer. In this study, we established the first comprehensive SLBP interaction network by affinity purification-mass spectrometry (AP-MS) analysis, and further demonstrated arsenic enhanced the association between SLBP and a crucial chaperone complex containing heat shock proteins (HSPs) and ERp44. Strikingly, knockdown of these proteins markedly rescued the protein level of SLBP under arsenic exposure conditions, and abolished the increasing migration capacity of BEAS-2B cells induced by arsenic. Taken together, our study provides a potential new mechanism that a chaperone complex containing HSPs and ERp44 attenuates the stability of SLBP under both normal and arsenic exposure conditions, which could be essential for arsenic-induced high cell migration.
Collapse
Affiliation(s)
- Ruoyu Zhao
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China.,The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Binghao Wang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Yan Guo
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Jingzi Zhang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Danqi Chen
- Department of Environmental Medicine & Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Wei Ming He
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yong Juan Zhao
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yibing Ding
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Chunyuan Jin
- Department of Environmental Medicine & Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
| | - Chaojun Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Yue Zhao
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| | - Wei Ren
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University & Clinical Cancer Institute of Nanjing University, Nanjing, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School & Chemistry and Biomedicine Innovation Center of Nanjing University, Nanjing, China
| |
Collapse
|
12
|
Kelleher ES. Protein-Protein Interactions Shape Genomic Autoimmunity in the Adaptively Evolving Rhino-Deadlock-Cutoff Complex. Genome Biol Evol 2021; 13:6296839. [PMID: 34115120 PMCID: PMC8290110 DOI: 10.1093/gbe/evab132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 12/23/2022] Open
Abstract
The Piwi-interacting RNA (piRNA) pathway is a genomic defense system that controls the movement of transposable elements (TEs) through transcriptional and post-transcriptional silencing. Although TE defense is critical to ensuring germline genome integrity, it is equally critical that the piRNA pathway avoids autoimmunity in the form of silencing host genes. Ongoing cycles of selection for expanded control of invading TEs, followed by selection for increased specificity to reduce impacts on host genes, are proposed to explain the frequent signatures of adaptive evolution among piRNA pathway proteins. However, empirical tests of this model remain limited, particularly with regards to selection against genomic autoimmunity. I examined three adaptively evolving piRNA proteins, Rhino, Deadlock, and Cutoff, for evidence of interspecific divergence in autoimmunity between Drosophila melanogaster and Drosophila simulans. I tested a key prediction of the autoimmunity hypothesis that foreign heterospecific piRNA proteins will exhibit enhanced autoimmunity, due to the absence of historical selection against off-target effects. Consistent with this prediction, full-length D. simulans Cutoff, as well as the D. simulans hinge and chromo domains of Rhino, exhibit expanded regulation of D. melanogaster genes. I further demonstrate that this autoimmunity is dependent on known incompatibilities between D. simulans proteins or domains and their interacting partners in D. melanogaster. My observations reveal that the same protein–protein interaction domains that are interfaces of adaptive evolution in Rhino and Cutoff also determine their potential for autoimmunity.
Collapse
|
13
|
Potter-Birriel JM, Gonsalvez GB, Marzluff WF. A region of SLBP outside the mRNA-processing domain is essential for deposition of histone mRNA into the Drosophila egg. J Cell Sci 2021; 134:jcs.251728. [PMID: 33408246 DOI: 10.1242/jcs.251728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/21/2020] [Indexed: 01/01/2023] Open
Abstract
Replication-dependent histone mRNAs are the only cellular mRNAs that are not polyadenylated, ending in a stemloop instead of a polyA tail, and are normally regulated coordinately with DNA replication. Stemloop-binding protein (SLBP) binds the 3' end of histone mRNA, and is required for processing and translation. During Drosophila oogenesis, large amounts of histone mRNAs and proteins are deposited in the developing oocyte. The maternally deposited histone mRNA is synthesized in stage 10B oocytes after the nurse cells complete endoreduplication. We report that in wild-type stage 10B oocytes, the histone locus bodies (HLBs), formed on the histone genes, produce histone mRNAs in the absence of phosphorylation of Mxc, which is normally required for histone gene expression in S-phase cells. Two mutants of SLBP, one with reduced expression and another with a 10-amino-acid deletion, fail to deposit sufficient histone mRNA in the oocyte, and do not transcribe the histone genes in stage 10B. Mutations in a putative SLBP nuclear localization sequence overlapping the deletion phenocopy the deletion. We conclude that a high concentration of SLBP in the nucleus of stage 10B oocytes is essential for histone gene transcription.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Jennifer Michelle Potter-Birriel
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Interdisciplinary Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Graydon B Gonsalvez
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912 , USA
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA .,Interdisciplinary Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
14
|
Dual RNA 3'-end processing of H2A.X messenger RNA maintains DNA damage repair throughout the cell cycle. Nat Commun 2021; 12:359. [PMID: 33441544 PMCID: PMC7807067 DOI: 10.1038/s41467-020-20520-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022] Open
Abstract
Phosphorylated H2A.X is a critical chromatin marker of DNA damage repair (DDR) in higher eukaryotes. However, H2A.X gene expression remains relatively uncharacterised. Replication-dependent (RD) histone genes generate poly(A)- mRNA encoding new histones to package DNA during replication. In contrast, replication-independent (RI) histone genes synthesise poly(A)+ mRNA throughout the cell cycle, translated into histone variants that confer specific epigenetic patterns on chromatin. Remarkably H2AFX, encoding H2A.X, is a hybrid histone gene, generating both poly(A)+ and poly(A)- mRNA isoforms. Here we report that the selective removal of either mRNA isoform reveals different effects in different cell types. In some cells, RD H2A.X poly(A)- mRNA generates sufficient histone for deposition onto DDR associated chromatin. In contrast, cells making predominantly poly(A)+ mRNA require this isoform for de novo H2A.X synthesis, required for efficient DDR. This highlights the importance of differential H2A.X mRNA 3’-end processing in the maintenance of effective DDR. H2A.X histone variant gene encodes poly(A)+ and poly(A)- mRNA isoforms which are differentially expressed depending on cell lines. Here the authors show that upon DNA damage, cells expressing more poly(A)+ isoform require this isoform for de novo H2A.X synthesis while cells with more poly(A)- isoform have sufficient H2A.X present in chromatin.
Collapse
|
15
|
Uggenti C, Lepelley A, Depp M, Badrock AP, Rodero MP, El-Daher MT, Rice GI, Dhir S, Wheeler AP, Dhir A, Albawardi W, Frémond ML, Seabra L, Doig J, Blair N, Martin-Niclos MJ, Della Mina E, Rubio-Roldán A, García-Pérez JL, Sproul D, Rehwinkel J, Hertzog J, Boland-Auge A, Olaso R, Deleuze JF, Baruteau J, Brochard K, Buckley J, Cavallera V, Cereda C, De Waele LMH, Dobbie A, Doummar D, Elmslie F, Koch-Hogrebe M, Kumar R, Lamb K, Livingston JH, Majumdar A, Lorenço CM, Orcesi S, Peudenier S, Rostasy K, Salmon CA, Scott C, Tonduti D, Touati G, Valente M, van der Linden H, Van Esch H, Vermelle M, Webb K, Jackson AP, Reijns MAM, Gilbert N, Crow YJ. cGAS-mediated induction of type I interferon due to inborn errors of histone pre-mRNA processing. Nat Genet 2020; 52:1364-1372. [PMID: 33230297 DOI: 10.1038/s41588-020-00737-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/09/2020] [Indexed: 12/25/2022]
Abstract
Inappropriate stimulation or defective negative regulation of the type I interferon response can lead to autoinflammation. In genetically uncharacterized cases of the type I interferonopathy Aicardi-Goutières syndrome, we identified biallelic mutations in LSM11 and RNU7-1, which encode components of the replication-dependent histone pre-mRNA-processing complex. Mutations were associated with the misprocessing of canonical histone transcripts and a disturbance of linker histone stoichiometry. Additionally, we observed an altered distribution of nuclear cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) and enhanced interferon signaling mediated by the cGAS-stimulator of interferon genes (STING) pathway in patient-derived fibroblasts. Finally, we established that chromatin without linker histone stimulates cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) production in vitro more efficiently. We conclude that nuclear histones, as key constituents of chromatin, are essential in suppressing the immunogenicity of self-DNA.
Collapse
Affiliation(s)
- Carolina Uggenti
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Alice Lepelley
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Marine Depp
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Andrew P Badrock
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Mathieu P Rodero
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Marie-Thérèse El-Daher
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Gillian I Rice
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Somdutta Dhir
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ann P Wheeler
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ashish Dhir
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Waad Albawardi
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Marie-Louise Frémond
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Luis Seabra
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Jennifer Doig
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Natalie Blair
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Maria José Martin-Niclos
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Erika Della Mina
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France
| | - Alejandro Rubio-Roldán
- Centre for Genomics and Oncological Research (GENyO), Pfizer-University of Granada-Andalusian Regional Government, Parque Tecnico de la Ciencia de Salud, Granada, Spain
| | - Jose L García-Pérez
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
- Centre for Genomics and Oncological Research (GENyO), Pfizer-University of Granada-Andalusian Regional Government, Parque Tecnico de la Ciencia de Salud, Granada, Spain
| | - Duncan Sproul
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jonny Hertzog
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Anne Boland-Auge
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Robert Olaso
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine, Évry, France
| | - Julien Baruteau
- University College London Great Ormond Street Institute of Child Health, London, UK
| | - Karine Brochard
- Service de Médecine Interne Néphrologie Pédiatrique, Hôpital des Enfants, Toulouse, France
| | - Jonathan Buckley
- Department of Paediatric Nephrology, University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Vanessa Cavallera
- Child Neurology and Psychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | | | - Angus Dobbie
- Yorkshire Clinical Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Diane Doummar
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Département de Neuropédiatrie, Centre de Référence de Neurogénétique et Mouvements Anormaux de l'Enfant, Hôpital Armand Trousseau, Paris, France
| | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's, University of London, London, UK
| | - Margarete Koch-Hogrebe
- Department of Paediatric Neurology, Children's Hospital Datteln, Witten/Herdecke University, Datteln, Germany
| | - Ram Kumar
- Department of Paediatric Neurology, Alder Hey Children's National Health Service Foundation Trust, Liverpool, UK
| | - Kate Lamb
- Department of Paediatrics, Gloucestershire Royal Hospital, Gloucester, UK
| | - John H Livingston
- Department of Paediatric Neurology, Leeds Teaching Hospitals National Health Service Trust, Leeds, UK
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Children's Hospital, Bristol, UK
| | - Charles Marques Lorenço
- Faculdade de Medicina - Centro Universitário Estácio de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Simona Orcesi
- Child Neurology and Psychiatry Unit, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Sylviane Peudenier
- Centre de Référence des Déficiences Intellectuelles de Causes Rares et Polyhandicap, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Kevin Rostasy
- Department of Paediatric Neurology, Children's Hospital Datteln, Witten/Herdecke University, Datteln, Germany
| | - Caroline A Salmon
- Department of Paediatrics, Royal Surrey County Hospital, Guildford, UK
| | - Christiaan Scott
- University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Davide Tonduti
- Center for diagnosis and treatment of Leukodystrophies, Pediatric Neurology Unit, V. Buzzi Children's Hospital, Milano, Italy
| | - Guy Touati
- Reference Center for Inborn Errors of Metabolism-Department of Pediatrics, Hôpital des Enfants-Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Marialuisa Valente
- Genomic and Post-Genomic Center, Istituto di Ricovero e Cura a Carattere Scientifico, Mondino Foundation, Pavia, Italy
| | - Hélio van der Linden
- Department of Paediatric Neurology, Neurological Institute of Goiânia, Goiânia, Brazil
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Marie Vermelle
- Department of Paediatrics, Centre Hospitalier de Dunkerque, Dunkerque, France
| | - Kate Webb
- University of Cape Town, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Andrew P Jackson
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Martin A M Reijns
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Yanick J Crow
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK.
- University of Paris, Imagine Institute, Laboratory of Neurogenetics and Neuroinflammation, Paris, France.
| |
Collapse
|
16
|
Chen D, Chen QY, Wang Z, Zhu Y, Kluz T, Tan W, Li J, Wu F, Fang L, Zhang X, He R, Shen S, Sun H, Zang C, Jin C, Costa M. Polyadenylation of Histone H3.1 mRNA Promotes Cell Transformation by Displacing H3.3 from Gene Regulatory Elements. iScience 2020; 23:101518. [PMID: 32920490 PMCID: PMC7492993 DOI: 10.1016/j.isci.2020.101518] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 07/17/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
Replication-dependent canonical histone messenger RNAs (mRNAs) do not terminate with a poly(A) tail at the 3' end. We previously demonstrated that exposure to arsenic, an environmental carcinogen, induces polyadenylation of canonical histone H3.1 mRNA, causing transformation of human cells in vitro. Here we report that polyadenylation of H3.1 mRNA increases H3.1 protein, resulting in displacement of histone variant H3.3 at active promoters, enhancers, and insulator regions, leading to transcriptional deregulation, G2/M cell-cycle arrest, chromosome aneuploidy, and aberrations. In support of these observations, knocking down the expression of H3.3 induced cell transformation, whereas ectopic expression of H3.3 attenuated arsenic-induced cell transformation. Notably, arsenic exposure also resulted in displacement of H3.3 from active promoters, enhancers, and insulator regions. These data suggest that H3.3 displacement might be central to carcinogenesis caused by polyadenylation of H3.1 mRNA upon arsenic exposure. Our findings illustrate the importance of proper histone stoichiometry in maintaining genome integrity.
Collapse
Affiliation(s)
- Danqi Chen
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Qiao Yi Chen
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yusha Zhu
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Thomas Kluz
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Wuwei Tan
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Statistics, University of Virginia, Charlottesville, VA 22904, USA
| | - Jinquan Li
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Feng Wu
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Lei Fang
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Rongquan He
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Steven Shen
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Chunyuan Jin
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10010, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| |
Collapse
|
17
|
Hur W, Kemp JP, Tarzia M, Deneke VE, Marzluff WF, Duronio RJ, Di Talia S. CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies. Dev Cell 2020; 54:379-394.e6. [PMID: 32579968 DOI: 10.1016/j.devcel.2020.06.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/17/2020] [Accepted: 05/30/2020] [Indexed: 10/24/2022]
Abstract
Many membraneless organelles form through liquid-liquid phase separation, but how their size is controlled and whether size is linked to function remain poorly understood. The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of histone mRNAs. Here, we show that Drosophila HLBs form through phase separation. During embryogenesis, the size of HLBs is controlled in a precise and dynamic manner that is dependent on the cell cycle and zygotic histone gene activation. Control of HLB growth is achieved by a mechanism integrating nascent mRNAs at the histone locus, which facilitates phase separation, and the nuclear concentration of the scaffold protein multi-sex combs (Mxc), which is controlled by the activity of cyclin-dependent kinases. Reduced Cdk2 activity results in smaller HLBs and the appearance of nascent, misprocessed histone mRNAs. Thus, our experiments identify a mechanism linking nuclear body growth and size with gene expression.
Collapse
Affiliation(s)
- Woonyung Hur
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - James P Kemp
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tarzia
- LPTMC, CNRS-UMR 7600, Sorbonne Université, 4 Pl. Jussieu, 75005 Paris, France
| | - Victoria E Deneke
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA.
| |
Collapse
|
18
|
Chari S, Wilky H, Govindan J, Amodeo AA. Histone concentration regulates the cell cycle and transcription in early development. Development 2019; 146:dev.177402. [PMID: 31511251 DOI: 10.1242/dev.177402] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022]
Abstract
The early embryos of many animals, including flies, fish and frogs, have unusually rapid cell cycles and delayed onset of transcription. These divisions are dependent on maternally supplied RNAs and proteins including histones. Previous work suggests that the pool size of maternally provided histones can alter the timing of zygotic genome activation (ZGA) in frogs and fish. Here, we examine the effects of under- and overexpression of maternal histones in Drosophila embryogenesis. Decreasing histone concentration advances zygotic transcription, cell cycle elongation, Chk1 activation and gastrulation. Conversely, increasing histone concentration delays transcription and results in an additional nuclear cycle before gastrulation. Numerous zygotic transcripts are sensitive to histone concentration, and the promoters of histone-sensitive genes are associated with specific chromatin features linked to increased histone turnover. These include enrichment of the pioneer transcription factor Zelda, and lack of SIN3A and associated histone deacetylases. Our findings uncover a crucial regulatory role for histone concentrations in ZGA of Drosophila.
Collapse
Affiliation(s)
- Sudarshan Chari
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Henry Wilky
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jayalakshmi Govindan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Amanda A Amodeo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
19
|
Histone stress: an unexplored source of chromosomal instability in cancer? Curr Genet 2019; 65:1081-1088. [DOI: 10.1007/s00294-019-00967-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 01/24/2023]
|
20
|
Turner KJ, Hoyle J, Valdivia LE, Cerveny KL, Hart W, Mangoli M, Geisler R, Rees M, Houart C, Poole RJ, Wilson SW, Gestri G. Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure of cells to transition from proliferation to differentiation, retinal coloboma and midline axon guidance deficits. PLoS One 2019; 14:e0211073. [PMID: 30695021 PMCID: PMC6350959 DOI: 10.1371/journal.pone.0211073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/07/2019] [Indexed: 12/26/2022] Open
Abstract
Through forward genetic screening for mutations affecting visual system development, we identified prominent coloboma and cell-autonomous retinal neuron differentiation, lamination and retinal axon projection defects in eisspalte (ele) mutant zebrafish. Additional axonal deficits were present, most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp, which encodes a conserved RNA stem-loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when, and locations where, post-mitotic cells have differentiated in wild-type siblings. Indeed, RNAseq analysis showed down-regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated, for instance, in axon guidance, that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise, or promote transitions in, cell state and require the correct function of Slbp-dependent histone and chromatin regulatory genes.
Collapse
Affiliation(s)
- Katherine J. Turner
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Jacqueline Hoyle
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
- Department of Paediatrics and Child Health, University College London, London, United Kingdom
| | - Leonardo E. Valdivia
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Kara L. Cerveny
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Wendy Hart
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Maryam Mangoli
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Robert Geisler
- Karlsruhe Institute of Technology (KIT) Institute of Toxicology and Genetics, Eggenstein-Leopoldshafen, Germany
| | - Michele Rees
- Department of Paediatrics and Child Health, University College London, London, United Kingdom
| | - Corinne Houart
- Department of Developmental Neurobiology and MRC Centre for Developmental Disorders, Kings College London, London, United Kingdom
| | - Richard J. Poole
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Stephen W. Wilson
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
- * E-mail: (GG); (SWW)
| | - Gaia Gestri
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom
- * E-mail: (GG); (SWW)
| |
Collapse
|
21
|
He WX, Wu M, Liu Z, Li Z, Wang Y, Zhou J, Yu P, Zhang XJ, Zhou L, Gui JF. Oocyte-specific maternal Slbp2 is required for replication-dependent histone storage and early nuclear cleavage in zebrafish oogenesis and embryogenesis. RNA (NEW YORK, N.Y.) 2018; 24:1738-1748. [PMID: 30185624 PMCID: PMC6239174 DOI: 10.1261/rna.067090.118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/28/2018] [Indexed: 05/29/2023]
Abstract
Stem-loop binding protein (SLBP) is required for replication-dependent histone mRNA metabolism in mammals. Zebrafish possesses two slbps, and slbp1 is necessary for retinal neurogenesis. However, the detailed expression and function of slbp2 in zebrafish are still unknown. In this study, we first identified zebrafish slbp2 as an oocyte-specific maternal factor and then generated a maternal-zygotic slbp2 F3 homozygous mutant (MZslbp2Δ4-/-) using CRISPR/Cas9. The depletion of maternal Slbp2 disrupted early nuclear cleavage, which resulted in developmental arrest at the MBT stage. The developmental defects could be rescued in slbp2 transgenic MZslbp2Δ4-/- embryos. However, homozygous mutant MZslbp1Δ1-/- developed normally, indicating slbp1 is dispensable for zebrafish early embryogenesis. Through comparative proteome and transcriptome profiling between WT and MZslbp2Δ4-/- embryos, we identified many differentially expressed proteins and genes. In comparison with those in WT embryos, four replication-dependent histones, including H2a, H2b, H3, and H4, all reduced their expression, while histone variant h2afx significantly increased in MZslbp2Δ4-/- embryos at the 256-cell stage and high stage. Zebrafish Slbp2 can bind histone mRNA stem-loop in vitro, and the defects of MZslbp2Δ4-/- embryos can be partially rescued by overexpression of H2b. The current data indicate that maternal Slbp2 plays a pivotal role in the storage of replication-dependent histone mRNAs and proteins during zebrafish oogenesis.
Collapse
Affiliation(s)
- Wen-Xia He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
22
|
Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
Collapse
Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| |
Collapse
|
23
|
Biochemical Fractionation of Time-Resolved Drosophila Embryos Reveals Similar Transcriptomic Alterations in Replication Checkpoint and Histone mRNA Processing Mutants. J Mol Biol 2017; 429:3264-3279. [DOI: 10.1016/j.jmb.2017.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 11/22/2022]
|
24
|
Marzluff WF, Koreski KP. Birth and Death of Histone mRNAs. Trends Genet 2017; 33:745-759. [PMID: 28867047 DOI: 10.1016/j.tig.2017.07.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/24/2017] [Accepted: 07/28/2017] [Indexed: 12/22/2022]
Abstract
In metazoans, histone mRNAs are not polyadenylated but end in a conserved stem-loop. Stem-loop binding protein (SLBP) binds to the stem-loop and is required for all steps in histone mRNA metabolism. The genes for the five histone proteins are linked. A histone locus body (HLB) forms at each histone gene locus. It contains factors essential for transcription and processing of histone mRNAs, and couples transcription and processing. The active form of U7 snRNP contains the HLB component FLASH (FLICE-associated huge protein), the histone cleavage complex (HCC), and a subset of polyadenylation factors including the endonuclease CPSF73. Histone mRNAs are rapidly degraded when DNA replication is inhibited by a 3' to 5' pathway that requires extensive uridylation of mRNA decay intermediates.
Collapse
Affiliation(s)
- William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kaitlin P Koreski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
25
|
Alexiadis A, Delidakis C, Kalantidis K. Snipper, an Eri1 homologue, affects histone mRNA abundance and is crucial for normal Drosophila melanogaster development. FEBS Lett 2017. [PMID: 28626879 DOI: 10.1002/1873-3468.12719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The conserved 3'-5' RNA exonuclease ERI1 is implicated in RNA interference inhibition, 5.8S rRNA maturation and histone mRNA maturation and turnover. The single ERI1 homologue in Drosophila melanogaster Snipper (Snp) is a 3'-5' exonuclease, but its in vivo function remains elusive. Here, we report Snp requirement for normal Drosophila development, since its perturbation leads to larval arrest and tissue-specific downregulation results in abnormal tissue development. Additionally, Snp directly interacts with histone mRNA, and its depletion results in drastic reduction in histone transcript levels. We propose that Snp protects the 3'-ends of histone mRNAs and upon its absence, histone transcripts are readily degraded. This in turn may lead to cell cycle delay or arrest, causing growth arrest and developmental perturbations.
Collapse
Affiliation(s)
- Anastasios Alexiadis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| | - Christos Delidakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece.,Department of Biology, University of Crete, Heraklion, Greece
| |
Collapse
|
26
|
Data for the generation of RNA spatiotemporal distributions and interpretation of Chk1 and SLBP protein depletion phenotypes during Drosophila embryogenesis. Data Brief 2017; 13:28-31. [PMID: 28560279 PMCID: PMC5440278 DOI: 10.1016/j.dib.2017.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/31/2017] [Accepted: 05/03/2017] [Indexed: 11/22/2022] Open
Abstract
The data presented in this article is related to the research article entitled "Biochemical Fractionation of Time-Resolved Drosophila Embryos Reveals Similar Transcriptomic Alterations in Replication Checkpoint and Histone mRNA Processing Mutants" (Lefebvre et al., 2017) [1]. This article provides a spatiotemporal transcriptomic analysis of early embryogenesis and shows that mutations in the checkpoint factor grapes/Chk1 and the histone mRNA processing factor SLBP selectively impair zygotic gene expression. Here, lists of transcripts enriched in early syncytial embryos, late blastoderm embryos, cytoplasmic and nuclear extracts of blastoderm embryos are made public, along with transcription factor motif occurrence for genes enriched in each context. In addition, extensive lists of genes down-regulated upon Chk1 and SLBP protein depletion in embryos are released to enable further analyses.
Collapse
|
27
|
Duronio RJ, Marzluff WF. Coordinating cell cycle-regulated histone gene expression through assembly and function of the Histone Locus Body. RNA Biol 2017; 14:726-738. [PMID: 28059623 DOI: 10.1080/15476286.2016.1265198] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Metazoan replication-dependent (RD) histone genes encode the only known cellular mRNAs that are not polyadenylated. These mRNAs end instead in a conserved stem-loop, which is formed by an endonucleolytic cleavage of the pre-mRNA. The genes for all 5 histone proteins are clustered in all metazoans and coordinately regulated with high levels of expression during S phase. Production of histone mRNAs occurs in a nuclear body called the Histone Locus Body (HLB), a subdomain of the nucleus defined by a concentration of factors necessary for histone gene transcription and pre-mRNA processing. These factors include the scaffolding protein NPAT, essential for histone gene transcription, and FLASH and U7 snRNP, both essential for histone pre-mRNA processing. Histone gene expression is activated by Cyclin E/Cdk2-mediated phosphorylation of NPAT at the G1-S transition. The concentration of factors within the HLB couples transcription with pre-mRNA processing, enhancing the efficiency of histone mRNA biosynthesis.
Collapse
Affiliation(s)
- Robert J Duronio
- a Department of Biology , University of North Carolina , Chapel Hill , NC , USA.,b Department of Genetics , University of North Carolina , Chapel Hill , NC , USA.,c Integrative Program for Biological and Genome Sciences , University of North Carolina , Chapel Hill , NC , USA.,d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA
| | - William F Marzluff
- a Department of Biology , University of North Carolina , Chapel Hill , NC , USA.,c Integrative Program for Biological and Genome Sciences , University of North Carolina , Chapel Hill , NC , USA.,d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA.,e Department of Biochemistry and Biophysics , University of North Carolina , Chapel Hill , NC , USA
| |
Collapse
|
28
|
Chen QY, Brocato J, Laulicht F, Costa M. Mechanisms of Nickel Carcinogenesis. ESSENTIAL AND NON-ESSENTIAL METALS 2017. [DOI: 10.1007/978-3-319-55448-8_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
29
|
Dankert JF, Rona G, Clijsters L, Geter P, Skaar JR, Bermudez-Hernandez K, Sassani E, Fenyö D, Ueberheide B, Schneider R, Pagano M. Cyclin F-Mediated Degradation of SLBP Limits H2A.X Accumulation and Apoptosis upon Genotoxic Stress in G2. Mol Cell 2016; 64:507-519. [PMID: 27773672 DOI: 10.1016/j.molcel.2016.09.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/01/2016] [Accepted: 09/08/2016] [Indexed: 10/20/2022]
Abstract
SLBP (stem-loop binding protein) is a highly conserved factor necessary for the processing, translation, and degradation of H2AFX and canonical histone mRNAs. We identified the F-box protein cyclin F, a substrate recognition subunit of an SCF (Skp1-Cul1-F-box protein) complex, as the G2 ubiquitin ligase for SLBP. SLBP interacts with cyclin F via an atypical CY motif, and mutation of this motif prevents SLBP degradation in G2. Expression of an SLBP stable mutant results in increased loading of H2AFX mRNA onto polyribosomes, resulting in increased expression of H2A.X (encoded by H2AFX). Upon genotoxic stress in G2, high levels of H2A.X lead to persistent γH2A.X signaling, high levels of H2A.X phosphorylated on Tyr142, high levels of p53, and induction of apoptosis. We propose that cyclin F co-evolved with the appearance of stem-loops in vertebrate H2AFX mRNA to mediate SLBP degradation, thereby limiting H2A.X synthesis and cell death upon genotoxic stress.
Collapse
Affiliation(s)
- John F Dankert
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Linda Clijsters
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Phillip Geter
- Department of Microbiology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Jeffrey R Skaar
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Keria Bermudez-Hernandez
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Institute for System Genetics, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Institute for System Genetics, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Proteomics Resource Center, Office of Collaborative Science, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Robert Schneider
- Department of Microbiology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Department of Radiation Oncology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Howard Hughes Medical Institute, 522 First Avenue, SRB 1107, New York, NY 10016, USA.
| |
Collapse
|
30
|
Tatomer DC, Terzo E, Curry KP, Salzler H, Sabath I, Zapotoczny G, McKay DJ, Dominski Z, Marzluff WF, Duronio RJ. Concentrating pre-mRNA processing factors in the histone locus body facilitates efficient histone mRNA biogenesis. J Cell Biol 2016; 213:557-70. [PMID: 27241916 PMCID: PMC4896052 DOI: 10.1083/jcb.201504043] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/27/2016] [Indexed: 11/22/2022] Open
Abstract
Concentrating factors in nuclear bodies is thought to promote efficient gene expression. Tatomer et al. show that the histone locus body (HLB) concentrates pre-mRNA processing factors at replication-dependent histone genes, resulting in optimal 3′ end formation of histone mRNAs coupled with transcription termination. The histone locus body (HLB) assembles at replication-dependent histone genes and concentrates factors required for histone messenger RNA (mRNA) biosynthesis. FLASH (Flice-associated huge protein) and U7 small nuclear RNP (snRNP) are HLB components that participate in 3′ processing of the nonpolyadenylated histone mRNAs by recruiting the endonuclease CPSF-73 to histone pre-mRNA. Using transgenes to complement a FLASH mutant, we show that distinct domains of FLASH involved in U7 snRNP binding, histone pre-mRNA cleavage, and HLB localization are all required for proper FLASH function in vivo. By genetically manipulating HLB composition using mutations in FLASH, mutations in the HLB assembly factor Mxc, or depletion of the variant histone H2aV, we find that failure to concentrate FLASH and/or U7 snRNP in the HLB impairs histone pre-mRNA processing. This failure results in accumulation of small amounts of polyadenylated histone mRNA and nascent read-through transcripts at the histone locus. Thus, the HLB concentrates FLASH and U7 snRNP, promoting efficient histone mRNA biosynthesis and coupling 3′ end processing with transcription termination.
Collapse
Affiliation(s)
- Deirdre C Tatomer
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Esteban Terzo
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Kaitlin P Curry
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Harmony Salzler
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Ivan Sabath
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Grzegorz Zapotoczny
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Daniel J McKay
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| | - Zbigniew Dominski
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - William F Marzluff
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J Duronio
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| |
Collapse
|
31
|
Toompuu M, Kärblane K, Pata P, Truve E, Sarmiento C. ABCE1 is essential for S phase progression in human cells. Cell Cycle 2016; 15:1234-47. [PMID: 26985706 DOI: 10.1080/15384101.2016.1160972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
ABCE1 is a highly conserved protein universally present in eukaryotes and archaea, which is crucial for the viability of different organisms. First identified as RNase L inhibitor, ABCE1 is currently recognized as an essential translation factor involved in several stages of eukaryotic translation and ribosome biogenesis. The nature of vital functions of ABCE1, however, remains unexplained. Here, we study the role of ABCE1 in human cell proliferation and its possible connection to translation. We show that ABCE1 depletion by siRNA results in a decreased rate of cell growth due to accumulation of cells in S phase, which is accompanied by inefficient DNA synthesis and reduced histone mRNA and protein levels. We infer that in addition to the role in general translation, ABCE1 is involved in histone biosynthesis and DNA replication and therefore is essential for normal S phase progression. In addition, we analyze whether ABCE1 is implicated in transcript-specific translation via its association with the eIF3 complex subunits known to control the synthesis of cell proliferation-related proteins. The expression levels of a few such targets regulated by eIF3A, however, were not consistently affected by ABCE1 depletion.
Collapse
Affiliation(s)
- Marina Toompuu
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Kairi Kärblane
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Pille Pata
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Erkki Truve
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| | - Cecilia Sarmiento
- a Department of Gene Technology , Tallinn University of Technology , Tallinn , Estonia
| |
Collapse
|
32
|
Tatomer DC, Rizzardi LF, Curry KP, Witkowski AM, Marzluff WF, Duronio RJ. Drosophila Symplekin localizes dynamically to the histone locus body and tricellular junctions. Nucleus 2015; 5:613-25. [PMID: 25493544 DOI: 10.4161/19491034.2014.990860] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The scaffolding protein Symplekin is part of multiple complexes involved in generating and modifying the 3' end of mRNAs, including cleavage-polyadenylation, histone pre-mRNA processing and cytoplasmic polyadenylation. To study these functions in vivo, we examined the localization of Symplekin during development and generated mutations of the Drosophila Symplekin gene. Mutations in Symplekin that reduce Symplekin protein levels alter the efficiency of both poly A(+) and histone mRNA 3' end formation resulting in lethality or sterility. Histone mRNA synthesis takes place at the histone locus body (HLB) and requires a complex composed of Symplekin and several polyadenylation factors that associates with the U7 snRNP. Symplekin is present in the HLB in the early embryo when Cyclin E/Cdk2 is active and histone genes are expressed and is absent from the HLB in cells that have exited the cell cycle. During oogenesis, Symplekin is preferentially localized to HLBs during S-phase in endoreduplicating follicle cells when histone mRNA is synthesized. After the completion of endoreplication, Symplekin accumulates in the cytoplasm, in addition to the nucleoplasm, and localizes to tricellular junctions of the follicle cell epithelium. This localization depends on the RNA binding protein ypsilon schachtel. CPSF-73 and a number of mRNAs are localized at this same site, suggesting that Symplekin participates in cytoplasmic polyadenylation at tricellular junctions.
Collapse
Key Words
- CTD, RNA polymerase II C-terminal domain
- Drosophila
- HCC, histone cleavage complex
- HDE, histone downstream element
- HLB, histone locus body
- Madm, MLF1-adaptor molecule
- PAP, poly (A) polymerase
- PAS, poly A signal
- RNA processing, Symplekin
- Rp49, ribosomal protein L32
- SL, stem loop
- SLBP, stem loop binding protein
- Sym, Symplekin
- cas, castor
- gene expression
- histone mRNA
- nuclear bodies
- sop, ribosomal protein S2
- yps, ypsilon schachtel
Collapse
Affiliation(s)
- Deirdre C Tatomer
- a Department of Biology ; University of North Carolina ; Chapel Hill , NC USA
| | | | | | | | | | | |
Collapse
|
33
|
Brocato J, Chen D, Liu J, Fang L, Jin C, Costa M. A Potential New Mechanism of Arsenic Carcinogenesis: Depletion of Stem-Loop Binding Protein and Increase in Polyadenylated Canonical Histone H3.1 mRNA. Biol Trace Elem Res 2015; 166:72-81. [PMID: 25893362 PMCID: PMC4470754 DOI: 10.1007/s12011-015-0296-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/03/2015] [Indexed: 12/27/2022]
Abstract
Canonical histones are synthesized with a peak in S-phase, whereas histone variants are formed throughout the cell cycle. Unlike messenger RNA (mRNA) for all other genes with a poly(A) tail, canonical histone mRNAs contain a stem-loop structure at their 3'-ends. This stem-loop structure is the binding site for the stem-loop binding protein (SLBP), a protein involved in canonical histone mRNA processing. Recently, we found that arsenic depletes SLBP by enhancing its proteasomal degradation and epigenetically silencing the promoter of the SLBP gene. The loss of SLBP disrupts histone mRNA processing and induces aberrant polyadenylation of canonical histone H3.1 mRNA. Here, we present new data supporting the idea that the lack of SLBP allows the H3.1 mRNA to be polyadenylated using the downstream poly(A) signal. SLBP was also depleted in arsenic-transformed bronchial epithelial cells (BEAS-2B), which led us to hypothesize the involvement of SLBP and polyadenylated H3.1 mRNA in carcinogenesis. Here, for the first time, we report that overexpression of H3.1 polyadenylated mRNA, and knockdown of SLBP enhances anchorage-independent cell growth. A pcDNA-H3.1 vector with a poly(A) signal sequence was stably transfected into BEAS-2B cells. Polyadenylated H3.1 mRNA and exogenous H3.1 protein levels were significantly increased in cells containing the pcDNA-H3.1 vector. A soft agar assay revealed that cells containing the vector formed significantly higher numbers of colonies compared to wild-type cells. Moreover, small hairpin RNA for SLBP (shSLBP) was used to knockdown the expression of SLBP. Cells stably transfected with the shSLBP vector grew significantly more colonies in soft agar than cells transfected with a control vector. These data suggest that upregulation of polyadenylated H3.1 mRNA holds potential as a mechanism to facilitate carcinogenesis by toxicants such as arsenic that depletes SLBP.
Collapse
Affiliation(s)
- Jason Brocato
- Department of Environmental Medicine, NYU School of Medicine, NY, NY, 10016 USA
| | - Danqi Chen
- Department of Environmental Medicine, NYU School of Medicine, NY, NY, 10016 USA
| | - Jianli Liu
- Department of Environmental Medicine, NYU School of Medicine, NY, NY, 10016 USA
| | - Lei Fang
- Department of Environmental Medicine, NYU School of Medicine, NY, NY, 10016 USA
| | - Chunyuan Jin
- Department of Environmental Medicine, NYU School of Medicine, NY, NY, 10016 USA
| | - Max Costa
- Department of Environmental Medicine, NYU School of Medicine, NY, NY, 10016 USA
| |
Collapse
|
34
|
Welte MA. As the fat flies: The dynamic lipid droplets of Drosophila embryos. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1156-85. [PMID: 25882628 DOI: 10.1016/j.bbalip.2015.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/31/2015] [Accepted: 04/06/2015] [Indexed: 01/09/2023]
Abstract
Research into lipid droplets is rapidly expanding, and new cellular and organismal roles for these lipid-storage organelles are continually being discovered. The early Drosophila embryo is particularly well suited for addressing certain questions in lipid-droplet biology and combines technical advantages with unique biological phenomena. This review summarizes key features of this experimental system and the techniques available to study it, in order to make it accessible to researchers outside this field. It then describes the two topics most heavily studied in this system, lipid-droplet motility and protein sequestration on droplets, discusses what is known about the molecular players involved, points to open questions, and compares the results from Drosophila embryo studies to what it is known about lipid droplets in other systems.
Collapse
Affiliation(s)
- Michael A Welte
- Department of Biology University of Rochester, RC Box 270211, 317 Hutchison Hall, Rochester, NY 14627, USA.
| |
Collapse
|
35
|
Terzo EA, Lyons SM, Poulton JS, Temple BRS, Marzluff WF, Duronio RJ. Distinct self-interaction domains promote Multi Sex Combs accumulation in and formation of the Drosophila histone locus body. Mol Biol Cell 2015; 26:1559-74. [PMID: 25694448 PMCID: PMC4395134 DOI: 10.1091/mbc.e14-10-1445] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/12/2015] [Indexed: 11/11/2022] Open
Abstract
The Drosophila Multi Sex Combs (Mxc) protein is necessary for the recruitment of histone mRNA biosynthetic factors to the histone locus body (HLB). Mxc contains multiple domains required for HLB assembly and histone mRNA biosynthesis. Two N-terminal domains of Mxc are essential for promoting HLB assembly via a self-interaction. Nuclear bodies (NBs) are structures that concentrate proteins, RNAs, and ribonucleoproteins that perform functions essential to gene expression. How NBs assemble is not well understood. We studied the Drosophila histone locus body (HLB), a NB that concentrates factors required for histone mRNA biosynthesis at the replication-dependent histone gene locus. We coupled biochemical analysis with confocal imaging of both fixed and live tissues to demonstrate that the Drosophila Multi Sex Combs (Mxc) protein contains multiple domains necessary for HLB assembly. An important feature of this assembly process is the self-interaction of Mxc via two conserved N-terminal domains: a LisH domain and a novel self-interaction facilitator (SIF) domain immediately downstream of the LisH domain. Molecular modeling suggests that the LisH and SIF domains directly interact, and mutation of either the LisH or the SIF domain severely impairs Mxc function in vivo, resulting in reduced histone mRNA accumulation. A region of Mxc between amino acids 721 and 1481 is also necessary for HLB assembly independent of the LisH and SIF domains. Finally, the C-terminal 195 amino acids of Mxc are required for recruiting FLASH, an essential histone mRNA-processing factor, to the HLB. We conclude that multiple domains of the Mxc protein promote HLB assembly in order to concentrate factors required for histone mRNA biosynthesis.
Collapse
Affiliation(s)
- Esteban A Terzo
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Shawn M Lyons
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - John S Poulton
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Brenda R S Temple
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| |
Collapse
|
36
|
Skaar JR, Ferris AL, Wu X, Saraf A, Khanna KK, Florens L, Washburn MP, Hughes SH, Pagano M. The Integrator complex controls the termination of transcription at diverse classes of gene targets. Cell Res 2015; 25:288-305. [PMID: 25675981 PMCID: PMC4349240 DOI: 10.1038/cr.2015.19] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/22/2014] [Accepted: 12/25/2014] [Indexed: 02/08/2023] Open
Abstract
Complexes containing INTS3 and either NABP1 or NABP2 were initially characterized in DNA damage responses, but their biochemical function remained unknown. Using affinity purifications and HIV Integration targeting-sequencing (HIT-Seq), we find that these complexes are part of the Integrator complex, which binds RNA Polymerase II and regulates specific target genes. Integrator cleaves snRNAs as part of their processing to their mature form in a mechanism that is intimately coupled with transcription termination. However, HIT-Seq reveals that Integrator also binds to the 3' end of replication-dependent histones and promoter proximal regions of genes with polyadenylated transcripts. Depletion of Integrator subunits results in transcription termination failure, disruption of histone mRNA processing, and polyadenylation of snRNAs and histone mRNAs. Furthermore, promoter proximal binding of Integrator negatively regulates expression of genes whose transcripts are normally polyadenylated. Integrator recruitment to all three gene classes is DSIF-dependent, suggesting that Integrator functions as a termination complex at DSIF-dependent RNA Polymerase II pause sites.
Collapse
Affiliation(s)
- Jeffrey R Skaar
- Department of Pathology, Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, 522 First Avenue, New York, NY 10016, USA
| | - Andrea L Ferris
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anita Saraf
- The Stowers Institute for Medical Research, Kansas City, MO 6411, USA
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland 4006, Australia
| | - Laurence Florens
- The Stowers Institute for Medical Research, Kansas City, MO 6411, USA
| | - Michael P Washburn
- 1] The Stowers Institute for Medical Research, Kansas City, MO 6411, USA [2] Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Stephen H Hughes
- HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Michele Pagano
- 1] Department of Pathology, Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, 522 First Avenue, New York, NY 10016, USA [2] Howard Hughes Medical Institute, 522 First Avenue New York, NY 10016, USA
| |
Collapse
|
37
|
Horard B, Loppin B. Histone storage and deposition in the early Drosophila embryo. Chromosoma 2015; 124:163-75. [PMID: 25563491 DOI: 10.1007/s00412-014-0504-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Drosophila development initiates with the formation of a diploid zygote followed by the rapid division of embryonic nuclei. This syncytial phase of development occurs almost entirely under maternal control and ends when the blastoderm embryo cellularizes and activates its zygotic genome. The biosynthesis and storage of histones in quantity sufficient for chromatin assembly of several thousands of genome copies represent a unique challenge for the developing embryo. In this article, we have reviewed our current understanding of the mechanisms involved in the production, storage, and deposition of histones in the fertilized egg and during the exponential amplification of cleavage nuclei.
Collapse
Affiliation(s)
- Béatrice Horard
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire-CNRS UMR5534, Université Claude Bernard Lyon 1, University of Lyon, 69100, Villeurbanne, France
| | | |
Collapse
|
38
|
Imai F, Yoshizawa A, Matsuzaki A, Oguri E, Araragi M, Nishiwaki Y, Masai I. Stem-loop binding protein is required for retinal cell proliferation, neurogenesis, and intraretinal axon pathfinding in zebrafish. Dev Biol 2014; 394:94-109. [DOI: 10.1016/j.ydbio.2014.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/05/2014] [Accepted: 07/23/2014] [Indexed: 02/04/2023]
|
39
|
Brocato J, Fang L, Chervona Y, Chen D, Kiok K, Sun H, Tseng HC, Xu D, Shamy M, Jin C, Costa M. Arsenic induces polyadenylation of canonical histone mRNA by down-regulating stem-loop-binding protein gene expression. J Biol Chem 2014; 289:31751-31764. [PMID: 25266719 DOI: 10.1074/jbc.m114.591883] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The replication-dependent histone genes are the only metazoan genes whose messenger RNA (mRNA) does not terminate with a poly(A) tail at the 3'-end. Instead, the histone mRNAs display a stem-loop structure at their 3'-end. Stem-loop-binding protein (SLBP) binds the stem-loop and regulates canonical histone mRNA metabolism. Here we report that exposure to arsenic, a carcinogenic metal, decreased cellular levels of SLBP by inducing its proteasomal degradation and inhibiting SLBP transcription via epigenetic mechanisms. Notably, arsenic exposure dramatically increased polyadenylation of canonical histone H3.1 mRNA possibly through down-regulation of SLBP expression. The polyadenylated H3.1 mRNA induced by arsenic was not susceptible to normal degradation that occurs at the end of S phase, resulting in continued presence into mitosis, increased total H3.1 mRNA, and increased H3 protein levels. Excess expression of canonical histones have been shown to increase sensitivity to DNA damage as well as increase the frequency of missing chromosomes and induce genomic instability. Thus, polyadenylation of canonical histone mRNA following arsenic exposure may contribute to arsenic-induced carcinogenesis.
Collapse
Affiliation(s)
- Jason Brocato
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| | - Lei Fang
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| | - Yana Chervona
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| | - Danqi Chen
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| | - Kathrin Kiok
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| | - Hsiang-Chi Tseng
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| | - Dazhong Xu
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| | - Magdy Shamy
- Department of Environmental Sciences, Faculty of Meteorology, Environment, and Arid Land Agriculture, King Abdulaziz University, Jeddah 21432, Saudi Arabia
| | - Chunyuan Jin
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and.
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, New York, New York 10016 and
| |
Collapse
|
40
|
Abstract
Eukaryotes package DNA into nucleosomes that contain a core of histone proteins. During DNA replication, nucleosomes are disrupted and re-assembled with newly synthesized histones and DNA. Despite much progress, it is still unclear why higher eukaryotes contain multiple core histone genes, how chromatin assembly is controlled, and how these processes are coordinated with cell cycle progression. We used a histone null mutation of Drosophila melanogaster to show that histone supply levels, provided by a defined number of transgenic histone genes, regulate the length of S phase during the cell cycle. Lack of de novo histone supply not only extends S phase, but also causes a cell cycle arrest during G2 phase, and thus prevents cells from entering mitosis. Our results suggest a novel cell cycle surveillance mechanism that monitors nucleosome assembly without involving the DNA repair pathways and exerts its effect via suppression of CDC25 phosphatase String expression. DOI:http://dx.doi.org/10.7554/eLife.02443.001 As a cell prepares to divide, it goes through four distinct stages. First, it grows in size (G1 phase); next it copies its entire DNA content (S phase); then it grows some more (G2 phase); and, last, it splits into two new cells (M phase). During S phase, groups of histone proteins that normally stick together to tightly package the DNA are pulled apart in order to make the DNA accessible for copying. After the DNA has been duplicated, both copies of the DNA strand need to be repackaged. Therefore, after copying the DNA the cell rapidly reassembles the DNA–histone complexes (called nucleosomes), using a combination of old and newly synthesized histones to do so. A cell can adjust how quickly it copies DNA according to the availability of these histone proteins, which is important because copying DNA without the resources to package it could expose the DNA to damage. Here, Günesdogan et al. investigate how a cell controls these processes using a mutant of the fruit fly Drosophila melanogaster that completely lacks the genes required to make histones. Cells that lack histones copy their DNA very slowly but adding copies of histone genes back into these flies speeds up the rate at which DNA is copied. Günesdogan et al. ask whether the slower speed of DNA replication in cells without new histones is connected to preventing DNA damage. However, these cells can still copy all their DNA, despite being unable to package it, so the higher risk of making mistakes is not enough to stop S phase. In fact, indications suggest that DNA damage detection methods continue to work as normal in cells without histones: these cells can get all the way to the end of G2 phase without any problems. To go one step further and start splitting in two, a cell needs to switch on another gene, called string in the fruit fly and CDC25 in vertebrates, which makes an enzyme required for the cell division process. Normal cells switch on string during G2 phase, but cells that lack histones do not—and therefore do not enter M phase. Günesdogan et al. show that turning on string by a genetic trick is sufficient to overcome this cell cycle arrest and drive the cells into M phase. String could therefore form part of a surveillance mechanism that blocks cell division if DNA–histone complexes are not assembled correctly. DOI:http://dx.doi.org/10.7554/eLife.02443.002
Collapse
Affiliation(s)
- Ufuk Günesdogan
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Herbert Jäckle
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
| | - Alf Herzig
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany Abteilung Zelluläre Mikrobiologie, Max-Planck-Institut für Infektionsbiologie, Berlin, Germany
| |
Collapse
|
41
|
Yamamoto J, Hagiwara Y, Chiba K, Isobe T, Narita T, Handa H, Yamaguchi Y. DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes. Nat Commun 2014; 5:4263. [PMID: 24968874 DOI: 10.1038/ncomms5263] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/01/2014] [Indexed: 01/26/2023] Open
Abstract
The elongation factors DSIF and NELF are responsible for promoter-proximal RNA polymerase II (Pol II) pausing. NELF is also involved in 3' processing of replication-dependent histone genes, which produce non-polyadenylated mRNAs. Here we show that DSIF and NELF contribute to the synthesis of small nuclear RNAs (snRNAs) through their association with Integrator, the large multisubunit complex responsible for 3' processing of pre-snRNAs. In HeLa cells, Pol II, Integrator, DSIF and NELF accumulate at the 3' end of the U1 snRNA gene. Knockdown of NELF results in misprocessing of U1, U2, U4 and U5 snRNAs, while DSIF is required for proper transcription of these genes. Knocking down NELF also disrupts transcription termination and induces the production of polyadenylated U1 transcripts caused by an enhanced recruitment of cleavage stimulation factor. Our results indicate that NELF plays a key role in determining the post-transcriptional fate of Pol II-transcribed genes.
Collapse
Affiliation(s)
- Junichi Yamamoto
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yuri Hagiwara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Kunitoshi Chiba
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Tomoyasu Isobe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takashi Narita
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Hiroshi Handa
- Department of Nanoparticle Translational Research, Tokyo Medical University, Tokyo 160-8402, Japan
| | - Yuki Yamaguchi
- 1] Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan [2] PRESTO, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| |
Collapse
|
42
|
Li Z, Johnson MR, Ke Z, Chen L, Welte MA. Drosophila lipid droplets buffer the H2Av supply to protect early embryonic development. Curr Biol 2014; 24:1485-91. [PMID: 24930966 DOI: 10.1016/j.cub.2014.05.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/31/2014] [Accepted: 05/08/2014] [Indexed: 10/25/2022]
Abstract
Assembly of DNA into chromatin requires a delicate balancing act, as both dearth and excess of histones severely disrupt chromatin function [1-3]. In particular, cells need to carefully control histone stoichiometry: if different types of histones are incorporated into chromatin in an imbalanced manner, it can lead to altered gene expression, mitotic errors, and death [4-6]. Both the balance between individual core histones and the balance between core histones and histone variants are critical [5, 7]. Here, we find that in early Drosophila embryos, histone balance in the nuclei is regulated by lipid droplets, cytoplasmic fat-storage organelles [8]. Lipid droplets were previously known to function in long-term histone storage: newly laid embryos contain large amounts of excess histones generated during oogenesis [9], and the maternal supplies of core histone H2A and the histone variant H2Av are anchored to lipid droplets via the novel protein Jabba [3]. We find that in these embryos, synthesis of new H2A and H2Av is imbalanced, and that newly produced H2Av can be recruited to lipid droplets. When droplet sequestration is disrupted by mutating Jabba, embryos display an elevated H2Av/H2A ratio in nuclei as well as mitotic defects, reduced viability, and hypersensitivity to H2Av overexpression. We propose that in Drosophila embryos, lipid droplets serve as a histone buffer, not only storing maternal histones to support the early cell cycles but also transiently sequestering H2Av produced in excess and thus ensuring proper histone balance in the nucleus.
Collapse
Affiliation(s)
- Zhihuan Li
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Matthew R Johnson
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Zhonghe Ke
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lili Chen
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Michael A Welte
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
| |
Collapse
|
43
|
Rouhana L, Weiss JA, King RS, Newmark PA. PIWI homologs mediate histone H4 mRNA localization to planarian chromatoid bodies. Development 2014; 141:2592-601. [PMID: 24903754 DOI: 10.1242/dev.101618] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The well-known regenerative abilities of planarian flatworms are attributed to a population of adult stem cells called neoblasts that proliferate and differentiate to produce all cell types. A characteristic feature of neoblasts is the presence of large cytoplasmic ribonucleoprotein granules named chromatoid bodies, the function of which has remained largely elusive. This study shows that histone mRNAs are a common component of chromatoid bodies. Our experiments also demonstrate that accumulation of histone mRNAs, which is typically restricted to the S phase of eukaryotic cells, is extended during the cell cycle of neoblasts. The planarian PIWI homologs SMEDWI-1 and SMEDWI-3 are required for proper localization of germinal histone H4 (gH4) mRNA to chromatoid bodies. The association between histone mRNA and chromatoid body components extends beyond gH4 mRNA, since transcripts of other core histone genes were also found in these structures. Additionally, piRNAs corresponding to loci of every core histone type have been identified. Altogether, this work provides evidence that links PIWI proteins and chromatoid bodies to histone mRNA regulation in planarian stem cells. The molecular similarities between neoblasts and undifferentiated cells of other organisms raise the possibility that PIWI proteins might also regulate histone mRNAs in stem cells and germ cells of other metazoans.
Collapse
Affiliation(s)
- Labib Rouhana
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Jennifer A Weiss
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Ryan S King
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Phillip A Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| |
Collapse
|
44
|
Abstract
This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.
Collapse
Affiliation(s)
| | - Cornelius F. Boerkoel
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-604-875-2157; Fax: +1-604-875-2376
| |
Collapse
|
45
|
Iampietro C, Bergalet J, Wang X, Cody NAL, Chin A, Lefebvre FA, Douziech M, Krause HM, Lécuyer E. Developmentally regulated elimination of damaged nuclei involves a Chk2-dependent mechanism of mRNA nuclear retention. Dev Cell 2014; 29:468-81. [PMID: 24835465 DOI: 10.1016/j.devcel.2014.03.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 12/18/2013] [Accepted: 03/31/2014] [Indexed: 11/25/2022]
Abstract
The faithful execution of embryogenesis relies on the ability of organisms to respond to genotoxic stress and to eliminate defective cells that could otherwise compromise viability. In syncytial-stage Drosophila embryos, nuclei with excessive DNA damage undergo programmed elimination through an as-yet poorly understood process of nuclear fallout at the midblastula transition. We show that this involves a Chk2-dependent mechanism of mRNA nuclear retention that is induced by DNA damage and prevents the translation of specific zygotic mRNAs encoding key mitotic, cytoskeletal, and nuclear proteins required to maintain nuclear viability. For histone messages, we show that nuclear retention involves Chk2-mediated inactivation of the Drosophila stem loop binding protein (SLBP), the levels of which are specifically depleted in damaged nuclei following Chk2 phosphorylation, an event that contributes to nuclear fallout. These results reveal a layer of regulation within the DNA damage surveillance systems that safeguard genome integrity in eukaryotes.
Collapse
Affiliation(s)
- Carole Iampietro
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Julie Bergalet
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Xiaofeng Wang
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Neal A L Cody
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Ashley Chin
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Fabio Alexis Lefebvre
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada; Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Mélanie Douziech
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Henry M Krause
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada; Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada; Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada.
| |
Collapse
|
46
|
MIF4G domain containing protein regulates cell cycle and hepatic carcinogenesis by antagonizing CDK2-dependent p27 stability. Oncogene 2013; 34:237-45. [PMID: 24336329 DOI: 10.1038/onc.2013.536] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 11/09/2013] [Accepted: 11/11/2013] [Indexed: 12/16/2022]
Abstract
The CDK inhibitor p27(kip1) plays crucial roles in cell cycle regulation and cancer progression. Through yeast two-hybrid screening, we identified MIF4G domain containing protein (MIF4GD) as a novel binding partner for p27. The association of MIF4GD and p27 was verified using immunoprecipitation and glutathione S-transferase (GST) pull-down assays. Interaction with MIF4GD led to the stabilization of p27 both in the nucleus and in the cytoplasm in hepatocellular carcinoma (HCC) cells as a result of suppressed phosphorylation of p27 by CDK2 at threonine187. Serum stimulation decreased the levels of MIF4GD and p27 simultaneously. In addition, MIF4GD overexpression resulted in increased p27 levels and reduced cell proliferation, while knockdown of MIF4GD promoted cell cycle progression with decreased p27 levels in cells. Furthermore, overexpression of MIF4GD reduced colony formation and inhibited xenograft tumor growth in nude mice. Finally, we found that both MIF4GD and p27 were expressed at low levels in HCC tissues compared to non-cancerous tissues, and that low expression levels of MIF4GD and p27 were associated with significantly worse prognosis in HCC patients. Our results suggest that MIF4GD is a potential regulator of p27-dependent cell proliferation in HCC. These findings provide a rational framework for the development of potential HCC therapy by targeting the MIF4GD-p27 interaction.
Collapse
|
47
|
Sabath I, Skrajna A, Yang XC, Dadlez M, Marzluff WF, Dominski Z. 3'-End processing of histone pre-mRNAs in Drosophila: U7 snRNP is associated with FLASH and polyadenylation factors. RNA (NEW YORK, N.Y.) 2013; 19:1726-44. [PMID: 24145821 PMCID: PMC3884669 DOI: 10.1261/rna.040360.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
3'-End cleavage of animal replication-dependent histone pre-mRNAs is controlled by the U7 snRNP. Lsm11, the largest component of the U7-specific Sm ring, interacts with FLASH, and in mammalian nuclear extracts these two proteins form a platform that recruits the CPSF73 endonuclease and other polyadenylation factors to the U7 snRNP. FLASH is limiting, and the majority of the U7 snRNP in mammalian extracts exists as a core particle consisting of the U7 snRNA and the Sm ring. Here, we purified the U7 snRNP from Drosophila nuclear extracts and characterized its composition by mass spectrometry. In contrast to the mammalian U7 snRNP, a significant fraction of the Drosophila U7 snRNP contains endogenous FLASH and at least six subunits of the polyadenylation machinery: symplekin, CPSF73, CPSF100, CPSF160, WDR33, and CstF64. The same composite U7 snRNP is recruited to histone pre-mRNA for 3'-end processing. We identified a motif in Drosophila FLASH that is essential for the recruitment of the polyadenylation complex to the U7 snRNP and analyzed the role of other factors, including SLBP and Ars2, in 3'-end processing of Drosophila histone pre-mRNAs. SLBP that binds the upstream stem-loop structure likely recruits a yet-unidentified essential component(s) to the processing machinery. In contrast, Ars2, a protein previously shown to interact with FLASH in mammalian cells, is dispensable for processing in Drosophila. Our studies also demonstrate that Drosophila symplekin and three factors involved in cleavage and polyadenylation-CPSF, CstF, and CF Im-are present in Drosophila nuclear extracts in a stable supercomplex.
Collapse
Affiliation(s)
- Ivan Sabath
- Department of Biochemistry and Biophysics, Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Aleksandra Skrajna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 00-901 Warsaw, Poland
| | - Xiao-cui Yang
- Department of Biochemistry and Biophysics, Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 00-901 Warsaw, Poland
- Institute of Genetics and Biotechnology, Warsaw University, 02-106 Warsaw, Poland
| | - William F. Marzluff
- Department of Biochemistry and Biophysics, Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Zbigniew Dominski
- Department of Biochemistry and Biophysics, Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Corresponding authorE-mail
| |
Collapse
|
48
|
Abstract
A paper in this issue shows that histones H2a and H2b are stored in lipid droplets in Drosophila embryos complexed with the protein Jabba. In Jabba mutant embryos, histones H2a and H2b are degraded but embryos survive by translating stored histone mRNA.
Collapse
|
49
|
Mahajan K, Mahajan NP. WEE1 tyrosine kinase, a novel epigenetic modifier. Trends Genet 2013; 29:394-402. [PMID: 23537585 DOI: 10.1016/j.tig.2013.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/26/2012] [Accepted: 02/25/2013] [Indexed: 11/30/2022]
Abstract
The cell cycle requires cells to duplicate their chromatin, DNA, and histones, while retaining a subset of epigenetic marks, in a highly coordinated manner. The WEE1 kinase was identified as an important regulator during S phase, preventing entry into mitosis until DNA replication has been completed. Interestingly, WEE1 has also emerged as a key player in regulating histone synthesis. It phosphorylates histone H2B at tyrosine 37 in the nucleosomes found upstream of the histone gene cluster, and this suppresses histone transcription in late S phase. These observations highlight a dual role for WEE1 as both a mitotic gatekeeper and a surveyor of chromatin synthesis, providing a direct link between epigenetics and cell-cycle progression. Importantly, this link has implications for the design of novel epigenetic inhibitors targeting cancers that display elevated expression of this kinase.
Collapse
Affiliation(s)
- Kiran Mahajan
- Drug Discovery Department, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.
| | | |
Collapse
|
50
|
Li Z, Thiel K, Thul PJ, Beller M, Kühnlein RP, Welte MA. Lipid droplets control the maternal histone supply of Drosophila embryos. Curr Biol 2012; 22:2104-13. [PMID: 23084995 DOI: 10.1016/j.cub.2012.09.018] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 09/03/2012] [Accepted: 09/03/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Histones are essential for chromatin packing, yet free histones not incorporated into chromatin are toxic. While in most cells multiple regulatory mechanisms prevent accumulation of excess histones, early Drosophila embryos contain massive extranuclear histone stores, thought to be essential for development. Excess histones H2A, H2B, and H2Av are bound to lipid droplets, ubiquitous fat storage organelles especially abundant in embryos. It has been proposed that sequestration on lipid droplets allows safe transient storage of supernumerary histones. RESULTS Here, we critically test this sequestration hypothesis. We find that histones are anchored to lipid droplets via the previously uncharacterized protein Jabba: Jabba localizes to droplets, coimmunoprecipitates with histones, and is necessary to recruit histones to droplets. Jabba mutants lack the maternal H2A, H2B, and H2Av deposits altogether; presumably, these deposits are eliminated unless sequestered on droplets. Jabba mutant embryos compensate for this histone deficit by translating maternal histone mRNAs. However, when histone expression is mildly compromised, the maternal histone protein deposits are essential for proper early mitoses and for viability. CONCLUSIONS A growing number of proteins from other cellular compartments have been found to transiently associate with lipid droplets. Our studies provide the first insight into mechanism and functional relevance of this sequestration. We conclude that sequestration on lipid droplets allows embryos to build up extranuclear histone stores and provides histones for chromatin assembly during times of high demand. This work reveals a novel aspect of histone metabolism and establishes lipid droplets as functional storage sites for unstable or detrimental proteins.
Collapse
Affiliation(s)
- Zhihuan Li
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | | | | | | | | | | |
Collapse
|