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Wolfe MB, Schagat TL, Paulsen MT, Magnuson B, Ljungman M, Park D, Zhang C, Campbell ZT, Goldstrohm AC, Freddolino PL. Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis. RNA (NEW YORK, N.Y.) 2020; 26:1680-1703. [PMID: 32753408 PMCID: PMC7566576 DOI: 10.1261/rna.077362.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/30/2020] [Indexed: 05/27/2023]
Abstract
The human PUF-family proteins, PUM1 and PUM2, posttranscriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3'-UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady-state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a "rulebook" of key contextual features that differentiate functional versus nonfunctional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.
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Affiliation(s)
- Michael B Wolfe
- Department of Biological Chemistry and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Brian Magnuson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Daeyoon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Chi Zhang
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Peter L Freddolino
- Department of Biological Chemistry and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
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Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing. Methods 2018; 155:88-103. [PMID: 30529548 DOI: 10.1016/j.ymeth.2018.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022] Open
Abstract
Many open questions in RNA biology relate to the kinetics of gene expression and the impact of RNA binding regulatory factors on processing or decay rates of particular transcripts. Steady state measurements of RNA abundance obtained from RNA-seq approaches are not able to separate the effects of transcription from those of RNA decay in the overall abundance of any given transcript, instead only giving information on the (presumed steady-state) abundances of transcripts. Through the combination of metabolic labeling and high-throughput sequencing, several groups have been able to measure both transcription rates and decay rates of the entire transcriptome of an organism in a single experiment. This review focuses on the methodology used to specifically measure RNA decay at a global level. By comparing and contrasting approaches and describing the experimental protocols in a modular manner, we intend to provide both experienced and new researchers to the field the ability to combine aspects of various protocols to fit the unique needs of biological questions not addressed by current methods.
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Roberts TC, Hart JR, Kaikkonen MU, Weinberg MS, Vogt PK, Morris KV. Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR. Nat Protoc 2015; 10:1198-211. [PMID: 26182239 PMCID: PMC4790731 DOI: 10.1038/nprot.2015.076] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear run-on (NRO) is a method that measures transcriptional activity via the quantification of biochemically labeled nascent RNA molecules derived from nuclear isolates. Widespread use of this technique has been limited because of its technical difficulty relative to steady-state total mRNA analyses. Here we describe a detailed protocol for the quantification of transcriptional activity in human cell cultures. Nuclei are first isolated and NRO transcription is performed in the presence of bromouridine. Labeled nascent transcripts are purified by immunoprecipitation, and transcript levels are determined by reverse-transcription quantitative PCR (RT-qPCR). Data are then analyzed using standard techniques described elsewhere. This method is rapid (the protocol can be completed in 2 d) and cost-effective, exhibits negligible detection of background noise from unlabeled transcripts, requires no radioactive materials and can be performed from as few as 500,000 nuclei. It also takes advantage of the high sensitivity, specificity and dynamic range of RT-qPCR.
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Affiliation(s)
- Thomas C. Roberts
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, United Kingdom
- Sanford-Burnham Medical Research Institute, Development, Aging and Regeneration Program, 10901 N. Torrey pines Road, La Jolla, CA, 92037, USA
| | - Jonathan R. Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Minna U. Kaikkonen
- University of Eastern Finland, A.I. Virtanen institute, Department of Biotechnology and Molecular Medicine, P.O.B. 1627, 70211 Kuopio, Finland
| | - Marc S. Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, WITS 2050, South Africa
| | - Peter K. Vogt
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Kevin V. Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- School of Biotechnology and Biomedical Sciences, University of New South Wales, NSW 2052, Australia
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Abstract
Steady-state levels of cellular RNA are determined by both transcriptional rate and RNA half-life. Commonly used methods for transcriptional analysis are only capable of profiling total RNA and do not distinguish changes in synthesis and decay rates. Hence, a better understanding of the temporal dynamics of cellular response for a given condition at the transcriptional level requires techniques for the analysis of nascent transcripts. Here we describe a protocol that allows isolation of nascent transcripts with a copper-catalyzed azide-alkyne cycloaddition (CuAAC) also known as a click chemistry reaction.
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Affiliation(s)
- Ozlem Yildirim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
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5
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Ionizing radiation and glioblastoma exosomes: implications in tumor biology and cell migration. Transl Oncol 2013; 6:638-48. [PMID: 24466366 DOI: 10.1593/tlo.13640] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 09/25/2013] [Accepted: 10/30/2013] [Indexed: 12/12/2022] Open
Abstract
Exosomes are nanometer-sized lipid vesicles released ubiquitously by cells, which have been shown to have a normal physiological role, as well as influence the tumor microenvironment and aid metastasis. Recent studies highlight the ability of exosomes to convey tumor-suppressive and oncogenic mRNAs, microRNAs, and proteins to a receiving cell, subsequently activating downstream signaling pathways and influencing cellular phenotype. Here, we show that radiation increases the abundance of exosomes released by glioblastoma cells and normal astrocytes. Exosomes derived from irradiated cells enhanced the migration of recipient cells, and their molecular profiling revealed an abundance of molecules related to signaling pathways important for cell migration. In particular, connective tissue growth factor (CTGF) mRNA and insulin-like growth factor binding protein 2 (IGFBP2) protein levels were elevated, and coculture of nonirradiated cells with exosomes isolated from irradiated cells increased CTGF protein expression in the recipient cells. Additionally, these exosomes enhanced the activation of neurotrophic tyrosine kinase receptor type 1 (TrkA), focal adhesion kinase, Paxillin, and proto-oncogene tyrosine-protein kinase Src (Src) in recipient cells, molecules involved in cell migration. Collectively, our data suggest that radiation influences exosome abundance, specifically alters their molecular composition, and on uptake, promotes a migratory phenotype.
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Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Magnuson B, Wilson TE, Ljungman M. Use of Bru-Seq and BruChase-Seq for genome-wide assessment of the synthesis and stability of RNA. Methods 2013; 67:45-54. [PMID: 23973811 DOI: 10.1016/j.ymeth.2013.08.015] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/10/2013] [Accepted: 08/15/2013] [Indexed: 11/29/2022] Open
Abstract
Gene expression studies commonly examine total cellular RNA, which only provides information about its steady-state pool of RNA. It remains unclear whether differences in the steady-state reflects variable rates of transcription or RNA degradation. To specifically monitor RNA synthesis and degradation genome-wide, we developed Bru-Seq and BruChase-Seq. These assays are based on metabolic pulse-chase labeling of RNA using bromouridine (Bru). In Bru-Seq, recently labeled RNAs are sequenced to reveal spans of nascent transcription in the genome. In BruChase-Seq, cells are chased in uridine for different periods of time following Bru-labeling, allowing for the isolation of RNA populations of specific ages. Here we describe these methodologies in detail and highlight their usefulness in assessing RNA synthesis and stability as well as splicing kinetics with examples of specific genes from different human cell lines.
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Affiliation(s)
- Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI, USA
| | - Artur Veloso
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI, USA; Bioinformatics Program, University of Michigan, Ann Arbor, MI, USA
| | - Jayendra Prasad
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI, USA
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Emily A Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI, USA
| | - Brian Magnuson
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI, USA
| | - Thomas E Wilson
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan, Ann Arbor, MI, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
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Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc Natl Acad Sci U S A 2013; 110:2240-5. [PMID: 23345452 DOI: 10.1073/pnas.1219192110] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, micro RNAs (miRNAs), and RNA-binding proteins. Here, we present bromouride labeling and sequencing (Bru-Seq) and bromouridine pulse-chase and sequencing (BruChase-Seq) to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis and after exposure to the proinflammatory tumor necrosis factor (TNF). The inflammatory response in human cells involves rapid and dramatic changes in gene expression, and the Bru-Seq and BruChase-Seq techniques revealed a coordinated and complex regulation of gene expression both at the transcriptional and posttranscriptional levels. The combinatory analysis of both RNA synthesis and stability using Bru-Seq and BruChase-Seq allows for a much deeper understanding of mechanisms of gene regulation than afforded by the analysis of steady-state total RNA and should be useful in many biological settings.
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Fukuoka M, Uehara A, Niki K, Goto S, Kato D, Utsugi T, Ohtsu M, Murakami Y. Identification of preferentially reactivated genes during early G1 phase using nascent mRNA as an index of transcriptional activity. Biochem Biophys Res Commun 2012; 430:1005-10. [PMID: 23261446 DOI: 10.1016/j.bbrc.2012.12.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 12/11/2012] [Indexed: 11/19/2022]
Abstract
During mammalian mitosis, transcription is silenced due to dissociation of transcription factors from DNA and chromosome condensation. At the end of mitosis, transcription is reactivated through chromosome relaxation and reloading of these factors to the DNA. Early G1 genes, which are preferentially reactivated during M/G1 transition, are important for maintenance of cellular function and are known to be strictly regulated. As only few early G1 genes have been identified to date, screening for early G1 genes by genome-wide analysis using nascent mRNA could contribute to the elucidation of the regulatory mechanisms during early G1. Here, we performed a detailed expression analysis for the M/G1 transition of mammalian cells by microarray analysis of nascent mRNA, and identified 298 early G1 genes. Analysis of these genes provides two important insights. Firstly, certain motifs are enriched in the upstream sequences of early G1 genes; from this we could predict candidate cognate transcription factors, including Sp1, which is recruited to the DNA in the early G1 phase. Secondly, we discovered that neighboring genes of early G1 genes were also frequently up-regulated in the G1 phase. Information about these numerous newly identified early G1 genes will likely contribute to an understanding of the regulatory mechanisms of the early G1 genes.
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Affiliation(s)
- Masashi Fukuoka
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
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Tani H, Akimitsu N. Genome-wide technology for determining RNA stability in mammalian cells: historical perspective and recent advantages based on modified nucleotide labeling. RNA Biol 2012; 9:1233-8. [PMID: 23034600 DOI: 10.4161/rna.22036] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Changing the abundance of transcripts by regulated RNA degradation is a critical step in the control of various biological pathways. Recently, genome-wide inhibitor-free technologies for determining RNA stabilities in mammalian cells have been developed. In these methods, endogenous RNAs are pulse labeled by uridine analogs [e.g., 4-thiouridine (4sU), 5-etyniluridine (EU) and 5'-bromo-uridine (BrU)], followed by purification of labeled de novo RNAs. These technologies have revealed that the specific half-life of each mRNA is closely related to its physiological function. Genes with short-lived mRNAs are significantly enriched among regulatory genes, while genes with long-lived mRNAs are enriched among housekeeping genes. This review describes the recent progress of experimental procedures for measuring RNA stability.
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Affiliation(s)
- Hidenori Tani
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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Pérez-Ortín JE, Jordán-Pla A, Pelechano V. A genomic view of mRNA turnover in yeast. C R Biol 2011; 334:647-54. [DOI: 10.1016/j.crvi.2011.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 03/17/2011] [Indexed: 12/01/2022]
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Direct evidence for postmeiotic transcription during Drosophila melanogaster spermatogenesis. Genetics 2010; 186:431-3. [PMID: 20610406 DOI: 10.1534/genetics.110.118919] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Extensive gene expression during meiosis is a hallmark of spermatogenesis. Although it was generally accepted that RNA transcription ceases during meiosis, recent observations suggest that some transcription occurs in postmeiosis. To further resolve this issue, we provide direct evidence for the de novo transcription of RNA during the postmeiotic phases. These results strengthen the newly emerging notion that postmeiotic transcription is dynamic and integral to the overall process of spermatogenesis.
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Ohse K, Ohtsu M, Onoda F, Murakami Y. Development of effective isolation method of ES cells for analysis of differentiation. Biochem Biophys Res Commun 2009; 387:64-9. [PMID: 19559667 DOI: 10.1016/j.bbrc.2009.06.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 06/22/2009] [Indexed: 11/19/2022]
Abstract
Neuroectoderm development is a milestone of vertebrate neurogenesis. However, the molecular mechanism underlying the differentiation of neuroectoderm is still unclear, especially in mammals. ES cells co-cultured with PA6 cells can differentiate to neuroectoderm by the stromal cell-derived inducing activity method (SDIA method), but contamination of PA6 cells is an obstacle to the analysis of molecular mechanisms of differentiation. Here we describe a novel method by which differentiated ES cells are easily isolated from PA6 cells. We attempted to induce the differentiation of ES cells using paraformaldehyde-fixed PA6 cells. RT-PCR and DNA microarray analysis revealed that the background noise derived from contaminated PA6 cells disappeared when fixed PA6 cells were used. Furthermore, genes up-regulated during the differentiation of ES cells were expressed in a developing mouse embryo. Thus, our newly developed method will be very useful for identifying novel genes associated with mouse neuroectoderm development in vitro and in vivo.
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Affiliation(s)
- Kensuke Ohse
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba, Japan
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Friedel CC, Dölken L. Metabolic tagging and purification of nascent RNA: implications for transcriptomics. MOLECULAR BIOSYSTEMS 2009; 5:1271-8. [PMID: 19823741 DOI: 10.1039/b911233b] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gene expression profiling to analyze cellular responses against different stimuli or conditions is generally performed at the total cellular RNA level. This results in poor resolution of the temporal kinetics of the cellular response and a bias towards detecting up-regulation of short-lived transcripts. Furthermore, changes in transcription rate and RNA stability cannot be distinguished. These problems can be addressed by analyzing nascent RNA instead of total cellular RNA. Throughout the last few years methods have been developed for metabolic tagging and purification of nascent RNA. In this article, we review these experimental procedures and discuss their implications for large-scale gene expression profiling.
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Affiliation(s)
- Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-University Munich, Amalienstr. 17, 80333 München, Germany.
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Mammalian MCM loading in late-G(1) coincides with Rb hyperphosphorylation and the transition to post-transcriptional control of progression into S-phase. PLoS One 2009; 4:e5462. [PMID: 19421323 PMCID: PMC2674209 DOI: 10.1371/journal.pone.0005462] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 04/15/2009] [Indexed: 01/19/2023] Open
Abstract
Background Control of the onset of DNA synthesis in mammalian cells requires the coordinated assembly and activation of the pre-Replication Complex. In order to understand the regulatory events controlling preRC dynamics, we have investigated how the timing of preRC assembly relates temporally to other biochemical events governing progress into S-phase. Methodology/Principal Finding In murine and Chinese hamster (CHO) cells released from quiescence, the loading of the replicative MCM helicase onto chromatin occurs in the final 3–4 hrs of G1. Cdc45 and PCNA, both of which are required for G1-S transit, bind to chromatin at the G1-S transition or even earlier in G1, when MCMs load. An RNA polymerase II inhibitor (DRB) was added to synchronized murine keratinocytes to show that they are no longer dependent on new mRNA synthesis 3–4 hrs prior to S-phase entry, which is also true for CHO and human cells. Further, CHO cells can progress into S-phase on time, and complete S-phase, under conditions where new mRNA synthesis is significantly compromised, and such mRNA suppression causes no adverse effects on preRC dynamics prior to, or during, S-phase progression. Even more intriguing, hyperphosphorylation of Rb coincides with the start of MCM loading and, paradoxically, with the time in late-G1 when de novo mRNA synthesis is no longer rate limiting for progression into S-phase. Conclusions/Significance MCM, Cdc45, and PCNA loading, and the subsequent transit through G1-S, do not depend on concurrent new mRNA synthesis. These results indicate that mammalian cells pass through a distinct transition in late-G1 at which time Rb becomes hyperphosphorylated and MCM loading commences, but that after this transition the control of MCM, Cdc45, and PCNA loading and the onset of DNA replication are regulated at the post-transcriptional level.
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