101
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Kingston ER, Bartel DP. Global analyses of the dynamics of mammalian microRNA metabolism. Genome Res 2019; 29:1777-1790. [PMID: 31519739 PMCID: PMC6836734 DOI: 10.1101/gr.251421.119] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/29/2019] [Indexed: 12/30/2022]
Abstract
Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 110 ± 50 copies/cell/min, which exceeds rates reported for any mRNAs. These duplexes are rapidly loaded into Argonaute, with <30 min typically required for duplex loading and silencing-complex maturation. Within Argonaute, guide strands have stabilities that vary by 100-fold. Half-lives also vary globally between cell lines, with median values ranging from 11 to 34 h in mESCs and contact-inhibited MEFs, respectively. Moreover, relative half-lives for individual miRNAs vary between cell types, implying the influence of cell-specific factors in dictating turnover rate. The apparent influence of miRNA regions most important for targeting, together with the effect of one target on miR-7 accumulation, suggest that targets fulfill this role. Analysis of the tailing and trimming of miRNA 3' termini showed that the flux was typically greatest through the isoform tailed with a single uridine, although changes in this flux did not correspond to changes in stability, which suggested that the processes of tailing and trimming might be independent from that of decay. Together, these results establish a framework for describing the dynamics and regulation of miRNAs throughout their life cycle.
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Affiliation(s)
- Elena R Kingston
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David P Bartel
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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102
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Steinparzer I, Sedlyarov V, Rubin JD, Eislmayr K, Galbraith MD, Levandowski CB, Vcelkova T, Sneezum L, Wascher F, Amman F, Kleinova R, Bender H, Andrysik Z, Espinosa JM, Superti-Furga G, Dowell RD, Taatjes DJ, Kovarik P. Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions. Mol Cell 2019; 76:485-499.e8. [PMID: 31495563 DOI: 10.1016/j.molcel.2019.07.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 01/12/2023]
Abstract
Transcriptional responses to external stimuli remain poorly understood. Using global nuclear run-on followed by sequencing (GRO-seq) and precision nuclear run-on sequencing (PRO-seq), we show that CDK8 kinase activity promotes RNA polymerase II pause release in response to interferon-γ (IFN-γ), a universal cytokine involved in immunity and tumor surveillance. The Mediator kinase module contains CDK8 or CDK19, which are presumed to be functionally redundant. We implemented cortistatin A, chemical genetics, transcriptomics, and other methods to decouple their function while assessing enzymatic versus structural roles. Unexpectedly, CDK8 and CDK19 regulated different gene sets via distinct mechanisms. CDK8-dependent regulation required its kinase activity, whereas CDK19 governed IFN-γ responses through its scaffolding function (i.e., it was kinase independent). Accordingly, CDK8, not CDK19, phosphorylates the STAT1 transcription factor (TF) during IFN-γ stimulation, and CDK8 kinase inhibition blocked activation of JAK-STAT pathway TFs. Cytokines such as IFN-γ rapidly mobilize TFs to "reprogram" cellular transcription; our results implicate CDK8 and CDK19 as essential for this transcriptional reprogramming.
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Affiliation(s)
- Iris Steinparzer
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jonathan D Rubin
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Kevin Eislmayr
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Terezia Vcelkova
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Lucy Sneezum
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Florian Wascher
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Fabian Amman
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria; Department of Theoretical Chemistry of the University of Vienna, 1090 Vienna, Austria
| | - Renata Kleinova
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria
| | - Heather Bender
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zdenek Andrysik
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
| | - Pavel Kovarik
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, Vienna, Austria.
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103
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Abstract
Summary Global quantification of total RNA is used to investigate steady state levels of gene expression. However, being able to differentiate pre-existing RNA (that has been synthesized prior to a defined point in time) and newly transcribed RNA can provide invaluable information e.g. to estimate RNA half-lives or identify fast and complex regulatory processes. Recently, new techniques based on metabolic labeling and RNA-seq have emerged that allow to quantify new and old RNA: Nucleoside analogs are incorporated into newly transcribed RNA and are made detectable as point mutations in mapped reads. However, relatively infrequent incorporation events and significant sequencing error rates make the differentiation between old and new RNA a highly challenging task. We developed a statistical approach termed GRAND-SLAM that, for the first time, allows to estimate the proportion of old and new RNA in such an experiment. Uncertainty in the estimates is quantified in a Bayesian framework. Simulation experiments show our approach to be unbiased and highly accurate. Furthermore, we analyze how uncertainty in the proportion translates into uncertainty in estimating RNA half-lives and give guidelines for planning experiments. Finally, we demonstrate that our estimates of RNA half-lives compare favorably to other experimental approaches and that biological processes affecting RNA half-lives can be investigated with greater power than offered by any other method. GRAND-SLAM is freely available for non-commercial use at http://software.erhard-lab.de; R scripts to generate all figures are available at zenodo (doi: 10.5281/zenodo.1162340).
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Affiliation(s)
- Christopher Jürges
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Florian Erhard
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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104
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Gressel S, Schwalb B, Cramer P. The pause-initiation limit restricts transcription activation in human cells. Nat Commun 2019; 10:3603. [PMID: 31399571 PMCID: PMC6689055 DOI: 10.1038/s41467-019-11536-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/18/2019] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic gene transcription is often controlled at the level of RNA polymerase II (Pol II) pausing in the promoter-proximal region. Pausing Pol II limits the frequency of transcription initiation ('pause-initiation limit'), predicting that the pause duration must be decreased for transcriptional activation. To test this prediction, we conduct a genome-wide kinetic analysis of the heat shock response in human cells. We show that the pause-initiation limit restricts transcriptional activation at most genes. Gene activation generally requires the activity of the P-TEFb kinase CDK9, which decreases the duration of Pol II pausing and thereby enables an increase in the productive initiation frequency. The transcription of enhancer elements is generally not pause limited and can be activated without CDK9 activity. Our results define the kinetics of Pol II transcriptional regulation in human cells at all gene classes during a natural transcription response.
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Affiliation(s)
- Saskia Gressel
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
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105
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Muthmann N, Hartstock K, Rentmeister A. Chemo-enzymatic treatment of RNA to facilitate analyses. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1561. [PMID: 31392842 DOI: 10.1002/wrna.1561] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/17/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]
Abstract
Labeling RNA is a recurring problem to make RNA compatible with state-of-the-art methodology and comes in many flavors. Considering only cellular applications, the spectrum still ranges from site-specific labeling of individual transcripts, for example, for live-cell imaging of mRNA trafficking, to metabolic labeling in combination with next generation sequencing to capture dynamic aspects of RNA metabolism on a transcriptome-wide scale. Combining the specificity of RNA-modifying enzymes with non-natural substrates has emerged as a valuable strategy to modify RNA site- or sequence-specifically with functional groups suitable for subsequent bioorthogonal reactions and thus label RNA with reporter moieties such as affinity or fluorescent tags. In this review article, we will cover chemo-enzymatic approaches (a) for in vitro labeling of RNA for application in cells, (b) for treatment of total RNA, and (c) for metabolic labeling of RNA. This article is categorized under: RNA Processing < RNA Editing and Modification RNA Methods < RNA Analyses in vitro and In Silico RNA Methods < RNA Analyses in Cells.
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Affiliation(s)
- Nils Muthmann
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Katja Hartstock
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
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106
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On the optimal design of metabolic RNA labeling experiments. PLoS Comput Biol 2019; 15:e1007252. [PMID: 31390362 PMCID: PMC6699717 DOI: 10.1371/journal.pcbi.1007252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 08/19/2019] [Accepted: 07/08/2019] [Indexed: 01/16/2023] Open
Abstract
Massively parallel RNA sequencing (RNA-seq) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription, processing or decay. Regardless of advances in the experimental protocols and techniques, every experimentalist needs to specify the key aspects of experimental design: For example, which protocol should be used (biochemical separation vs. nucleotide conversion) and what is the optimal labeling time? In this work, we provide approximate answers to these questions using the asymptotic theory of optimal design. Specifically, we investigate, how the variance of degradation rate estimates depends on the time and derive the optimal time for any given degradation rate. Subsequently, we show that an increase in sample numbers should be preferred over an increase in sequencing depth. Lastly, we provide some guidance on use cases when laborious biochemical separation outcompetes recent nucleotide conversion based methods (such as SLAMseq) and show, how inefficient conversion influences the precision of estimates. Code and documentation can be found at https://github.com/dieterich-lab/DesignMetabolicRNAlabeling. Massively parallel RNA sequencing (RNA-seq) in combination with metabolic labeling has become the de facto standard approach to study alterations in RNA transcription, processing or decay. In our manuscript, we address several key aspects of experimental design: 1) The optimal labeling time, 2) the number of replicate samples over sequencing depth and 3) the choice of experimental protocol. We provide approximate answers to these questions using asymptotic theory of optimal design.
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107
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Hendriks GJ, Jung LA, Larsson AJM, Lidschreiber M, Andersson Forsman O, Lidschreiber K, Cramer P, Sandberg R. NASC-seq monitors RNA synthesis in single cells. Nat Commun 2019; 10:3138. [PMID: 31316066 PMCID: PMC6637240 DOI: 10.1038/s41467-019-11028-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/12/2019] [Indexed: 12/14/2022] Open
Abstract
Sequencing of newly synthesised RNA can monitor transcriptional dynamics with great sensitivity and high temporal resolution, but is currently restricted to populations of cells. Here, we develop new transcriptome alkylation-dependent single-cell RNA sequencing (NASC-seq), to monitor newly synthesised and pre-existing RNA simultaneously in single cells. We validate the method on pre-labelled RNA, and by demonstrating that more newly synthesised RNA was detected for genes with known high mRNA turnover. Monitoring RNA synthesis during Jurkat T-cell activation with NASC-seq reveals both rapidly up- and down-regulated genes, and that induced genes are almost exclusively detected as newly transcribed. Moreover, the newly synthesised and pre-existing transcriptomes after T-cell activation are distinct, confirming that NASC-seq simultaneously measures gene expression corresponding to two time points in single cells. Altogether, NASC-seq enables precise temporal monitoring of RNA synthesis at single-cell resolution during homoeostasis, perturbation responses and cellular differentiation.
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Affiliation(s)
- Gert-Jan Hendriks
- Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden
| | - Lisa A Jung
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Blickagången 16, 141 52, Huddinge, Sweden
| | - Anton J M Larsson
- Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden
| | - Michael Lidschreiber
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Blickagången 16, 141 52, Huddinge, Sweden
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Oscar Andersson Forsman
- Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden
| | - Katja Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Patrick Cramer
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Blickagången 16, 141 52, Huddinge, Sweden.
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Instiutet, Biomedicum, Solnavägen 9, 171 65, Solna, Sweden.
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108
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scSLAM-seq reveals core features of transcription dynamics in single cells. Nature 2019; 571:419-423. [DOI: 10.1038/s41586-019-1369-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 06/10/2019] [Indexed: 11/08/2022]
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109
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Russo J, Wilusz J. Trick or TREAT: A Scary-Good New Approach for Single-Molecule mRNA Decay Analysis. Mol Cell 2019; 68:476-477. [PMID: 29100051 DOI: 10.1016/j.molcel.2017.10.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this issue of Molecular Cell, Horvathova et al. (2017) have developed a powerful approach to single-molecule assessment of RNA decay in living cells by exploiting the ability of flavivirus RNA structural elements to trap XRN1 decay intermediates in dual-labeled reporter constructs.
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Affiliation(s)
- Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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110
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Baptista MAP, Dölken L. RNA dynamics revealed by metabolic RNA labeling and biochemical nucleoside conversions. Nat Methods 2019; 15:171-172. [PMID: 29489745 DOI: 10.1038/nmeth.4608] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marisa A P Baptista
- Institute of Virology and Immunobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute of Virology and Immunobiology, Julius Maximilian University of Würzburg, Würzburg, Germany
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111
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Wachutka L, Caizzi L, Gagneur J, Cramer P. Global donor and acceptor splicing site kinetics in human cells. eLife 2019; 8:45056. [PMID: 31025937 PMCID: PMC6548502 DOI: 10.7554/elife.45056] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 04/25/2019] [Indexed: 11/13/2022] Open
Abstract
RNA splicing is an essential part of eukaryotic gene expression. Although the mechanism of splicing has been extensively studied in vitro, in vivo kinetics for the two-step splicing reaction remain poorly understood. Here, we combine transient transcriptome sequencing (TT-seq) and mathematical modeling to quantify RNA metabolic rates at donor and acceptor splice sites across the human genome. Splicing occurs in the range of minutes and is limited by the speed of RNA polymerase elongation. Splicing kinetics strongly depends on the position and nature of nucleotides flanking splice sites, and on structural interactions between unspliced RNA and small nuclear RNAs in spliceosomal intermediates. Finally, we introduce the 'yield' of splicing as the efficiency of converting unspliced to spliced RNA and show that it is highest for mRNAs and independent of splicing kinetics. These results lead to quantitative models describing how splicing rates and yield are encoded in the human genome.
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Affiliation(s)
- Leonhard Wachutka
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Livia Caizzi
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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112
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Detection and quantification of RNA decay intermediates using XRN1-resistant reporter transcripts. Nat Protoc 2019; 14:1603-1633. [DOI: 10.1038/s41596-019-0152-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
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113
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Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nat Methods 2019; 16:429-436. [PMID: 31011185 DOI: 10.1038/s41592-019-0394-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/18/2019] [Indexed: 12/19/2022]
Abstract
Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We report a sequencing method for the measurement of replication fork movement on single molecules by detecting nucleotide analog signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect 5-bromodeoxyuridine (BrdU) incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse-labeling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20-160 kilobases to generate a whole-genome single-molecule map of DNA replication dynamics and discover a class of low-frequency stochastic origins in budding yeast. The D-NAscent software is available at https://github.com/MBoemo/DNAscent.git .
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114
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Krajewska M, Dries R, Grassetti AV, Dust S, Gao Y, Huang H, Sharma B, Day DS, Kwiatkowski N, Pomaville M, Dodd O, Chipumuro E, Zhang T, Greenleaf AL, Yuan GC, Gray NS, Young RA, Geyer M, Gerber SA, George RE. CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation. Nat Commun 2019; 10:1757. [PMID: 30988284 PMCID: PMC6465371 DOI: 10.1038/s41467-019-09703-y] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 03/26/2019] [Indexed: 02/07/2023] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) modulates transcription elongation by phosphorylating the carboxy-terminal domain of RNA polymerase II and selectively affects the expression of genes involved in the DNA damage response (DDR) and mRNA processing. Yet, the mechanisms underlying such selectivity remain unclear. Here we show that CDK12 inhibition in cancer cells lacking CDK12 mutations results in gene length-dependent elongation defects, inducing premature cleavage and polyadenylation (PCPA) and loss of expression of long (>45 kb) genes, a substantial proportion of which participate in the DDR. This early termination phenotype correlates with an increased number of intronic polyadenylation sites, a feature especially prominent among DDR genes. Phosphoproteomic analysis indicated that CDK12 directly phosphorylates pre-mRNA processing factors, including those regulating PCPA. These results support a model in which DDR genes are uniquely susceptible to CDK12 inhibition primarily due to their relatively longer lengths and lower ratios of U1 snRNP binding to intronic polyadenylation sites. Cdk12 is primarily involved in the regulation of DNA damage response (DDR) gene transcription as well as mRNA processing. Here, the authors demonstrate that CDK12 suppresses intronic polyadenylation, and that inhibition of this kinase primarily affects the expression of long genes with higher numbers of polyA sites, features common to many DDR genes.
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Affiliation(s)
- Malgorzata Krajewska
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ruben Dries
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Departments of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Andrew V Grassetti
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA
| | - Sofia Dust
- Institute of Structural Biology, University of Bonn, 53127, Bonn, Germany
| | - Yang Gao
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Hao Huang
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bandana Sharma
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA
| | - Daniel S Day
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Nicholas Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Monica Pomaville
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA
| | - Oliver Dodd
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA
| | - Edmond Chipumuro
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Arno L Greenleaf
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Guo-Cheng Yuan
- Departments of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard School of Public Health, Boston, MA, 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, 53127, Bonn, Germany
| | - Scott A Gerber
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA
| | - Rani E George
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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115
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Global identification of functional microRNA-mRNA interactions in Drosophila. Nat Commun 2019; 10:1626. [PMID: 30967537 PMCID: PMC6456604 DOI: 10.1038/s41467-019-09586-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 03/11/2019] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. Here, we generated a transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila.
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116
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Suzuki H, Okamoto-Katsuyama M, Suwa T, Maeda R, Tamura TA, Yamaguchi Y. TLP-mediated global transcriptional repression after double-strand DNA breaks slows down DNA repair and induces apoptosis. Sci Rep 2019; 9:4868. [PMID: 30890736 PMCID: PMC6425004 DOI: 10.1038/s41598-019-41057-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/18/2019] [Indexed: 11/16/2022] Open
Abstract
Transcription and DNA damage repair act in a coordinated manner. Recent studies have shown that double-strand DNA breaks (DSBs) are repaired in a transcription-coupled manner. Active transcription results in a faster recruitment of DSB repair factors and expedites DNA repair. On the other hand, transcription is repressed by DNA damage through multiple mechanisms. We previously reported that TLP, a TATA box-binding protein (TBP) family member that functions as a transcriptional regulator, is also involved in DNA damage-induced apoptosis. However, the mechanism by which TLP affects DNA damage response was largely unknown. Here we show that TLP-mediated global transcriptional repression after DSBs is crucial for apoptosis induction by DNA-damaging agents such as etoposide and doxorubicin. Compared to control cells, TLP-knockdown cells were resistant to etoposide-induced apoptosis and exhibited an elevated level of global transcription after etoposide exposure. DSBs were efficiently removed in transcriptionally hyperactive TLP-knockdown cells. However, forced transcriptional shutdown using transcriptional inhibitors α-amanitin and 5,6-dichloro-1-ß-D-ribofuranosylbenzimidazole (DRB) slowed down DSB repair and resensitized TLP-knockdown cells to etoposide. Taken together, these results indicate that TLP is a critical determinant as to how cells respond to DSBs and triggers apoptosis to cells that have sustained DNA damage.
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Affiliation(s)
- Hidefumi Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8501, Japan
| | - Mayumi Okamoto-Katsuyama
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8501, Japan
| | - Tetsufumi Suwa
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8501, Japan
| | - Ryo Maeda
- Graduate School of Science, Chiba University, 1-33 Yayoicho, Chiba, 263-8522, Japan
| | - Taka-Aki Tamura
- Graduate School of Science, Chiba University, 1-33 Yayoicho, Chiba, 263-8522, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8501, Japan.
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117
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Dantoft W, Robertson KA, Watkins WJ, Strobl B, Ghazal P. Metabolic Regulators Nampt and Sirt6 Serially Participate in the Macrophage Interferon Antiviral Cascade. Front Microbiol 2019; 10:355. [PMID: 30886604 PMCID: PMC6409323 DOI: 10.3389/fmicb.2019.00355] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/11/2019] [Indexed: 11/13/2022] Open
Abstract
Molecular determinants underlying interferon (IFN)-macrophage biology can help delineate enzyme systems, pathways and mechanisms for enabling host-directed therapeutic approaches against infection. Notably, while the IFN antiviral response is known to be directly coupled to mevalonate-sterol biosynthesis, mechanistic insight for providing host pathway-therapeutic targets remain incomplete. Here, we show that Nampt and Sirt6 are coordinately regulated upon immune activation of macrophages and contribute to the IFN-sterol antiviral response. In silico analysis of the Nampt and Sirt6 promoter regions identified multiple core immune gene-regulatory transcription factor sites, including Stat1, implicating a molecular link to IFN control. Experimentally, we show using a range of genetically IFN-defective macrophages that the expression of Nampt is stringently regulated by the Jak/Stat-pathway while Sirt6 activation is temporally displaced in a partial IFN-dependent manner. We further show that pharmacological inhibition of Nampt and small interfering RNA (siRNA)-mediated inhibition of Nampt and Sirt6 promotes viral growth of cytomegalovirus in both fibroblasts and macrophages. Our results support the notion of pharmacologically exploiting immune regulated enzyme systems of macrophages for use as an adjuvant-based therapy for augmenting host protective pathway responses to infection.
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Affiliation(s)
- Widad Dantoft
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Kevin A Robertson
- Division of Infection and Pathway Medicine, School of Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - W John Watkins
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Peter Ghazal
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom.,Division of Infection and Pathway Medicine, School of Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
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118
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Venters CC, Oh JM, Di C, So BR, Dreyfuss G. U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene Regulation. Cold Spring Harb Perspect Biol 2019; 11:11/2/a032235. [PMID: 30709878 DOI: 10.1101/cshperspect.a032235] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent observations showed that nascent RNA polymerase II transcripts, pre-mRNAs, and noncoding RNAs are highly susceptible to premature 3'-end cleavage and polyadenylation (PCPA) from numerous intronic cryptic polyadenylation signals (PASs). The importance of this in gene regulation was not previously appreciated as PASs, despite their prevalence, were thought to be active in terminal exons at gene ends. Unexpectedly, antisense oligonucleotide interference with U1 snRNA base-pairing to 5' splice sites, which is necessary for U1 snRNP's (U1) function in splicing, caused widespread PCPA in metazoans. This uncovered U1's PCPA suppression activity, termed telescripting, as crucial for full-length transcription in thousands of vertebrate genes, providing a general role in transcription elongation control. Progressive intron-size expansion in metazoan evolution greatly increased PCPA vulnerability and dependence on U1 telescripting. We describe how these observations unfolded and discuss U1 telescripting's role in shaping the transcriptome.
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Affiliation(s)
- Christopher C Venters
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Jung-Min Oh
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Chao Di
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Byung Ran So
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Gideon Dreyfuss
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
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119
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120
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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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121
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Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1513. [PMID: 30370679 DOI: 10.1002/wrna.1513] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
Cellular RNA levels are the result of a juggling act between RNA transcription, processing, and degradation. By tuning one or more of these parameters, cells can rapidly alter the available pool of transcripts in response to stimuli. While RNA sequencing (RNA-seq) is a vital method to quantify RNA levels genome-wide, it is unable to capture the dynamics of different RNA populations at steady-state or distinguish between different mechanisms that induce changes to the steady-state (i.e., altered rate of transcription vs. degradation). The dynamics of different RNA populations can be studied by targeted incorporation of noncanonical nucleosides. 4-Thiouridine (s4 U) is a commonly used and versatile RNA metabolic label that allows the study of many properties of RNA metabolism from synthesis to degradation. Numerous experimental strategies have been developed that leverage the power of s4 U to label newly transcribed RNA in whole cells, followed by enrichment with activated disulfides or chemistry to induce C mutations at sites of s4 U during sequencing. This review presents existing methods to study RNA population dynamics genome-wide using s4 U metabolic labeling, as well as a discussion of considerations and challenges when designing s4 U metabolic labeling experiments. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Jeremy A Schofield
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
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122
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Baptista T, Devys D. Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity. J Vis Exp 2018. [PMID: 30394386 DOI: 10.3791/57982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Global defects in RNA polymerase II transcription might be overlooked by transcriptomic studies analyzing steady-state RNA. Indeed, the global decrease in mRNA synthesis has been shown to be compensated by a simultaneous decrease in mRNA degradation to restore normal steady-state levels. Hence, the genome-wide quantification of mRNA synthesis, independently from mRNA decay, is the best direct reflection of RNA polymerase II transcriptional activity. Here, we discuss a method using non-perturbing metabolic labeling of nascent RNAs in Saccharomyces cerevisiae (S. cerevisiae). Specifically, the cells are cultured for 6 min with a uracil analog, 4-thiouracil, and the labeled newly transcribed RNAs are purified and quantified to determine the synthesis rates of all individual mRNA. Moreover, using labeled Schizosaccharomyces pombe cells as internal standard allows comparing mRNA synthesis in different S. cerevisiae strains. Using this protocol and fitting the data with a dynamic kinetic model, the corresponding mRNA decay rates can be determined.
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Affiliation(s)
- Tiago Baptista
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg;
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123
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Yamada T, Akimitsu N. Contributions of regulated transcription and mRNA decay to the dynamics of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1508. [PMID: 30276972 DOI: 10.1002/wrna.1508] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022]
Abstract
Organisms have acquired sophisticated regulatory networks that control gene expression in response to cellular perturbations. Understanding of the mechanisms underlying the coordinated changes in gene expression in response to external and internal stimuli is a fundamental issue in biology. Recent advances in high-throughput technologies have enabled the measurement of diverse biological information, including gene expression levels, kinetics of gene expression, and interactions among gene expression regulatory molecules. By coupling these technologies with quantitative modeling, we can now uncover the biological roles and mechanisms of gene regulation at the system level. This review consists of two parts. First, we focus on the methods using uridine analogs that measure synthesis and decay rates of RNAs, which demonstrate how cells dynamically change the regulation of gene expression in response to both internal and external cues. Second, we discuss the underlying mechanisms of these changes in kinetics, including the functions of transcription factors and RNA-binding proteins. Overall, this review will help to clarify a system-level view of gene expression programs in cells. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Regulation of RNA Stability RNA Methods > RNA Analyses in vitro and In Silico.
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Affiliation(s)
- Toshimichi Yamada
- Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
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124
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Chan LY, Mugler CF, Heinrich S, Vallotton P, Weis K. Non-invasive measurement of mRNA decay reveals translation initiation as the major determinant of mRNA stability. eLife 2018; 7:32536. [PMID: 30192227 PMCID: PMC6152797 DOI: 10.7554/elife.32536] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 08/13/2018] [Indexed: 12/15/2022] Open
Abstract
The cytoplasmic abundance of mRNAs is strictly controlled through a balance of production and degradation. Whereas the control of mRNA synthesis through transcription has been well characterized, less is known about the regulation of mRNA turnover, and a consensus model explaining the wide variations in mRNA decay rates remains elusive. Here, we combine non-invasive transcriptome-wide mRNA production and stability measurements with selective and acute perturbations to demonstrate that mRNA degradation is tightly coupled to the regulation of translation, and that a competition between translation initiation and mRNA decay -but not codon optimality or elongation- is the major determinant of mRNA stability in yeast. Our refined measurements also reveal a remarkably dynamic transcriptome with an average mRNA half-life of only 4.8 min - much shorter than previously thought. Furthermore, global mRNA destabilization by inhibition of translation initiation induces a dose-dependent formation of processing bodies in which mRNAs can decay over time.
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Affiliation(s)
- Leon Y Chan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Christopher F Mugler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | | | | | - Karsten Weis
- Department of Biochemistry, ETH Zurich, Zurich, Switzerland
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125
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Duffy EE, Canzio D, Maniatis T, Simon MD. Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleic Acids Res 2018; 46:6996-7005. [PMID: 29986098 PMCID: PMC6101502 DOI: 10.1093/nar/gky556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/04/2018] [Accepted: 06/14/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-thiouridine (s4U) metabolic labeling and solid phase chemistry. This one-step enrichment procedure captures s4U-RNA by using highly efficient methane thiosulfonate (MTS) chemistry in an immobilized format. Like solution-based methods, this solid-phase enrichment can distinguish mature RNAs (mRNA) with differential stability, and can be used to reveal transient RNAs such as enhancer RNAs (eRNAs) and primary microRNAs (pri-miRNAs) from short metabolic labeling. Most importantly, the efficiency of this solid-phase chemistry made possible the first large scale measurements of RNA polymerase II (RNAPII) elongation rates in mouse cortical neurons. Thus, our approach provides the means to study regulation of RNA metabolism in specific tissue contexts as a means to better understand gene expression in vivo.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
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126
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Bertalovitz AC, Badhey MLO, McDonald TV. Synonymous nucleotide modification of the KCNH2 gene affects both mRNA characteristics and translation of the encoded hERG ion channel. J Biol Chem 2018; 293:12120-12136. [PMID: 29907571 PMCID: PMC6078446 DOI: 10.1074/jbc.ra118.001805] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/06/2018] [Indexed: 11/06/2022] Open
Abstract
Synonymous nucleotide variation is increasingly recognized as a factor than can affect protein expression, but the underlying mechanisms are incompletely understood. Here, we investigated whether synonymous changes could affect expression of the potassium voltage-gated channel subfamily H member 2 (KCNH2) gene, encoding the human ether-a-go-go-related gene (hERG) ion channel, which is linked to hereditary cardiac arrhythmia. We examined a previously described synthetic version (hERG-codon modified (CM)) with synonymous substitutions designed to reduce GC content, rare codons, and mRNA secondary structure relative to the native construct (hERG-NT). hERG-CM exhibited lower protein expression than hERG-NT in HEK293T cells. We found that the steady-state abundance of hERG-NT mRNA was greater than hERG-CM because of an enhanced transcription rate and increased mRNA stability for hERG-NT. Translation of hERG-CM was independently reduced, contributing to the overall greater synthesis of hERG-NT channel protein. This was partially offset, however, by a higher aggregation of a newly synthesized hERG-NT channel, resulting in nonfunctional protein. Regional mRNA analyses of chimeras of hERG-NT and hERG-CM revealed that synonymous changes in the 5' segments of the coding region had the greatest influence on hERG synthesis at both the mRNA and protein levels. Taken together, these results indicate that synonymous nucleotide variations within the coding region, particularly in the 5' region of the hERG mRNA, can affect both transcription and translation. These findings support the notion that greater attention should be given to the effects of synonymous genetic variation when analyzing hERG DNA sequences in the study of hereditary cardiac disease.
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Affiliation(s)
- Alexander C Bertalovitz
- Department of Molecular Pharmacology, Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Bronx, New York 10461; Department of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612
| | - Marika L Osterbur Badhey
- Department of Molecular Pharmacology, Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Thomas V McDonald
- Department of Molecular Pharmacology, Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Bronx, New York 10461; Department of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612.
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127
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Freimer JW, Hu TJ, Blelloch R. Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells. eLife 2018; 7:38014. [PMID: 30044225 PMCID: PMC6086665 DOI: 10.7554/elife.38014] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/24/2018] [Indexed: 01/29/2023] Open
Abstract
Translation and mRNA degradation are intimately connected, yet the mechanisms that link them are not fully understood. Here, we studied these mechanisms in embryonic stem cells (ESCs). Transcripts showed a wide range of stabilities, which correlated with their relative translation levels and that did not change during early ESC differentiation. The protein DHH1 links translation to mRNA stability in yeast; however, loss of the mammalian homolog, DDX6, in ESCs did not disrupt the correlation across transcripts. Instead, the loss of DDX6 led to upregulated translation of microRNA targets, without concurrent changes in mRNA stability. The Ddx6 knockout cells were phenotypically and molecularly similar to cells lacking all microRNAs (Dgcr8 knockout ESCs). These data show that the loss of DDX6 can separate the two canonical functions of microRNAs: translational repression and transcript destabilization. Furthermore, these data uncover a central role for translational repression independent of transcript destabilization in defining the downstream consequences of microRNA loss.
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Affiliation(s)
- Jacob W Freimer
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, United States.,Department of Urology, University of California, San Francisco, San Francisco, United States
| | - T J Hu
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, United States.,Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, United States.,Department of Urology, University of California, San Francisco, San Francisco, United States
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128
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Painter HJ, Chung NC, Sebastian A, Albert I, Storey JD, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun 2018; 9:2656. [PMID: 29985403 PMCID: PMC6037754 DOI: 10.1038/s41467-018-04966-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/31/2018] [Indexed: 01/12/2023] Open
Abstract
Genome-wide analysis of transcription in the malaria parasite Plasmodium falciparum has revealed robust variation in steady-state mRNA abundance throughout the 48-h intraerythrocytic developmental cycle (IDC), suggesting that this process is highly dynamic and tightly regulated. Here, we utilize rapid 4-thiouracil (4-TU) incorporation via pyrimidine salvage to specifically label, capture, and quantify newly-synthesized RNA transcripts at every hour throughout the IDC. This high-resolution global analysis of the transcriptome captures the timing and rate of transcription for each newly synthesized mRNA in vivo, revealing active transcription throughout all IDC stages. Using a statistical model to predict the mRNA dynamics contributing to the total mRNA abundance at each timepoint, we find varying degrees of transcription and stabilization for each mRNA corresponding to developmental transitions. Finally, our results provide new insight into co-regulation of mRNAs throughout the IDC through regulatory DNA sequence motifs, thereby expanding our understanding of P. falciparum mRNA dynamics. Transcriptomic analysis often doesn’t differentiate between newly synthesized and stabilized mRNAs. Using rapid 4-thiouracil incorporation, Painter et al. here define genome-wide active transcription throughout Plasmodium blood-stage developmental stages and identify associated regulatory DNA sequence motifs.
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Affiliation(s)
- Heather J Painter
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Neo Christopher Chung
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - John D Storey
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, 08544, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
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129
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Pendleton KE, Park SK, Hunter OV, Bresson SM, Conrad NK. Balance between MAT2A intron detention and splicing is determined cotranscriptionally. RNA (NEW YORK, N.Y.) 2018; 24:778-786. [PMID: 29563249 PMCID: PMC5959247 DOI: 10.1261/rna.064899.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/16/2018] [Indexed: 05/22/2023]
Abstract
Transcriptome analysis of human cells has revealed that intron retention controls the expression of a large number of genes with diverse cellular functions. Detained introns (DI) constitute a subgroup of transcripts with retained introns that are not exported to the cytoplasm but instead remain in the nucleus. Previous studies reported that the splicing of DIs in the CLK1 transcript is post-transcriptionally induced to produce mature mRNA in the absence of new transcription. Thus, CLK1-DI serves as a precursor or "reservoir" for the CLK1 mRNA. However, whether this is a universal mechanism for gene regulation by intron detention remains unknown. The MAT2A gene encodes S-adenosylmethionine (SAM) synthetase and it contains a DI that is regulated in response to intracellular SAM levels. We used three independent assays to assess the precursor-product relationship between MAT2A-DI and MAT2A mRNA. In contrast to CLK1-DI, these data support a model in which the MAT2A-DI transcript is not a precursor to mRNA but is instead a "dead-end" RNA fated for nuclear decay. Additionally, we show that in SAM-deprived conditions the cotranscriptional splicing of MAT2A detained introns increases. We conclude that polyadenylated RNAs with DIs can have at least two distinct fates. They can serve as nuclear reservoirs of pre-mRNAs available for rapid induction by the cell, or they constitute dead-end RNAs that are degraded in the nucleus.
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Affiliation(s)
- Kathryn E Pendleton
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sung-Kyun Park
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Olga V Hunter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Stefan M Bresson
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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130
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Chen YT, Chang IYF, Liu H, Ma CP, Kuo YP, Shih CT, Shih YH, Kang L, Tan BCM. Tumor-associated intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation. J Biol Chem 2018; 293:10158-10171. [PMID: 29769310 DOI: 10.1074/jbc.ra117.001197] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/29/2018] [Indexed: 01/02/2023] Open
Abstract
Processing of the eukaryotic transcriptome is a dynamic regulatory mechanism that confers genetic diversity, and splicing and adenosine to inosine (A-to-I) RNA editing are well-characterized examples of such processing. Growing evidence reveals the cross-talk between the splicing and RNA editing, but there is a paucity of substantial evidence for its mechanistic details and contribution in a physiological context. Here, our findings demonstrate that tumor-associated differential RNA editing, in conjunction with splicing machinery, regulates the expression of variants of HNRPLL, a gene encoding splicing factor. We discovered an HNRPLL transcript variant containing an additional exon 12A (E12A), which is a substrate of ADAR1 and ADAR2. Adenosine deaminases acting on RNA (ADAR) direct deaminase-dependent expression of the E12A transcript, and ADAR-mediated regulation of E12A is largely splicing-based, and does not affect the stability or nucleocytoplasmic distribution of the transcript. Furthermore, ADAR-mediated modification of exon 12A generates an enhancer for the oncogenic splicing factor SRSF1 and consequently promotes the frequency of alternative splicing. Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.
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Affiliation(s)
- Yi-Tung Chen
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | | | - Hsuan Liu
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,Molecular Medicine Research Center.,Department of Biochemistry, College of Medicine, and.,the Division of Colon and Rectal Surgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Chung-Pei Ma
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Yu-Ping Kuo
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Chieh-Tien Shih
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Ying-Hsin Shih
- the Department of Biomedical Sciences, College of Medicine
| | - Lin Kang
- the Edward Via College of Osteopathic Medicine, Blacksburg, Virginia 24060, and
| | - Bertrand Chin-Ming Tan
- From the Graduate Institute of Biomedical Sciences, College of Medicine, .,the Department of Biomedical Sciences, College of Medicine.,Molecular Medicine Research Center.,the Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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131
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Sun W, Gao Q, Schaefke B, Hu Y, Chen W. Pervasive allele-specific regulation on RNA decay in hybrid mice. Life Sci Alliance 2018; 1:e201800052. [PMID: 30456349 PMCID: PMC6238540 DOI: 10.26508/lsa.201800052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 02/05/2023] Open
Abstract
Cellular RNA abundance is determined by both RNA transcription and decay. Therefore, change in RNA abundance, which can drive phenotypic diversity between different species, could arise from genetic variants affecting either process. However, previous studies in the evolution of RNA expression have been largely focused on transcription. Here, to globally investigate the effects of cis-regulatory divergence on RNA decay in mammals for the first time, we quantified allele-specific differences in RNA decay rates (ASD) in an F1 hybrid mouse. Out of 8,815 genes with sufficient data, we identified 621 genes exhibiting significant cis-divergence. Systematic analysis of these genes revealed that the genetic variants affecting microRNA binding and RNA secondary structures contribute to the observed divergences. Finally, we demonstrated that although the divergences in RNA abundance were predominantly determined by allelic differences in RNA transcription, most genes with significant ASD did not exhibit significant difference in RNA abundance. For these genes, the apparently compensatory effect between the allelic differences in RNA transcription and ASD suggests that changes in RNA decay could serve as important means to stabilize RNA abundances during mammalian evolution.
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Affiliation(s)
- Wei Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Laboratory for Functional and Medical Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Qingsong Gao
- Laboratory for Functional and Medical Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Bernhard Schaefke
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Yuhui Hu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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132
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Kofoed RH, Betzer C, Lykke-Andersen S, Molska E, Jensen PH. Investigation of RNA Synthesis Using 5-Bromouridine Labelling and Immunoprecipitation. J Vis Exp 2018. [PMID: 29782024 DOI: 10.3791/57056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
When steady state RNA levels are compared between two conditions, it is not possible to distinguish whether changes are caused by alterations in production or degradation of RNA. This protocol describes a method for measurement of RNA production, using 5-Bromouridine labelling of RNA followed by immunoprecipitation, which enables investigation of RNA synthesized within a short timeframe (e.g., 1 h). The advantage of 5-Bromouridine-labelling and immunoprecipitation over the use of toxic transcriptional inhibitors, such as α-amanitin and actinomycin D, is that there are no or very low effects on cell viability during short-term use. However, because 5-Bromouridine-immunoprecipitation only captures RNA produced within the short labelling time, slowly produced as well as rapidly degraded RNA can be difficult to measure by this method. The 5-Bromouridine-labelled RNA captured by 5-Bromouridine-immunoprecipitation can be analyzed by reverse transcription, quantitative polymerase chain reaction, and next generation sequencing. All types of RNA can be investigated, and the method is not limited to measuring mRNA as is presented in this example.
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Affiliation(s)
- Rikke H Kofoed
- DANDRITE - Danish Research Institute of Translational Neuroscience, Dept. of Biomedicine, Aarhus University;
| | - Cristine Betzer
- DANDRITE - Danish Research Institute of Translational Neuroscience, Dept. of Biomedicine, Aarhus University
| | | | - Ewa Molska
- Dept. of Molecular Biology and Genetics, Aarhus University
| | - Poul H Jensen
- DANDRITE - Danish Research Institute of Translational Neuroscience, Dept. of Biomedicine, Aarhus University;
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133
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Lugowski A, Nicholson B, Rissland OS. DRUID: a pipeline for transcriptome-wide measurements of mRNA stability. RNA (NEW YORK, N.Y.) 2018; 24:623-632. [PMID: 29438994 PMCID: PMC5900561 DOI: 10.1261/rna.062877.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 02/01/2018] [Indexed: 05/21/2023]
Abstract
Control of messenger RNA (mRNA) stability is an important aspect of gene regulation. The gold standard for measuring mRNA stability transcriptome-wide uses metabolic labeling, biochemical isolation of labeled RNA populations, and high-throughput sequencing. However, difficult normalization procedures have inhibited widespread adoption of this approach. Here, we present DRUID (for determination of rates using intron dynamics), a new computational pipeline that is robust, easy to use, and freely available. Our pipeline uses endogenous introns to normalize time course data and yields reproducible half-lives, even with data sets that were otherwise unusable. DRUID can handle data sets from a variety of organisms, spanning yeast to humans, and we even applied it retroactively on published data sets. We anticipate that DRUID will allow broad application of metabolic labeling for studies of transcript stability.
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Affiliation(s)
- Andrew Lugowski
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Beth Nicholson
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Olivia S Rissland
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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134
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Lin D, Hiron TK, O'Callaghan CA. Intragenic transcriptional interference regulates the human immune ligand MICA. EMBO J 2018; 37:embj.201797138. [PMID: 29643123 DOI: 10.15252/embj.201797138] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 12/27/2022] Open
Abstract
Many human genes have tandem promoters driving overlapping transcription, but the value of this distributed promoter configuration is generally unclear. Here we show that MICA, a gene encoding a ligand for the activating immune receptor NKG2D, contains a conserved upstream promoter that expresses a noncoding transcript. Transcription from the upstream promoter represses the downstream standard promoter activity in cis through transcriptional interference. The effect of transcriptional interference depends on the strength of transcription from the upstream promoter and can be described quantitatively by a simple reciprocal repressor function. Transcriptional interference coincides with recruitment at the standard downstream promoter of the FACT histone chaperone complex, which is involved in nucleosomal remodelling during transcription. The mechanism is invoked in the regulation of MICA expression by the physiological inputs interferon-γ and interleukin-4 that act on the upstream promoter. Genome-wide analysis indicates that transcriptional interference between tandem intragenic promoters may constitute a general mechanism with widespread importance in human transcriptional regulation.
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Affiliation(s)
- Da Lin
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas K Hiron
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christopher A O'Callaghan
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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135
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A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms. Sci Rep 2018; 8:5742. [PMID: 29636505 PMCID: PMC5893539 DOI: 10.1038/s41598-018-24039-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/21/2018] [Indexed: 01/06/2023] Open
Abstract
To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured transcription rate (TR), mRNA abundance (RA) and translation activity (TA). This revealed multiple insights. First, the three parameters displayed systematic statistical differences. Sequentially more genes exhibited extreme (low or high) expression values from TR to RA, and then to TA; that is, cellular coordination of multiple transcriptome regulatory mechanisms leads to sequentially enhanced gene expression selectivity as the genetic information flow from the genome to the proteome. Second, contribution of the stabilization-by-translation regulatory mechanism to the cellular coordination process was assessed. The data enabled an estimation of mRNA stability, revealing a moderate but significant positive correlation between mRNA stability and translation activity. Third, the proportion of mRNA occupied by un-translated regions (UTR) exhibited a negative relationship with the level of this correlation, and was thus a major determinant of the mode of regulation of the mRNA. High-UTR-proportion mRNAs tend to defy the stabilization-by-translation regulatory mechanism, staying out of the polysome but remaining stable; mRNAs with little UTRs largely followed this regulation. In summary, we quantitatively delineated the relationship among multiple transcriptome regulation parameters, i.e., cellular coordination of corresponding regulatory mechanisms.
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136
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Herpes Simplex Virus 1 Dramatically Alters Loading and Positioning of RNA Polymerase II on Host Genes Early in Infection. J Virol 2018; 92:JVI.02184-17. [PMID: 29437966 DOI: 10.1128/jvi.02184-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/19/2018] [Indexed: 12/11/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) transcription is mediated by cellular RNA polymerase II (Pol II). Recent studies investigating how Pol II transcription of host genes is altered after HSV-1 are conflicting. Chromatin immunoprecipitation sequencing (ChIP-seq) studies suggest that Pol II is almost completely removed from host genes at 4 h postinfection (hpi), while 4-thiouridine (4SU) labeling experiments show that host transcription termination is extended at 7 hpi, implying that a significant amount of Pol II remains associated with host genes in infected cells. To address this discrepancy, we used precision nuclear run-on analysis (PRO-seq) to determine the location of Pol II to single-base-pair resolution in combination with quantitative reverse transcription-PCR (qRT-PCR) analysis at 3 hpi. HSV-1 decreased Pol II on approximately two-thirds of cellular genes but increased Pol II on others. For more than 85% of genes for which transcriptional termination could be statistically assessed, Pol II was displaced to positions downstream of the normal termination zone, suggesting extensive termination defects. Pol II amounts at the promoter, promoter-proximal pause site, and gene body were also modulated in a gene-specific manner. qRT-PCR of selected RNAs showed that HSV-1-induced extension of the termination zone strongly correlated with decreased RNA and mRNA accumulation. However, HSV-1-induced increases of Pol II occupancy on genes without termination zone extension correlated with increased cytoplasmic mRNA. Functional grouping of genes with increased Pol II occupancy suggested an upregulation of exosome secretion and downregulation of apoptosis, both of which are potentially beneficial to virus production.IMPORTANCE This study provides a map of RNA polymerase II location on host genes after infection with HSV-1 with greater detail than previous ChIP-seq studies and rectifies discrepancies between ChIP-seq data and 4SU labeling experiments with HSV-1. The data show the effects that a given change in RNA Pol II location on host genes has on the abundance of different RNA types, including nuclear, polyadenylated mRNA and cytoplasmic, polyadenylated mRNA. It gives a clearer understanding of how HSV-1 augments host transcription of some genes to provide an environment favorable to HSV-1 replication.
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137
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Hennig T, Michalski M, Rutkowski AJ, Djakovic L, Whisnant AW, Friedl MS, Jha BA, Baptista MAP, L'Hernault A, Erhard F, Dölken L, Friedel CC. HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes. PLoS Pathog 2018; 14:e1006954. [PMID: 29579120 PMCID: PMC5886697 DOI: 10.1371/journal.ppat.1006954] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/05/2018] [Accepted: 02/28/2018] [Indexed: 12/02/2022] Open
Abstract
Lytic herpes simplex virus 1 (HSV-1) infection triggers disruption of transcription termination (DoTT) of most cellular genes, resulting in extensive intergenic transcription. Similarly, cellular stress responses lead to gene-specific transcription downstream of genes (DoG). In this study, we performed a detailed comparison of DoTT/DoG transcription between HSV-1 infection, salt and heat stress in primary human fibroblasts using 4sU-seq and ATAC-seq. Although DoTT at late times of HSV-1 infection was substantially more prominent than DoG transcription in salt and heat stress, poly(A) read-through due to DoTT/DoG transcription and affected genes were significantly correlated between all three conditions, in particular at earlier times of infection. We speculate that HSV-1 either directly usurps a cellular stress response or disrupts the transcription termination machinery in other ways but with similar consequences. In contrast to previous reports, we found that inhibition of Ca2+ signaling by BAPTA-AM did not specifically inhibit DoG transcription but globally impaired transcription. Most importantly, HSV-1-induced DoTT, but not stress-induced DoG transcription, was accompanied by a strong increase in open chromatin downstream of the affected poly(A) sites. In its extent and kinetics, downstream open chromatin essentially matched the poly(A) read-through transcription. We show that this does not cause but rather requires DoTT as well as high levels of transcription into the genomic regions downstream of genes. This raises intriguing new questions regarding the role of histone repositioning in the wake of RNA Polymerase II passage downstream of impaired poly(A) site recognition. Recently, we reported that productive herpes simplex virus 1 (HSV-1) infection leads to disruption of transcription termination (DoTT) of most but not all cellular genes. This results in extensive transcription beyond poly(A) sites and into downstream genes. Subsequently, cellular stress responses were found to trigger transcription downstream of genes (DoG) for >10% of protein-coding genes. Here, we directly compared the two phenomena in HSV-1 infection, salt and heat stress and observed significant overlaps between the affected genes. We speculate that HSV-1 either directly usurps a cellular stress response or disrupts the transcription termination machinery in other ways with similar consequences. In addition, we show that inhibition of calcium signaling does not specifically inhibit stress-induced DoG transcription but globally impairs RNA polymerase I, II and III transcription. Finally, HSV-1-induced DoTT, but not stress-induced DoG transcription, was accompanied by a strong increase in chromatin accessibility downstream of affected poly(A) sites. In its kinetics and extent, this essentially matched poly(A) read-through transcription but does not cause but rather requires DoTT. We hypothesize that this results from impaired histone repositioning when RNA Polymerase II enters downstream intergenic regions of genes affected by DoTT.
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Affiliation(s)
- Thomas Hennig
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | - Andrzej J Rutkowski
- Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lara Djakovic
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Adam W Whisnant
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Marie-Sophie Friedl
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Bhaskar Anand Jha
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Marisa A P Baptista
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Anne L'Hernault
- Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Florian Erhard
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institut für Virologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.,Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
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138
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Davari K, Lichti J, Friedel CC, Glasmacher E. Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation. J Vis Exp 2018. [PMID: 29578509 PMCID: PMC5931490 DOI: 10.3791/56752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Upon activation, cells rapidly change their functional programs and, thereby, their gene expression profile. Massive changes in gene expression occur, for example, during cellular differentiation, morphogenesis, and functional stimulation (such as activation of immune cells), or after exposure to drugs and other factors from the local environment. Depending on the stimulus and cell type, these changes occur rapidly and at any possible level of gene regulation. Displaying all molecular processes of a responding cell to a certain type of stimulus/drug is one of the hardest tasks in molecular biology. Here, we describe a protocol that enables the simultaneous analysis of multiple layers of gene regulation. We compare, in particular, transcription factor binding (Chromatin-immunoprecipitation-sequencing (ChIP-seq)), de novo transcription (4-thiouridine-sequencing (4sU-seq)), mRNA processing, and turnover as well as translation (ribosome profiling). By combining these methods, it is possible to display a detailed and genome-wide course of action. Sequencing newly transcribed RNA is especially recommended when analyzing rapidly adapting or changing systems, since this depicts the transcriptional activity of all genes during the time of 4sU exposure (irrespective of whether they are up- or downregulated). The combinatorial use of total RNA-seq and ribosome profiling additionally allows the calculation of RNA turnover and translation rates. Bioinformatic analysis of high-throughput sequencing results allows for many means for analysis and interpretation of the data. The generated data also enables tracking co-transcriptional and alternative splicing, just to mention a few possible outcomes. The combined approach described here can be applied for different model organisms or cell types, including primary cells. Furthermore, we provide detailed protocols for each method used, including quality controls, and discuss potential problems and pitfalls.
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Affiliation(s)
- Kathrin Davari
- Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München
| | - Johannes Lichti
- Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München
| | | | - Elke Glasmacher
- Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München; Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg;
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139
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Etoposide-induced DNA damage affects multiple cellular pathways in addition to DNA damage response. Oncotarget 2018; 9:24122-24139. [PMID: 29844877 PMCID: PMC5963631 DOI: 10.18632/oncotarget.24517] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/10/2018] [Indexed: 02/06/2023] Open
Abstract
DNA damage response (DDR) coordinates lesion repair and checkpoint activation. DDR is intimately connected with transcription. However, the relationship between DDR and transcription has not been clearly established. We report here RNA-sequencing analyses of MCF7 cells containing double-strand breaks induced by etoposide. While etoposide does not apparently cause global changes in mRNA abundance, it altered some gene expression. At the setting of fold alteration ≥ 2 and false discovery rate (FDR) ≤ 0.001, FDR < 0.05, or p < 0.05, etoposide upregulated 96, 268, or 860 genes and downregulated 41, 133, or 503 genes in MCF7 cells. Among these differentially expressed genes (DEGs), the processes of biogenesis, metabolism, cell motility, signal transduction, and others were affected; the pathways of Ras GTPase activity, RNA binding, cytokine-mediated signaling, kinase regulatory activity, protein binding, and translation were upregulated, and those pathways related to coated vesicle, calmodulin binding, and microtubule-based movement were downregulated. We further identified RABL6, RFTN2, FAS-AS1, and TCEB3CL as new DDR-affected genes in MCF7 and T47D cells. By metabolic labelling using 4-thiouridine, we observed dynamic alterations in the transcription of these genes in etoposide-treated MCF7 and T47D cells. During 0-2 hour etoposide treatment, RABL6 transcription was robustly increased at 0.5 and 1 hour in MCF7 cells and at 2 hours in T47D cells, while FAS-AS1 transcription was dramatically and steadily elevated in both cell lines. Taken together, we demonstrate dynamic alterations in transcription and that these changes affect multiple cellular processes in etoposide-induced DDR.
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140
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Duffy DJ, Krstic A, Schwarzl T, Halasz M, Iljin K, Fey D, Haley B, Whilde J, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W. Wnt signalling is a bi-directional vulnerability of cancer cells. Oncotarget 2018; 7:60310-60331. [PMID: 27531891 PMCID: PMC5312386 DOI: 10.18632/oncotarget.11203] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 07/26/2016] [Indexed: 12/30/2022] Open
Abstract
Wnt signalling is involved in the formation, metastasis and relapse of a wide array of cancers. However, there is ongoing debate as to whether activation or inhibition of the pathway holds the most promise as a therapeutic treatment for cancer, with conflicting evidence from a variety of tumour types. We show that Wnt/β-catenin signalling is a bi-directional vulnerability of neuroblastoma, malignant melanoma and colorectal cancer, with hyper-activation or repression of the pathway both representing a promising therapeutic strategy, even within the same cancer type. Hyper-activation directs cancer cells to undergo apoptosis, even in cells oncogenically driven by β-catenin. Wnt inhibition blocks proliferation of cancer cells and promotes neuroblastoma differentiation. Wnt and retinoic acid co-treatments synergise, representing a promising combination treatment for MYCN-amplified neuroblastoma. Additionally, we report novel cross-talks between MYCN and β-catenin signalling, which repress normal β-catenin mediated transcriptional regulation. A β-catenin target gene signature could predict patient outcome, as could the expression level of its DNA binding partners, the TCF/LEFs. This β-catenin signature provides a tool to identify neuroblastoma patients likely to benefit from Wnt-directed therapy. Taken together, we show that Wnt/β-catenin signalling is a bi-directional vulnerability of a number of cancer entities, and potentially a more broadly conserved feature of malignant cells.
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Affiliation(s)
- David J Duffy
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Current address: The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA
| | - Aleksandar Krstic
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Thomas Schwarzl
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Current address: European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Melinda Halasz
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Bridget Haley
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Jenny Whilde
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | | | - Vidal Fey
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Matthias Fischer
- Department of Paediatric Haematology and Oncology and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Frank Westermann
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kai-Oliver Henrich
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Bannert
- Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Desmond G Higgins
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.,School of Medicine, University College Dublin, Belfield, Dublin, Ireland
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141
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Cleary MD. Uncovering cell type-specific complexities of gene expression and RNA metabolism by TU-tagging and EC-tagging. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e315. [PMID: 29369522 DOI: 10.1002/wdev.315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/07/2017] [Accepted: 12/19/2017] [Indexed: 01/17/2023]
Abstract
Cell type-specific transcription is a key determinant of cell fate and function. An ongoing challenge in biology is to develop robust and stringent biochemical methods to explore gene expression with cell type specificity. This challenge has become even greater as researchers attempt to apply high-throughput RNA analysis methods under in vivo conditions. TU-tagging and EC-tagging are in vivo biosynthetic RNA tagging techniques that allow spatial and temporal specificity in RNA purification. Spatial specificity is achieved through targeted expression of pyrimidine salvage enzymes (uracil phosphoribosyltransferase and cytosine deaminase) and temporal specificity is achieved by controlling exposure to bioorthogonal substrates of these enzymes (4-thiouracil and 5-ethynylcytosine). Tagged RNAs can be purified from total RNA extracted from an animal or tissue and used in transcriptome profiling analyses. In addition to identifying cell type-specific mRNA profiles, these techniques are applicable to noncoding RNAs and can be used to measure RNA transcription and decay. Potential applications of TU-tagging and EC-tagging also include fluorescent RNA imaging and selective definition of RNA-protein interactions. TU-tagging and EC-tagging hold great promise for supporting research at the intersection of RNA biology and developmental biology. This article is categorized under: Technologies > Analysis of the Transcriptome.
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Affiliation(s)
- Michael D Cleary
- Molecular Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California
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142
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Hinze F, Drewe-Boss P, Milek M, Ohler U, Landthaler M, Gotthardt M. Expanding the map of protein-RNA interaction sites via cell fusion followed by PAR-CLIP. RNA Biol 2018; 15:359-368. [PMID: 29028411 DOI: 10.1080/15476286.2017.1384120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
PAR-CLIP (photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation) facilitates the identification and mapping of protein/RNA interactions. So far, it has been limited to select cell-lines as it requires efficient 4SU uptake. To increase transcriptome complexity and thus identify additional RNA-protein interaction sites we fused HEK 293 T-Rex cells (HEK293-Y) that express the RNA binding protein YBX1 with PC12 cells expressing eGFP (PC12-eGFP). The resulting hybrids enable PAR-CLIP on a neuronally expanded transcriptome (Fusion-CLIP) and serve as a proof of principle. The fusion cells express both parental marker genes YBX1 and eGFP and the expanded transcriptome contains human and rat transcripts. PAR-CLIP of fused cells versus the parental HEK293-Y identified 768 novel RNA targets of YBX1. We were able to trace the origin of the majority of the short PAR-CLIP reads as they differentially mapped to the human and rat genome. Furthermore, Fusion-CLIP expanded the CAUC RNA binding motif of YBX1 to UCUUUNNCAUC. The fusion of HEK293-Y and PC12-eGFP cells resulted in cells with a diverse genome expressing human and rat transcripts that enabled the identification of novel YBX1 substrates. The technique allows the expansion of the HEK 293 transcriptome and makes PAR-CLIP available to fusion cells of diverse origin.
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Affiliation(s)
- Florian Hinze
- a Neuromuscular and Cardiovascular Cell Biology, Max-Delbrück-Center for Molecular Medicine , Berlin , Germany.,e DZHK (German Center for Cardiovascular Research), Partner Site Berlin , Berlin , Germany
| | - Philipp Drewe-Boss
- b Computational Regulatory Genomics, Max-Delbrück-Center for Molecular Medicine , Berlin , Germany
| | - Miha Milek
- c RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine , Berlin , Germany
| | - Uwe Ohler
- b Computational Regulatory Genomics, Max-Delbrück-Center for Molecular Medicine , Berlin , Germany
| | - Markus Landthaler
- c RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine , Berlin , Germany.,d IRI Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin , Berlin , Germany
| | - Michael Gotthardt
- a Neuromuscular and Cardiovascular Cell Biology, Max-Delbrück-Center for Molecular Medicine , Berlin , Germany.,e DZHK (German Center for Cardiovascular Research), Partner Site Berlin , Berlin , Germany
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143
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Tiana M, Acosta-Iborra B, Puente-Santamaría L, Hernansanz-Agustin P, Worsley-Hunt R, Masson N, García-Rio F, Mole D, Ratcliffe P, Wasserman WW, Jimenez B, del Peso L. The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia. Nucleic Acids Res 2018; 46:120-133. [PMID: 29059365 PMCID: PMC5758878 DOI: 10.1093/nar/gkx951] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 10/02/2017] [Accepted: 10/06/2017] [Indexed: 01/02/2023] Open
Abstract
Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. To identify genes regulated by hypoxia at the transcriptional level, we pulse-labeled HUVEC cells with 4-thiouridine and sequenced nascent transcripts. Then, we searched genome-wide binding profiles from the ENCODE project for factors that correlated with changes in transcription and identified binding of several components of the Sin3A co-repressor complex, including SIN3A, SAP30 and HDAC1/2, proximal to genes repressed by hypoxia. SIN3A interference revealed that it participates in the downregulation of 75% of the hypoxia-repressed genes in endothelial cells. Unexpectedly, it also blunted the induction of 47% of the upregulated genes, suggesting a role for this corepressor in gene induction. In agreement, ChIP-seq experiments showed that SIN3A preferentially localizes to the promoter region of actively transcribed genes and that SIN3A signal was enriched in hypoxia-repressed genes, prior exposure to the stimulus. Importantly, SINA3 occupancy was not altered by hypoxia in spite of changes in H3K27ac signal. In summary, our results reveal a prominent role for SIN3A in the transcriptional response to hypoxia and suggest a model where modulation of the associated histone deacetylase activity, rather than its recruitment, determines the transcriptional output.
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Affiliation(s)
- Maria Tiana
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Barbara Acosta-Iborra
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
| | - Laura Puente-Santamaría
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
| | - Pablo Hernansanz-Agustin
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
- Servicio Inmunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria del hospital de La Princesa, 28006 Madrid, Spain
| | - Rebecca Worsley-Hunt
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada
| | - Norma Masson
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Francisco García-Rio
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Servicio de Neumología, Hospital Universitario La Paz, Instituto de Investigación Sanitaria del hospital de La Paz, 28029 Madrid, Spain
| | - David Mole
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford OX3 7BN, UK
| | - Peter Ratcliffe
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada
| | - Benilde Jimenez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Luis del Peso
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
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144
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Silencing of the lncRNA Zeb2-NAT facilitates reprogramming of aged fibroblasts and safeguards stem cell pluripotency. Nat Commun 2018; 9:94. [PMID: 29311544 PMCID: PMC5758807 DOI: 10.1038/s41467-017-01921-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/24/2017] [Indexed: 12/17/2022] Open
Abstract
Aging imposes a barrier to somatic cell reprogramming through poorly understood mechanisms. Here, we report that fibroblasts from old mice express higher levels of Zeb2, a transcription factor that activates epithelial-to-mesenchymal transition. Synthesis of Zeb2 protein is controlled by a natural antisense transcript named Zeb2-NAT. We show that transfection of adult fibroblasts with specific LNA Gapmers induces a robust downregulation of Zeb2-NAT transcripts and Zeb2 protein and enhances the reprogramming of old fibroblasts into pluripotent cells. We further demonstrate that Zeb2-NAT expression is precociously activated by differentiation stimuli in embryonic stem (ES) cells. By knocking down Zeb2-NAT, we were able to maintain ES cells challenged with commitment signals in the ground state of pluripotency. In conclusion, our study identifies a long noncoding RNA that is overlapping and antisense to the Zeb2 locus as a target for rejuvenation strategies. The efficiency of somatic cell reprogramming is lowered by ageing. Here the authors show that the transcription factor Zeb2 and its long non-coding RNA Zeb2-NAT are expressed at high levels in older fibroblasts and their inhibition increases reprogramming efficiency.
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145
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c-Myc Represses Transcription of Epstein-Barr Virus Latent Membrane Protein 1 Early after Primary B Cell Infection. J Virol 2018; 92:JVI.01178-17. [PMID: 29118124 DOI: 10.1128/jvi.01178-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022] Open
Abstract
Recent evidence has shown that the Epstein-Barr virus (EBV) oncogene LMP1 is not expressed at high levels early after EBV infection of primary B cells, despite its being essential for the long-term outgrowth of immortalized lymphoblastoid cell lines (LCLs). In this study, we found that expression of LMP1 increased 50-fold between 7 days postinfection and the LCL state. Metabolic labeling of nascent transcribed mRNA indicated that this was primarily a transcription-mediated event. EBNA2, the key viral transcription factor regulating LMP1, and CTCF, an important chromatin insulator, were recruited to the LMP1 locus similarly early and late after infection. However, the activating histone H3K9Ac mark was enriched at the LMP1 promoter in LCLs relative to that in infected B cells early after infection. We found that high c-Myc activity in EBV-infected lymphoma cells as well as overexpression of c-Myc in an LCL model system repressed LMP1 transcription. Finally, we found that chemical inhibition of c-Myc both in LCLs and early after primary B cell infection increased LMP1 expression. These data support a model in which high levels of endogenous c-Myc activity induced early after primary B cell infection directly repress LMP1 transcription.IMPORTANCE EBV is a highly successful pathogen that latently infects more than 90% of adults worldwide and is also causally associated with a number of B cell malignancies. During the latent life cycle, EBV expresses a set of viral oncoproteins and noncoding RNAs with the potential to promote cancer. Critical among these is the viral latent membrane protein LMP1. Prior work suggests that LMP1 is essential for EBV to immortalize B cells, but our recent work indicates that LMP1 is not produced at high levels during the first few weeks after infection. Here we show that transcription of the LMP1 gene can be negatively regulated by a host transcription factor, c-Myc. Ultimately, understanding the regulation of EBV oncogenes will allow us to better treat cancers that rely on these viral products for survival.
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146
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Sun W, Chen W. Metabolic Labeling of Newly Synthesized RNA with 4sU to in Parallel Assess RNA Transcription and Decay. Methods Mol Biol 2018; 1720:25-34. [PMID: 29236249 DOI: 10.1007/978-1-4939-7540-2_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The development of genome-wide RNA profiling technologies greatly facilitates the global analysis of gene expression. However, such technologies alone could not distinguish the contribution to cellular RNA abundance by transcription versus decay. To overcome such limitation, metabolic labeling of newly synthesized RNA with 4-thiouridine (4sU) combined with genome-wide RNA profiling was used to in parallel measure RNA transcription and decay. Here, we describe the detailed protocol for using metabolic labeling with 4sU to separate newly synthesized RNA from the preexisting RNA in mammalian cells.
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Affiliation(s)
- Wei Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen City, Nanshan District, China
- Laboratory for Functional and Medical Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen City, Nanshan District, China.
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen City, Nanshan District, China.
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147
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Marzi MJ, Nicassio F. Uncovering the Stability of Mature miRNAs by 4-Thio-Uridine Metabolic Labeling. Methods Mol Biol 2018; 1823:141-152. [PMID: 29959679 DOI: 10.1007/978-1-4939-8624-8_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are an evolutionary conserved class of short, single-stranded noncoding RNAs (<18-22 nt in length) that act in posttranscriptional regulation of gene expression in higher eukaryotes. The abundance of a miRNA is a key feature in control of its activity and, therefore, a number of mechanisms finely regulate miRNA levels, acting at both transcriptional and posttranscriptional level. Recent evidences, including our research, highlighted the role of miRNA decay as a mechanism controlling the miRNA pool. We describe in this chapter an optimized methodology to determine miRNA degradation rates in mammalian cells. Our approach is based on metabolic pulse labeling with 4-thiouridine (4sU), a uridine analog that is incorporated in nascent RNA and allows thiol-specific biotinylation and selective pull-down of labeled RNA. In particular, given the long average half-life and the complex biogenetic process of miRNAs, we developed a "pulse-chase" protocol where 4sU is removed from the medium after a long labeling period (2-3 h pulse), and labeled RNA is purified at different time points to measure the decay of labeled molecules. By combining the 4sU-based "pulse-chase" approach with high-throughput small RNA sequencing (sRNAseq), it is possible to quantify at genome-wide level miRNA degradation rates.
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Affiliation(s)
- Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
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148
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Impact of Methods on the Measurement of mRNA Turnover. Int J Mol Sci 2017; 18:ijms18122723. [PMID: 29244760 PMCID: PMC5751324 DOI: 10.3390/ijms18122723] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/04/2017] [Accepted: 12/08/2017] [Indexed: 12/25/2022] Open
Abstract
The turnover of the RNA molecules is determined by the rates of transcription and RNA degradation. Several methods have been developed to study RNA turnover since the beginnings of molecular biology. Here we summarize the main methods to measure RNA half-life: transcription inhibition, gene control, and metabolic labelling. These methods were used to detect the cellular activity of the mRNAs degradation machinery, including the exo-ribonuclease Xrn1 and the exosome. On the other hand, the study of the differential stability of mature RNAs has been hampered by the fact that different methods have often yielded inconsistent results. Recent advances in the systematic comparison of different method variants in yeast have permitted the identification of the least invasive methodologies that reflect half-lives the most faithfully, which is expected to open the way for a consistent quantitative analysis of the determinants of mRNA stability.
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149
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Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL. Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods 2017; 14:1198-1204. [PMID: 28945705 PMCID: PMC5712218 DOI: 10.1038/nmeth.4435] [Citation(s) in RCA: 320] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/28/2017] [Indexed: 02/07/2023]
Abstract
Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM seq), an orthogonal-chemistry-based RNA sequencing technology that detects 4-thiouridine (s4U) incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM seq enabled rapid access to RNA-polymerase-II-dependent gene expression dynamics in the context of total RNA. We validated the method in mouse embryonic stem cells by showing that the RNA-polymerase-II-dependent transcriptional output scaled with Oct4/Sox2/Nanog-defined enhancer activity, and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N6-methyladenosine. SLAM seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective and scalable manner.
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Affiliation(s)
- Veronika A. Herzog
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Brian Reichholf
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Pooja Bhat
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Thomas R. Burkard
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Wiebke Wlotzka
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, Medical University of Vienna, University of Vienna, Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
| | - Stefan L. Ameres
- Institute of Molecular Biotechnology (IMBA), Vienna Biocenter Campus (VBC), 1030 Vienna, Austria
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150
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Poling BC, Price AM, Luftig MA, Cullen BR. The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis. Virology 2017; 512:113-123. [PMID: 28950226 DOI: 10.1016/j.virol.2017.09.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/05/2017] [Accepted: 09/18/2017] [Indexed: 10/18/2022]
Abstract
The Epstein-Barr virus (EBV) miR-BHRF1 microRNA (miRNA) cluster has been shown to facilitate B-cell transformation and promote the rapid growth of the resultant lymphoblastoid cell lines (LCLs). However, we find that expression of physiological levels of the miR-BHRF1 miRNAs in LCLs transformed with a miR-BHRF1 null mutant (∆123) fails to increase their growth rate. We demonstrate that the pri-miR-BHRF1-2 and 1-3 stem-loops are present in the 3'UTR of transcripts encoding EBNA-LP and that excision of pre-miR-BHRF1-2 and 1-3 by Drosha destabilizes these mRNAs and reduces expression of the encoded protein. Therefore, mutational inactivation of pri-miR-BHRF1-2 and 1-3 in the ∆123 mutant upregulates the expression of not only EBNA-LP but also EBNA-LP-regulated mRNAs and proteins, including LMP1. We hypothesize that this overexpression causes the reduced transformation capacity of the ∆123 EBV mutant. Thus, in addition to regulating cellular mRNAs in trans, miR-BHRF1-2 and 1-3 also regulate EBNA-LP mRNA expression in cis.
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Affiliation(s)
- Brigid Chiyoko Poling
- Department of Molecular Genetics & Microbiology and Center for Virology, Duke University Medical Center, Durham, NC, USA.
| | - Alexander M Price
- Department of Molecular Genetics & Microbiology and Center for Virology, Duke University Medical Center, Durham, NC, USA.
| | - Micah A Luftig
- Department of Molecular Genetics & Microbiology and Center for Virology, Duke University Medical Center, Durham, NC, USA.
| | - Bryan R Cullen
- Department of Molecular Genetics & Microbiology and Center for Virology, Duke University Medical Center, Durham, NC, USA.
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