101
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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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102
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Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD. TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nat Methods 2018; 15:221-225. [PMID: 29355846 PMCID: PMC5831505 DOI: 10.1038/nmeth.4582] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 12/14/2017] [Indexed: 12/18/2022]
Abstract
RNA sequencing (RNA-seq) offers a snapshot of cellular RNA populations, but not temporal information about the sequenced RNA. Here we report TimeLapse-seq, which uses oxidative-nucleophilic-aromatic substitution to convert 4-thiouridine into cytidine analogs, yielding apparent U-to-C mutations that mark new transcripts upon sequencing. TimeLapse-seq is a single-molecule approach that is adaptable to many applications and reveals RNA dynamics and induced differential expression concealed in traditional RNA-seq.
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Affiliation(s)
- Jeremy A Schofield
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Lea Kiefer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Meaghan C Sullivan
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, USA
- Chemical Biology Institute, Yale University, West Haven, Connecticut, USA
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103
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The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding. Cell Metab 2018; 27:404-418.e7. [PMID: 29358041 PMCID: PMC6996513 DOI: 10.1016/j.cmet.2017.12.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/05/2017] [Accepted: 12/15/2017] [Indexed: 12/21/2022]
Abstract
The mechanisms by which feeding and fasting drive rhythmic gene expression for physiological adaptation to daily rhythm in nutrient availability are not well understood. Here we show that, upon feeding, the RNA-binding protein NONO accumulates within speckle-like structures in liver cell nuclei. Combining RNA-immunoprecipitation and sequencing (RIP-seq), we find that an increased number of RNAs are bound by NONO after feeding. We further show that NONO binds and regulates the rhythmicity of genes involved in nutrient metabolism post-transcriptionally. Finally, we show that disrupted rhythmicity of NONO target genes has profound metabolic impact. Indeed, NONO-deficient mice exhibit impaired glucose tolerance and lower hepatic glycogen and lipids. Accordingly, these mice shift from glucose storage to fat oxidation, and therefore remain lean throughout adulthood. In conclusion, our study demonstrates that NONO post-transcriptionally coordinates circadian mRNA expression of metabolic genes with the feeding/fasting cycle, thereby playing a critical role in energy homeostasis.
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104
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Catarino RR, Stark A. Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. Genes Dev 2018; 32:202-223. [PMID: 29491135 PMCID: PMC5859963 DOI: 10.1101/gad.310367.117] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enhancers are important genomic regulatory elements directing cell type-specific transcription. They assume a key role during development and disease, and their identification and functional characterization have long been the focus of scientific interest. The advent of next-generation sequencing and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based genome editing has revolutionized the means by which we study enhancer biology. In this review, we cover recent developments in the prediction of enhancers based on chromatin characteristics and their identification by functional reporter assays and endogenous DNA perturbations. We discuss that the two latter approaches provide different and complementary insights, especially in assessing enhancer sufficiency and necessity for transcription activation. Furthermore, we discuss recent insights into mechanistic aspects of enhancer function, including findings about cofactor requirements and the role of post-translational histone modifications such as monomethylation of histone H3 Lys4 (H3K4me1). Finally, we survey how these approaches advance our understanding of transcription regulation with respect to promoter specificity and transcriptional bursting and provide an outlook covering open questions and promising developments.
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Affiliation(s)
- Rui R Catarino
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
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105
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Sander J, Schultze JL, Yosef N. ImpulseDE: detection of differentially expressed genes in time series data using impulse models. Bioinformatics 2018; 33:757-759. [PMID: 27797772 DOI: 10.1093/bioinformatics/btw665] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
Summary Perturbations in the environment lead to distinctive gene expression changes within a cell. Observed over time, those variations can be characterized by single impulse-like progression patterns. ImpulseDE is an R package suited to capture these patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes across time points from a single or between two time courses from two experiments. To optimize running time, the code uses clustering and multi-threading. By applying ImpulseDE , we demonstrate its power to represent underlying biology of gene expression in microarray and RNA-Seq data. Availability and Implementation ImpulseDE is available on Bioconductor ( https://bioconductor.org/packages/ImpulseDE/ ). Contact niryosef@berkeley.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jil Sander
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, 53115, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, 53115, Germany.,Single Cell Genomics and Epigenomics Unit at the University of Bonn and the German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Nir Yosef
- Electrical Engineering and Computer Science, Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720-1776, USA
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106
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Gagnon JA, Obbad K, Schier AF. The primary role of zebrafish nanog is in extra-embryonic tissue. Development 2018; 145:dev.147793. [PMID: 29180571 DOI: 10.1242/dev.147793] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 11/07/2017] [Indexed: 12/17/2022]
Abstract
The role of the zebrafish transcription factor Nanog has been controversial. It has been suggested that Nanog is primarily required for the proper formation of the extra-embryonic yolk syncytial layer (YSL) and only indirectly regulates gene expression in embryonic cells. In an alternative scenario, Nanog has been proposed to directly regulate transcription in embryonic cells during zygotic genome activation. To clarify the roles of Nanog, we performed a detailed analysis of zebrafish nanog mutants. Whereas zygotic nanog mutants survive to adulthood, maternal-zygotic (MZnanog) and maternal mutants exhibit developmental arrest at the blastula stage. In the absence of Nanog, YSL formation and epiboly are abnormal, embryonic tissue detaches from the yolk, and the expression of dozens of YSL and embryonic genes is reduced. Epiboly defects can be rescued by generating chimeric embryos of MZnanog embryonic tissue with wild-type vegetal tissue that includes the YSL and yolk cell. Notably, cells lacking Nanog readily respond to Nodal signals and when transplanted into wild-type hosts proliferate and contribute to embryonic tissues and adult organs from all germ layers. These results indicate that zebrafish Nanog is necessary for proper YSL development but is not directly required for embryonic cell differentiation.
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Affiliation(s)
- James A Gagnon
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kamal Obbad
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA .,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.,The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
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107
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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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108
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O'Neil JD, Ammit AJ, Clark AR. MAPK p38 regulates inflammatory gene expression via tristetraprolin: Doing good by stealth. Int J Biochem Cell Biol 2018; 94:6-9. [PMID: 29128684 PMCID: PMC6562201 DOI: 10.1016/j.biocel.2017.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022]
Abstract
Tristetraprolin (TTP) is an RNA-destabilizing protein that exerts profound anti-inflammatory effects by inhibiting the expression of tumour necrosis factor and many other inflammatory mediators. The mitogen-activated protein kinase (MAPK) p38 signaling pathway controls the strength and duration of inflammatory responses by regulating both the expression and function of TTP. The kinase MK2 (MAPK activated kinase 2) is activated by MAPK p38, and in turn phosphorylates TTP at two critical serine residues. One consequence of these phosphorylations is the protection of TTP from proteasome-mediated degradation. Another consequence is the loss of mRNA destabilizing activity. The control of TTP expression and function by the MAPK p38 pathway provides an elegant mechanism for coupling the on and off phases of inflammatory responses, and dictating the precise kinetics of expression of individual inflammatory mediators.
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Affiliation(s)
- J D O'Neil
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, United Kingdom
| | - A J Ammit
- Woolcock Emphysema Centre, Woolcock Institute of Medical Research, University of Sydney, New South Wales, Australia; School of Life Sciences, Faculty of Science, University of Technology, Sydney, New South Wales, Australia
| | - A R Clark
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2WB, United Kingdom.
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109
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Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. eLife 2017; 6:32537. [PMID: 29280736 PMCID: PMC5762160 DOI: 10.7554/elife.32537] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
Production of most eukaryotic mRNAs requires splicing of introns from pre-mRNA. The splicing reaction requires definition of splice sites, which are initially recognized in either intron-spanning (‘intron definition’) or exon-spanning (‘exon definition’) pairs. To understand how exon and intron length and splice site recognition mode impact splicing, we measured splicing rates genome-wide in Drosophila, using metabolic labeling/RNA sequencing and new mathematical models to estimate rates. We found that the modal intron length range of 60–70 nt represents a local maximum of splicing rates, but that much longer exon-defined introns are spliced even faster and more accurately. We observed unexpectedly low variation in splicing rates across introns in the same gene, suggesting the presence of gene-level influences, and we identified multiple gene level variables associated with splicing rate. Together our data suggest that developmental and stress response genes may have preferentially evolved exon definition in order to enhance the rate or accuracy of splicing.
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Affiliation(s)
- Athma A Pai
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Kayla McCue
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Adam Burkholder
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle, United States
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Christopher B Burge
- Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, United States
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110
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Wang C, Wang L, Ding Y, Lu X, Zhang G, Yang J, Zheng H, Wang H, Jiang Y, Xu L. LncRNA Structural Characteristics in Epigenetic Regulation. Int J Mol Sci 2017; 18:ijms18122659. [PMID: 29292750 PMCID: PMC5751261 DOI: 10.3390/ijms18122659] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/24/2017] [Accepted: 11/26/2017] [Indexed: 12/27/2022] Open
Abstract
The rapid development of new generation sequencing technology has deepened the understanding of genomes and functional products. RNA-sequencing studies in mammals show that approximately 85% of the DNA sequences have RNA products, for which the length greater than 200 nucleotides (nt) is called long non-coding RNAs (lncRNA). LncRNAs now have been shown to play important epigenetic regulatory roles in key molecular processes, such as gene expression, genetic imprinting, histone modification, chromatin dynamics, and other activities by forming specific structures and interacting with all kinds of molecules. This paper mainly discusses the correlation between the structure and function of lncRNAs with the recent progress in epigenetic regulation, which is important to the understanding of the mechanism of lncRNAs in physiological and pathological processes.
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Affiliation(s)
- Chenguang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Lianzong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Yu Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Xiaoyan Lu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Guosi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Jiaxin Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Hewei Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Hong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
| | - Liangde Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
- Training Center for Students Innovation and Entrepreneurship Education, Harbin Medical University, Harbin 150081, China.
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111
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Rabani M, Pieper L, Chew GL, Schier AF. A Massively Parallel Reporter Assay of 3' UTR Sequences Identifies In Vivo Rules for mRNA Degradation. Mol Cell 2017; 68:1083-1094.e5. [PMID: 29225039 DOI: 10.1016/j.molcel.2017.11.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022]
Abstract
The stability of mRNAs is regulated by signals within their sequences, but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR-seq, a combination of massively parallel reporter assays and regression models, to survey the dynamics of tens of thousands of 3' UTR sequences during early zebrafish embryogenesis. UTR-seq revealed two temporal degradation programs: a maternally encoded early-onset program and a late-onset program that accelerated degradation after zygotic genome activation. Three signals regulated early-onset rates: stabilizing poly-U and UUAG sequences and destabilizing GC-rich signals. Three signals explained late-onset degradation: miR-430 seeds, AU-rich sequences, and Pumilio recognition sites. Sequence-based regression models translated 3' UTRs into their unique decay patterns and predicted the in vivo effect of sequence signals on mRNA stability. Their application led to the successful design of artificial 3' UTRs that conferred specific mRNA dynamics. UTR-seq provides a general strategy to uncover the rules of RNA cis regulation.
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Affiliation(s)
- Michal Rabani
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lindsey Pieper
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Guo-Liang Chew
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; The Broad Institute, Cambridge, MA 02140, USA.
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112
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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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113
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Cheng J, Maier KC, Avsec Ž, Rus P, Gagneur J. Cis-regulatory elements explain most of the mRNA stability variation across genes in yeast. RNA (NEW YORK, N.Y.) 2017; 23:1648-1659. [PMID: 28802259 PMCID: PMC5648033 DOI: 10.1261/rna.062224.117] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/31/2017] [Indexed: 05/09/2023]
Abstract
The stability of mRNA is one of the major determinants of gene expression. Although a wealth of sequence elements regulating mRNA stability has been described, their quantitative contributions to half-life are unknown. Here, we built a quantitative model for Saccharomyces cerevisiae based on functional mRNA sequence features that explains 59% of the half-life variation between genes and predicts half-life at a median relative error of 30%. The model revealed a new destabilizing 3' UTR motif, ATATTC, which we functionally validated. Codon usage proves to be the major determinant of mRNA stability. Nonetheless, single-nucleotide variations have the largest effect when occurring on 3' UTR motifs or upstream AUGs. Analyzing mRNA half-life data of 34 knockout strains showed that the effect of codon usage not only requires functional decapping and deadenylation, but also the 5'-to-3' exonuclease Xrn1, the nonsense-mediated decay genes, but not no-go decay. Altogether, this study quantitatively delineates the contributions of mRNA sequence features on stability in yeast, reveals their functional dependencies on degradation pathways, and allows accurate prediction of half-life from mRNA sequence.
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Affiliation(s)
- Jun Cheng
- Department of Informatics, Technical University of Munich, 85748 Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Žiga Avsec
- Department of Informatics, Technical University of Munich, 85748 Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Petra Rus
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, 85748 Garching, Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 München, Germany
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114
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Dukler N, Booth GT, Huang YF, Tippens N, Waters CT, Danko CG, Lis JT, Siepel A. Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome Res 2017; 27:1816-1829. [PMID: 29025894 PMCID: PMC5668940 DOI: 10.1101/gr.222935.117] [Citation(s) in RCA: 19] [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: 03/16/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022]
Abstract
Most studies of responses to transcriptional stimuli measure changes in cellular mRNA concentrations. By sequencing nascent RNA instead, it is possible to detect changes in transcription in minutes rather than hours and thereby distinguish primary from secondary responses to regulatory signals. Here, we describe the use of PRO-seq to characterize the immediate transcriptional response in human cells to celastrol, a compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory, and obesity-controlling effects. Celastrol is known to elicit a cellular stress response resembling the response to heat shock, but the transcriptional basis of this response remains unclear. Our analysis of PRO-seq data for K562 cells reveals dramatic transcriptional effects soon after celastrol treatment at a broad collection of both coding and noncoding transcription units. This transcriptional response occurred in two major waves, one within 10 min, and a second 40-60 min after treatment. Transcriptional activity was generally repressed by celastrol, but one distinct group of genes, enriched for roles in the heat shock response, displayed strong activation. Using a regression approach, we identified key transcription factors that appear to drive these transcriptional responses, including members of the E2F and RFX families. We also found sequence-based evidence that particular transcription factors drive the activation of enhancers. We observed increased polymerase pausing at both genes and enhancers, suggesting that pause release may be widely inhibited during the celastrol response. Our study demonstrates that a careful analysis of PRO-seq time-course data can disentangle key aspects of a complex transcriptional response, and it provides new insights into the activity of a powerful pharmacological agent.
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Affiliation(s)
- Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Nathaniel Tippens
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10065, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Colin T Waters
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14850, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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115
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Tudek A, Schmid M, Jensen TH. Nuclear Decay Factors Crack Up mRNA. Mol Cell 2017; 65:775-776. [PMID: 28257696 DOI: 10.1016/j.molcel.2017.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this issue of Molecular Cell, Bresson et al. (2017) show that the nuclear RNA decay factors Nab3 and Mtr4 reshape the coding transcriptome during glucose starvation in budding yeast, placing nuclear mRNA metabolism as an important contributor of gene expression regulation.
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Affiliation(s)
- Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark.
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116
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Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Aguet F, Gelfand E, Ardlie K, Weitz DA, Rozenblatt-Rosen O, Zhang F, Regev A. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods 2017; 14:955-958. [PMID: 28846088 PMCID: PMC5623139 DOI: 10.1038/nmeth.4407] [Citation(s) in RCA: 636] [Impact Index Per Article: 90.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/13/2017] [Indexed: 11/20/2022]
Abstract
Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.
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Affiliation(s)
- Naomi Habib
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
- Broad Institute of MIT and Harvard, Cambridge MA
- McGovern Institute, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge
MA
| | | | - Anindita Basu
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Tyler Burks
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
| | - Karthik Shekhar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
| | - Sourav R. Choudhury
- Broad Institute of MIT and Harvard, Cambridge MA
- McGovern Institute, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge
MA
| | | | | | | | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
- Department of Physics, Harvard University, Cambridge, MA
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge MA
- McGovern Institute, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge
MA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
- Howard Hughes Medical Institute, Department of Biology, Koch Institute of Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge MA
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117
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Li HB, Tong J, Zhu S, Batista PJ, Duffy EE, Zhao J, Bailis W, Cao G, Kroehling L, Chen Y, Wang G, Broughton JP, Chen YG, Kluger Y, Simon MD, Chang HY, Yin Z, Flavell RA. m 6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature 2017; 548:338-342. [PMID: 28792938 PMCID: PMC5729908 DOI: 10.1038/nature23450] [Citation(s) in RCA: 643] [Impact Index Per Article: 91.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 06/30/2017] [Indexed: 12/28/2022]
Abstract
N6 -methyladenosine (m6A) is the most common and abundant messenger RNA modification, modulated by ‘writers’, ‘erasers’ and ‘readers’ of this mark 1,2. In vitro data have shown that m6A influences all fundamental aspects of mRNA metabolism, mainly mRNA stability, to determine stem cell fates 3,4. However, its in vivo physiological function in mammals and adult mammalian cells is still unknown. Here we show that deletion of m6A ‘writer’ protein METTL3 in mouse T cells disrupts T cell homeostasis and differentiation. In a lymphopenic mouse adoptive transfer model, naive Mettl3 deficient T cells failed to undergo homeostatic expansion and remarkably remained in the naïve state up through 12 weeks, thereby preventing colitis. Consistent with these observations, the mRNAs of SOCS family genes encoding STAT- signaling inhibitory proteins, Socs1, Socs3 and Cish, were marked by m6A, exhibited slower mRNA decay and increased mRNAs and protein expression levels in Mettl3 deficient naïve T cells. This increased SOCS family activity consequently inhibited IL-7 mediated STAT5 activation and T cell homeostatic proliferation and differentiation. We also found that m6A plays important roles for inducible degradation of Socs mRNAs in response to IL-7 signaling in order to reprogram Naïve T cells for proliferation and differentiation. Our study elucidates for the first time the in vivo biological role of m6A modification in T cell mediated pathogenesis and reveals a novel mechanism of T cell homeostasis and signal-dependent induction of mRNA degradation.
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Affiliation(s)
- Hua-Bing Li
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Jiyu Tong
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Shu Zhu
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Pedro J Batista
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Erin E Duffy
- Department of Molecular Biophysics &Biochemistry, Yale University, New Haven, Connecticut 06511, USA.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Jun Zhao
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Will Bailis
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Guangchao Cao
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Lina Kroehling
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Yuanyuan Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Institute of Surgical Research, Daping Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Geng Wang
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - James P Broughton
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Y Grace Chen
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Matthew D Simon
- Department of Molecular Biophysics &Biochemistry, Yale University, New Haven, Connecticut 06511, USA.,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Howard Y Chang
- Center for Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
| | - Zhinan Yin
- The First Affiliated Hospital, Biomedical Translational Research Institute and Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou 510632, China
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA
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118
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Chen T, van Steensel B. Comprehensive analysis of nucleocytoplasmic dynamics of mRNA in Drosophila cells. PLoS Genet 2017; 13:e1006929. [PMID: 28771467 PMCID: PMC5557608 DOI: 10.1371/journal.pgen.1006929] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 08/15/2017] [Accepted: 07/17/2017] [Indexed: 01/14/2023] Open
Abstract
Eukaryotic mRNAs undergo a cycle of transcription, nuclear export, and degradation. A major challenge is to obtain a global, quantitative view of these processes. Here we measured the genome-wide nucleocytoplasmic dynamics of mRNA in Drosophila cells by metabolic labeling in combination with cellular fractionation. By mathematical modeling of these data we determined rates of transcription, export and cytoplasmic decay for 5420 genes. We characterized these kinetic rates and investigated links with mRNA features, RNA-binding proteins (RBPs) and chromatin states. We found prominent correlations between mRNA decay rate and transcript size, while nuclear export rates are linked to the size of the 3'UTR. Transcription, export and decay rates are each associated with distinct spectra of RBPs. Specific classes of genes, such as those encoding cytoplasmic ribosomal proteins, exhibit characteristic combinations of rate constants, suggesting modular control. Binding of splicing factors is associated with faster rates of export, and our data suggest coordinated regulation of nuclear export of specific functional classes of genes. Finally, correlations between rate constants suggest global coordination between the three processes. Our approach provides insights into the genome-wide nucleocytoplasmic kinetics of mRNA and should be generally applicable to other cell systems. All mRNAs start from production in the nucleus, undergo exportation through nuclear pores and finally are degraded in the cytoplasm. A comprehensive characterization of the kinetic rates of all mRNAs is an important prerequisite for a global understanding of the regulation of the transcriptome and the cell. By conducting a time-series experiment and building a mathematical model, we trace the dynamics of mRNAs from the nucleus to the cytoplasm and determine the rates at each kinetic step at transcriptome-wide level. This information allows us to associate mRNA kinetic rates with a wealth of biological features and made some intriguing discoveries. We show mRNA decay is positively linked to transcript length while mRNA export is negatively linked to the length of the 3' UTR. We show binding of splicing factors is associated with faster rates of mRNA export. We provide evidence for global coordination between nuclear export an decay of mRNA. We show genes sharing specific functions tend to have similar nucleoplasmic kinetics, in which ribosomal proteins possessing special kinetic features exclusively stand out. Altogether, our integrated approach to quantitatively determine the rates of kinetic steps on a gene-by-gene basis provides a blueprint to obtain the global understanding of RNA regulation.
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Affiliation(s)
- Tao Chen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail:
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119
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Bohlen CJ, Bennett FC, Tucker AF, Collins HY, Mulinyawe SB, Barres BA. Diverse Requirements for Microglial Survival, Specification, and Function Revealed by Defined-Medium Cultures. Neuron 2017; 94:759-773.e8. [PMID: 28521131 DOI: 10.1016/j.neuron.2017.04.043] [Citation(s) in RCA: 413] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 03/31/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022]
Abstract
Microglia, the resident macrophages of the CNS, engage in various CNS-specific functions that are critical for development and health. To better study microglia and the properties that distinguish them from other tissue macrophage populations, we have optimized serum-free culture conditions to permit robust survival of highly ramified adult microglia under defined-medium conditions. We find that astrocyte-derived factors prevent microglial death ex vivo and that this activity results from three primary components, CSF-1/IL-34, TGF-β2, and cholesterol. Using microglial cultures that have never been exposed to serum, we demonstrate a dramatic and lasting change in phagocytic capacity after serum exposure. Finally, we find that mature microglia rapidly lose signature gene expression after isolation, and that this loss can be reversed by engrafting cells back into an intact CNS environment. These data indicate that the specialized gene expression profile of mature microglia requires continuous instructive signaling from the intact CNS.
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Affiliation(s)
- Christopher J Bohlen
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - F Chris Bennett
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew F Tucker
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannah Y Collins
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sara B Mulinyawe
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ben A Barres
- Department of Neurobiology, Stanford University School of Medicine, Stanford, CA 94305, USA
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120
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The control of inflammation via the phosphorylation and dephosphorylation of tristetraprolin: a tale of two phosphatases. Biochem Soc Trans 2017; 44:1321-1337. [PMID: 27911715 PMCID: PMC5095909 DOI: 10.1042/bst20160166] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 12/14/2022]
Abstract
Twenty years ago, the first description of a tristetraprolin (TTP) knockout mouse highlighted the fundamental role of TTP in the restraint of inflammation. Since then, work from several groups has generated a detailed picture of the expression and function of TTP. It is a sequence-specific RNA-binding protein that orchestrates the deadenylation and degradation of several mRNAs encoding inflammatory mediators. It is very extensively post-translationally modified, with more than 30 phosphorylations that are supported by at least two independent lines of evidence. The phosphorylation of two particular residues, serines 52 and 178 of mouse TTP (serines 60 and 186 of the human orthologue), has profound effects on the expression, function and localisation of TTP. Here, we discuss the control of TTP biology via its phosphorylation and dephosphorylation, with a particular focus on recent advances and on questions that remain unanswered.
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121
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Uvarovskii A, Dieterich C. pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments. Bioinformatics 2017; 33:3305-3307. [DOI: 10.1093/bioinformatics/btx368] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alexey Uvarovskii
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg, Germany
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122
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Wagner A, Regev A, Yosef N. Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol 2017; 34:1145-1160. [PMID: 27824854 DOI: 10.1038/nbt.3711] [Citation(s) in RCA: 375] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Single-cell genomics has now made it possible to create a comprehensive atlas of human cells. At the same time, it has reopened definitions of a cell's identity and of the ways in which identity is regulated by the cell's molecular circuitry. Emerging computational analysis methods, especially in single-cell RNA sequencing (scRNA-seq), have already begun to reveal, in a data-driven way, the diverse simultaneous facets of a cell's identity, from discrete cell types to continuous dynamic transitions and spatial locations. These developments will eventually allow a cell to be represented as a superposition of 'basis vectors', each determining a different (but possibly dependent) aspect of cellular organization and function. However, computational methods must also overcome considerable challenges-from handling technical noise and data scale to forming new abstractions of biology. As the scale of single-cell experiments continues to increase, new computational approaches will be essential for constructing and characterizing a reference map of cell identities.
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Affiliation(s)
- Allon Wagner
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA
| | - Aviv Regev
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, Massachusetts, USA
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123
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Andrianne M, Assabban A, La C, Mogilenko D, Salle DS, Fleury S, Doumont G, Van Simaeys G, Nedospasov SA, Blackshear PJ, Dombrowicz D, Goriely S, Van Maele L. Tristetraprolin expression by keratinocytes controls local and systemic inflammation. JCI Insight 2017; 2:92979. [PMID: 28570274 DOI: 10.1172/jci.insight.92979] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/03/2017] [Indexed: 12/22/2022] Open
Abstract
Tristetraprolin (TTP, encoded by the Zfp36 gene) regulates the mRNA stability of several important cytokines. Due to the critical role of this RNA-binding protein in the control of inflammation, TTP deficiency leads to the spontaneous development of a complex inflammatory syndrome. So far, this phenotype has been largely attributed to dysregulated production of TNF and IL‑23 by myeloid cells, such as macrophages or DCs. Here, we generated mice with conditional deletion of TTP in keratinocytes (Zfp36fl/flK14-Cre mice, referred to herein as Zfp36ΔEP mice). Unlike DC-restricted (CD11c-Cre) or myeloid cell-restricted (LysM-Cre) TTP ablation, these mice developed exacerbated inflammation in the imiquimod-induced psoriasis model. Furthermore, Zfp36ΔEP mice progressively developed a spontaneous pathology with systemic inflammation, psoriatic-like skin lesions, and dactylitis. Finally, we provide evidence that keratinocyte-derived TNF production drives these different pathological features. In summary, these findings expand current views on the initiation of psoriasis and related arthritis by revealing the keratinocyte-intrinsic role of TTP.
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Affiliation(s)
- Mathieu Andrianne
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO) and Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Assiya Assabban
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO) and Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Caroline La
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO) and Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Denis Mogilenko
- Université de Lille, Inserm, Institut Pasteur de Lille, CHU Lille, Lille, France
| | | | - Sébastien Fleury
- Université de Lille, Inserm, Institut Pasteur de Lille, CHU Lille, Lille, France
| | - Gilles Doumont
- Centre of Microscopy and Molecular Imaging (CMMI), ULB, Charleroi (Gosselies), Belgium
| | - Gaëtan Van Simaeys
- Centre of Microscopy and Molecular Imaging (CMMI), ULB, Charleroi (Gosselies), Belgium.,Department of Nuclear Medicine, Hôpital Erasme, ULB, Brussels, Belgium
| | - Sergei A Nedospasov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences and Lomonosov Moscow State University, Moscow, Russia
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA.,Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
| | - David Dombrowicz
- Université de Lille, Inserm, Institut Pasteur de Lille, CHU Lille, Lille, France
| | - Stanislas Goriely
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO) and Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Laurye Van Maele
- Walloon Excellence in Lifesciences and Biotechnology (WELBIO) and Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
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124
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Uhlitz F, Sieber A, Wyler E, Fritsche-Guenther R, Meisig J, Landthaler M, Klinger B, Blüthgen N. An immediate-late gene expression module decodes ERK signal duration. Mol Syst Biol 2017; 13:928. [PMID: 28468958 PMCID: PMC5448165 DOI: 10.15252/msb.20177554] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RAF‐MEK‐ERK signalling pathway controls fundamental, often opposing cellular processes such as proliferation and apoptosis. Signal duration has been identified to play a decisive role in these cell fate decisions. However, it remains unclear how the different early and late responding gene expression modules can discriminate short and long signals. We obtained both protein phosphorylation and gene expression time course data from HEK293 cells carrying an inducible construct of the proto‐oncogene RAF. By mathematical modelling, we identified a new gene expression module of immediate–late genes (ILGs) distinct in gene expression dynamics and function. We find that mRNA longevity enables these ILGs to respond late and thus translate ERK signal duration into response amplitude. Despite their late response, their GC‐rich promoter structure suggested and metabolic labelling with 4SU confirmed that transcription of ILGs is induced immediately. A comparative analysis shows that the principle of duration decoding is conserved in PC12 cells and MCF7 cells, two paradigm cell systems for ERK signal duration. Altogether, our findings suggest that ILGs function as a gene expression module to decode ERK signal duration.
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Affiliation(s)
- Florian Uhlitz
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anja Sieber
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Raphaela Fritsche-Guenther
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Johannes Meisig
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Bertram Klinger
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nils Blüthgen
- IRI Life Sciences & Institute for Theoretical Biology, Humboldt Universität Berlin, Berlin, Germany .,Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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125
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Michel M, Demel C, Zacher B, Schwalb B, Krebs S, Blum H, Gagneur J, Cramer P. TT-seq captures enhancer landscapes immediately after T-cell stimulation. Mol Syst Biol 2017; 13:920. [PMID: 28270558 PMCID: PMC5371733 DOI: 10.15252/msb.20167507] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To monitor transcriptional regulation in human cells, rapid changes in enhancer and promoter activity must be captured with high sensitivity and temporal resolution. Here, we show that the recently established protocol TT-seq ("transient transcriptome sequencing") can monitor rapid changes in transcription from enhancers and promoters during the immediate response of T cells to ionomycin and phorbol 12-myristate 13-acetate (PMA). TT-seq maps eRNAs and mRNAs every 5 min after T-cell stimulation with high sensitivity and identifies many new primary response genes. TT-seq reveals that the synthesis of 1,601 eRNAs and 650 mRNAs changes significantly within only 15 min after stimulation, when standard RNA-seq does not detect differentially expressed genes. Transcription of enhancers that are primed for activation by nucleosome depletion can occur immediately and simultaneously with transcription of target gene promoters. Our results indicate that enhancer transcription is a good proxy for enhancer regulatory activity in target gene activation, and establish TT-seq as a tool for monitoring the dynamics of enhancer landscapes and transcription programs during cellular responses and differentiation.
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Affiliation(s)
- Margaux Michel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carina Demel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Benedikt Zacher
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Krebs
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julien Gagneur
- Department of Informatics, Technische Universität München, Garching, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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126
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m 6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature 2017; 542:475-478. [PMID: 28192787 PMCID: PMC5323276 DOI: 10.1038/nature21355] [Citation(s) in RCA: 404] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 12/22/2016] [Indexed: 12/23/2022]
Abstract
The maternal-to-zygotic transition (MZT) is one of the most profound and orchestrated processes during the early life of embryos, yet factors that shape the temporal pattern of vertebrate MZT are largely unknown. Here we show that over one-third of zebrafish maternal messenger RNAs (mRNAs) can be N6-methyladenosine (m6A) modified, and the clearance of these maternal mRNAs is facilitated by an m6A-binding protein, Ythdf2. Removal of Ythdf2 in zebrafish embryos decelerates the decay of m6A-modified maternal mRNAs and impedes zygotic genome activation. These embryos fail to initiate timely MZT, undergo cell cycle pause, and remain developmentally delayed throughout larval life. Our study reveals m6A-dependent RNA decay as a previously unidentified maternally driven mechanism that regulates maternal mRNA clearance during zebrafish MZT, highlighting the critical role of m6A mRNA methylation in transcriptome switching and animal development.
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127
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Stewart-Ornstein J, Lahav G. Integrating genomic information and signaling dynamics for efficient cancer therapy. CURRENT OPINION IN SYSTEMS BIOLOGY 2017; 1:38-43. [PMID: 28944311 PMCID: PMC5608455 DOI: 10.1016/j.coisb.2016.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The field of cancer systems biology has made great strides in understanding oncogenic pathway signaling and enumerating mutations involved in oncogenesis. However, application of these datasets to patient stratification, and to the design of personalized therapy, is in its infancy. We review BRAF and BRCA mutant targeted therapy, where patient stratification has had critical, albeit mixed success. We contrast the work on genomic targeted therapy with orthogonal studies on the dynamics of signaling pathways for designing optimal treatment schedules. We suggest that an integrated approach, combining genomic data and the dynamics of signaling pathways, is required for developing pathway specific computational models and for systematic deployment of targeted combination regimes. The field of cancer systems biology has made great strides in understanding oncogenic pathway signaling and enumerating mutations involved in oncogenesis. However, application of the existing approaches and datasets to patient stratification, and to the design of personalized therapy, is in its infancy. Here we discuss an integrated approach combining genomic data and the dynamics of signaling pathway to develop pathway specific computational models and the systematic deployment of targeted combination regimes. We review recent studies and existing datasets in the field of cancer systems biology and highlight potentially fruitful synergies between the different strands of this discipline.
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Affiliation(s)
| | - Galit Lahav
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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128
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Zacher B, Michel M, Schwalb B, Cramer P, Tresch A, Gagneur J. Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN. PLoS One 2017; 12:e0169249. [PMID: 28056037 PMCID: PMC5215863 DOI: 10.1371/journal.pone.0169249] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/14/2016] [Indexed: 12/22/2022] Open
Abstract
Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today’s largest compendium of chromatin assays. Extensive benchmarks demonstrate that GenoSTAN generally identifies promoters and enhancers with significantly higher accuracy than previous methods. Moreover, GenoSTAN-derived promoters and enhancers showed significantly higher enrichment of complex trait-associated genetic variants than current annotations. Altogether, GenoSTAN provides an easy-to-use tool to define promoters and enhancers in any system, and our annotation of human transcriptional cis-regulatory elements constitutes a rich resource for future research in biology and medicine.
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Affiliation(s)
- Benedikt Zacher
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität Munich, Germany
- * E-mail: (BZ); (AT); (JG)
| | - Margaux Michel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Achim Tresch
- Department of Biology, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail: (BZ); (AT); (JG)
| | - Julien Gagneur
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität Munich, Germany
- * E-mail: (BZ); (AT); (JG)
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129
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Heyn P, Neugebauer KM. Purification of Zygotically Transcribed RNA through Metabolic Labeling of Early Zebrafish Embryos. Methods Mol Biol 2017; 1605:121-131. [PMID: 28456961 DOI: 10.1007/978-1-4939-6988-3_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Early embryonic development in all known metazoans is characterized by a transcriptionally silent phase, during which development is under control of maternally loaded protein and RNA. The zygotic genome becomes transcriptionally active after a series of rapid reductive cleavage divisions. In this chapter, we present a method to metabolically label, purify, and analyze newly transcribed RNAs in early zebrafish embryos. We previously used this method, which is adaptable to other embryos and systems, to determine the onset of zygotic transcription activation and identify the first zygotic transcripts.
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Affiliation(s)
- Patricia Heyn
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Karla M Neugebauer
- Molecular Biophysics & Biochemistry, Yale University, 333 Cedar St, New Haven, CT, 06520, USA.
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130
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Kumagai Y, Vandenbon A, Teraguchi S, Akira S, Suzuki Y. Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs. BMC Genomics 2016; 17:1032. [PMID: 28155712 PMCID: PMC5259865 DOI: 10.1186/s12864-016-3325-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Immune cells have to change their gene expression patterns dynamically in response to external stimuli such as lipopolysaccharide (LPS). The gene expression is regulated at multiple steps in eukaryotic cells, in which control of RNA levels at both the transcriptional level and the post-transcriptional level plays important role. Impairment of the control leads to aberrant immune responses such as excessive or impaired production of cytokines. However, genome-wide studies focusing on the post-transcriptional control were relatively rare until recently. Moreover, several RNA cis elements and RNA-binding proteins have been found to be involved in the process, but our general understanding remains poor, partly because identification of regulatory RNA motifs is very challenging in spite of its importance. We took advantage of genome-wide measurement of RNA degradation in combination with estimation of degradation kinetics by qualitative approach, and performed de novo prediction of RNA sequence and structure motifs. METHODS To classify genes by their RNA degradation kinetics, we first measured RNA degradation time course in mouse dendritic cells after LPS stimulation and the time courses were clustered to estimate degradation kinetics and to find patterns in the kinetics. Then genes were clustered by their similarity in degradation kinetics patterns. The 3' UTR sequences of a cluster was subjected to de novo sequence or structure motif prediction. RESULTS The quick degradation kinetics was found to be strongly associated with lower gene expression level, immediate regulation (both induction and repression) of gene expression level, and longer 3' UTR length. De novo sequence motif prediction found AU-rich element-like and TTP-binding sequence-like motifs which are enriched in quickly degrading genes. De novo structure motif prediction found a known functional motif, namely stem-loop structure containing sequence bound by RNA-binding protein Roquin and Regnase-1, as well as unknown motifs. CONCLUSIONS The current study indicated that degradation kinetics patterns lead to classification different from that by gene expression and the differential classification facilitates identification of functional motifs. Identification of novel motif candidates implied post-transcriptional controls different from that by known pairs of RNA-binding protein and RNA motif.
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Affiliation(s)
- Yutaro Kumagai
- Quantitative Immunology Research Unit, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka, 565-0871, Japan.
| | - Alexis Vandenbon
- Immuno-Genomics Research Unit, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Shunsuke Teraguchi
- Quantitative Immunology Research Unit, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka, 565-0871, Japan.
| | - Shizuo Akira
- Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
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131
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Alpert T, Herzel L, Neugebauer KM. Perfect timing: splicing and transcription rates in living cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27873472 DOI: 10.1002/wrna.1401] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 12/27/2022]
Abstract
An important step toward understanding gene regulation is the elucidation of the time necessary for the completion of individual steps. Measurement of reaction rates can reveal potential nodes for regulation. For example, measurements of in vivo transcription elongation rates reveal regulation by DNA sequence, gene architecture, and chromatin. Pre-mRNA splicing is regulated by transcription elongation rates and vice versa, yet the rates of RNA processing reactions remain largely elusive. Since the 1980s, numerous model systems and approaches have been used to determine the precise timing of splicing in vivo. Because splicing can be co-transcriptional, the position of Pol II when splicing is detected has been used as a proxy for time by some investigators. In addition to these 'distance-based' measurements, 'time-based' measurements have been possible through live cell imaging, metabolic labeling of RNA, and gene induction. Yet splicing rates can be convolved by the time it takes for transcription, spliceosome assembly and spliceosome disassembly. The variety of assays and systems used has, perhaps not surprisingly, led to reports of widely differing splicing rates in vivo. Recently, single molecule RNA-seq has indicated that splicing occurs more quickly than previously deduced. Here we comprehensively review these findings and discuss evidence that splicing and transcription rates are closely coordinated, facilitating the efficiency of gene expression. On the other hand, introduction of splicing delays through as yet unknown mechanisms provide opportunity for regulation. More work is needed to understand how cells optimize the rates of gene expression for a range of biological conditions. WIREs RNA 2017, 8:e1401. doi: 10.1002/wrna.1401 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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132
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Integrative classification of human coding and noncoding genes through RNA metabolism profiles. Nat Struct Mol Biol 2016; 24:86-96. [PMID: 27870833 DOI: 10.1038/nsmb.3325] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/18/2016] [Indexed: 12/26/2022]
Abstract
Pervasive transcription of the human genome results in a heterogeneous mix of coding RNAs and long noncoding RNAs (lncRNAs). Only a small fraction of lncRNAs have demonstrated regulatory functions, thus making functional lncRNAs difficult to distinguish from nonfunctional transcriptional byproducts. This difficulty has resulted in numerous competing human lncRNA classifications that are complicated by a steady increase in the number of annotated lncRNAs. To address these challenges, we quantitatively examined transcription, splicing, degradation, localization and translation for coding and noncoding human genes. We observed that annotated lncRNAs had lower synthesis and higher degradation rates than mRNAs and discovered mechanistic differences explaining slower lncRNA splicing. We grouped genes into classes with similar RNA metabolism profiles, containing both mRNAs and lncRNAs to varying extents. These classes exhibited distinct RNA metabolism, different evolutionary patterns and differential sensitivity to cellular RNA-regulatory pathways. Our classification provides an alternative to genomic context-driven annotations of lncRNAs.
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133
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Abstract
We give an overview of experimental and computational methods to estimate RNA metabolism rates genome-wide. We then advocate a local definition of RNA metabolism rate at the level of individual phosphodiester bonds. Rates of formation and disappearance of individual bonds are unambiguously defined, in contrast to rates of complete transcripts. We show that over previous approaches, the recently developed transient transcriptome sequencing (TT-seq) protocol allows for estimation of metabolism rates of individual bonds with least positional bias.
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Affiliation(s)
- Leonhard Wachutka
- a Department of Informatics , Technical University of Munich, Garching bei München , Germany
| | - Julien Gagneur
- a Department of Informatics , Technical University of Munich, Garching bei München , Germany
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134
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Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res 2016; 26:1397-1410. [PMID: 27470110 PMCID: PMC5052061 DOI: 10.1101/gr.207902.116] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/27/2016] [Indexed: 12/27/2022]
Abstract
RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3′-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1000 cDNA libraries, each from an individual pancreatic islet cell. ESAT identified nine distinct cell types, three distinct β-cell types, and a complex interplay between hormone secretion and vascularization. ESAT, then, offers a much-needed and generally applicable computational pipeline for either bulk or single-cell RNA end-sequencing.
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Affiliation(s)
- Alan Derr
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Chaoxing Yang
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Rapolas Zilionis
- Department of System Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Institute of Biotechnology, Vilnius University, LT 02241 Vilnius, Lithuania
| | - Alexey Sergushichev
- Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia; Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
| | - David M Blodgett
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Sambra Redick
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Rita Bortell
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - David M Harlan
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dale L Greiner
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Allon Klein
- Department of System Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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135
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Gao Y, Wang J, Zheng Y, Zhang J, Chen S, Zhao F. Comprehensive identification of internal structure and alternative splicing events in circular RNAs. Nat Commun 2016; 7:12060. [PMID: 27350239 PMCID: PMC4931246 DOI: 10.1038/ncomms12060] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/20/2016] [Indexed: 02/06/2023] Open
Abstract
Although previous studies demonstrated circular RNAs (circRNAs) does not exclusively comprise mRNA exons, no study has extensively explored their internal structure. By combining an algorithm with long-read sequencing data and experimental validation, we, for the first time, comprehensively investigate internal components of circRNAs in 10 human cell lines and 62 fruit fly samples, and reveal the prevalence of alternative splicing (AS) events within circRNAs. Significantly, a large proportion of circRNA AS exons can hardly be detected in mRNAs and are enriched with binding sites of distinct splicing factors from those enriched in mRNA exons. We find that AS events in circRNAs have a preference towards nucleus localization and exhibit tissue- and developmental stage-specific expression patterns. This study suggests an independent regulation on the biogenesis or decay of AS events in circRNAs and the identified circular AS isoforms provide targets for future studies on circRNA formation and function.
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Affiliation(s)
- Yuan Gao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zheng
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyang Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Chen
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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136
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Schwalb B, Michel M, Zacher B, Frühauf K, Demel C, Tresch A, Gagneur J, Cramer P. TT-seq maps the human transient transcriptome. Science 2016; 352:1225-8. [DOI: 10.1126/science.aad9841] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/06/2016] [Indexed: 12/14/2022]
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137
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Sedlyarov V, Fallmann J, Ebner F, Huemer J, Sneezum L, Ivin M, Kreiner K, Tanzer A, Vogl C, Hofacker I, Kovarik P. Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution. Mol Syst Biol 2016; 12:868. [PMID: 27178967 PMCID: PMC4988506 DOI: 10.15252/msb.20156628] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Precise regulation of mRNA decay is fundamental for robust yet not exaggerated inflammatory responses to pathogens. However, a global model integrating regulation and functional consequences of inflammation‐associated mRNA decay remains to be established. Using time‐resolved high‐resolution RNA binding analysis of the mRNA‐destabilizing protein tristetraprolin (TTP), an inflammation‐limiting factor, we qualitatively and quantitatively characterize TTP binding positions in the transcriptome of immunostimulated macrophages. We identify pervasive destabilizing and non‐destabilizing TTP binding, including a robust intronic binding, showing that TTP binding is not sufficient for mRNA destabilization. A low degree of flanking RNA structuredness distinguishes occupied from silent binding motifs. By functionally relating TTP binding sites to mRNA stability and levels, we identify a TTP‐controlled switch for the transition from inflammatory into the resolution phase of the macrophage immune response. Mapping of binding positions of the mRNA‐stabilizing protein HuR reveals little target and functional overlap with TTP, implying a limited co‐regulation of inflammatory mRNA decay by these proteins. Our study establishes a functionally annotated and navigable transcriptome‐wide atlas (http://ttp-atlas.univie.ac.at) of cis‐acting elements controlling mRNA decay in inflammation.
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Affiliation(s)
- Vitaly Sedlyarov
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Jörg Fallmann
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Florian Ebner
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Jakob Huemer
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Lucy Sneezum
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Masa Ivin
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Kristina Kreiner
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Andrea Tanzer
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ivo Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark
| | - Pavel Kovarik
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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138
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New insights into the multidimensional concept of macrophage ontogeny, activation and function. Nat Immunol 2016; 17:34-40. [PMID: 26681460 DOI: 10.1038/ni.3324] [Citation(s) in RCA: 539] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/15/2015] [Indexed: 11/08/2022]
Abstract
Macrophages have protective roles in immunity to pathogens, tissue development, homeostasis and repair following damage. Maladaptive immunity and inflammation provoke changes in macrophage function that are causative of disease. Despite a historical wealth of knowledge about macrophages, recent advances have revealed unknown aspects of their development and function. Following development, macrophages are activated by diverse signals. Such tissue microenvironmental signals together with epigenetic changes influence macrophage development, activation and functional diversity, with consequences in disease and homeostasis. We discuss here how recent discoveries in these areas have led to a multidimensional concept of macrophage ontogeny, activation and function. In connection with this, we also discuss how technical advances facilitate a new roadmap for the isolation and analysis of macrophages at high resolution.
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139
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Rutenberg-Schoenberg M, Sexton AN, Simon MD. The Properties of Long Noncoding RNAs That Regulate Chromatin. Annu Rev Genomics Hum Genet 2016; 17:69-94. [PMID: 27147088 DOI: 10.1146/annurev-genom-090314-024939] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Beyond coding for proteins, RNA molecules have well-established functions in the posttranscriptional regulation of gene expression. Less clear are the upstream roles of RNA in regulating transcription and chromatin-based processes in the nucleus. RNA is transcribed in the nucleus, so it is logical that RNA could play diverse and broad roles that would impact human physiology. Indeed, this idea is supported by well-established examples of noncoding RNAs that affect chromatin structure and function. There has been dramatic growth in studies focused on the nuclear roles of long noncoding RNAs (lncRNAs). Although little is known about the biochemical mechanisms of these lncRNAs, there is a developing consensus regarding the challenges of defining lncRNA function and mechanism. In this review, we examine the definition, discovery, functions, and mechanisms of lncRNAs. We emphasize areas where challenges remain and where consensus among laboratories has underscored the exciting ways in which human lncRNAs may affect chromatin biology.
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Affiliation(s)
- Michael Rutenberg-Schoenberg
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Alec N Sexton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
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140
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Oesterreich FC, Herzel L, Straube K, Hujer K, Howard J, Neugebauer KM. Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II. Cell 2016; 165:372-381. [PMID: 27020755 PMCID: PMC4826323 DOI: 10.1016/j.cell.2016.02.045] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/04/2016] [Accepted: 02/21/2016] [Indexed: 01/01/2023]
Abstract
Protein-coding genes in eukaryotes are transcribed by RNA polymerase II (Pol II) and introns are removed from pre-mRNA by the spliceosome. Understanding the time lag between Pol II progression and splicing could provide mechanistic insights into the regulation of gene expression. Here, we present two single-molecule nascent RNA sequencing methods that directly determine the progress of splicing catalysis as a function of Pol II position. Endogenous genes were analyzed on a global scale in budding yeast. We show that splicing is 50% complete when Pol II is only 45 nt downstream of introns, with the first spliced products observed as introns emerge from Pol II. Perturbations that slow the rate of spliceosome assembly or speed up the rate of transcription caused splicing delays, showing that regulation of both processes determines in vivo splicing profiles. We propose that matched rates streamline the gene expression pathway, while allowing regulation through kinetic competition.
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Affiliation(s)
| | - Lydia Herzel
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Korinna Straube
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Katja Hujer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Jonathon Howard
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M. Neugebauer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
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141
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Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc 2016; 11:499-524. [PMID: 26890679 PMCID: PMC4941947 DOI: 10.1038/nprot.2016.015] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A protocol is described for sequencing the transcriptome of a cell nucleus. Nuclei are isolated from specimens and sorted by FACS, cDNA libraries are constructed and RNA-seq is performed, followed by data analysis. Some steps follow published methods (Smart-seq2 for cDNA synthesis and Nextera XT barcoded library preparation) and are not described in detail here. Previous single-cell approaches for RNA-seq from tissues include cell dissociation using protease treatment at 30 °C, which is known to alter the transcriptome. We isolate nuclei at 4 °C from tissue homogenates, which cause minimal damage. Nuclear transcriptomes can be obtained from postmortem human brain tissue stored at -80 °C, making brain archives accessible for RNA-seq from individual neurons. The method also allows investigation of biological features unique to nuclei, such as enrichment of certain transcripts and precursors of some noncoding RNAs. By following this procedure, it takes about 4 d to construct cDNA libraries that are ready for sequencing.
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Affiliation(s)
| | | | - Mark Novotny
- J. Craig Venter Institute, La Jolla, California, USA
| | | | - Benjamin Lacar
- Salk Institute for Biological Studies, La Jolla, California, USA
| | - Kunal Bhutani
- J. Craig Venter Institute, La Jolla, California, USA
| | - Sara B Linker
- Salk Institute for Biological Studies, La Jolla, California, USA
| | - Son Pham
- Salk Institute for Biological Studies, La Jolla, California, USA
| | - Jennifer A Erwin
- Salk Institute for Biological Studies, La Jolla, California, USA
| | | | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Martin Kelder
- Salk Institute for Biological Studies, La Jolla, California, USA
| | | | | | - Francisco Diez Fuertes
- J. Craig Venter Institute, La Jolla, California, USA
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Jun Lee
- LeGene Biosciences, San Diego, California, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Fred H Gage
- Salk Institute for Biological Studies, La Jolla, California, USA
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142
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Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S, Cramer P, Gagneur J. Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol 2016; 12:857. [PMID: 26883383 PMCID: PMC4770384 DOI: 10.15252/msb.20156526] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
To decrypt the regulatory code of the genome, sequence elements must be defined that determine the kinetics of RNA metabolism and thus gene expression. Here, we attempt such decryption in an eukaryotic model organism, the fission yeast S. pombe. We first derive an improved genome annotation that redefines borders of 36% of expressed mRNAs and adds 487 non‐coding RNAs (ncRNAs). We then combine RNA labeling in vivo with mathematical modeling to obtain rates of RNA synthesis and degradation for 5,484 expressed RNAs and splicing rates for 4,958 introns. We identify functional sequence elements in DNA and RNA that control RNA metabolic rates and quantify the contributions of individual nucleotides to RNA synthesis, splicing, and degradation. Our approach reveals distinct kinetics of mRNA and ncRNA metabolism, separates antisense regulation by transcription interference from RNA interference, and provides a general tool for studying the regulatory code of genomes.
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Affiliation(s)
- Philipp Eser
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Leonhard Wachutka
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kerstin C Maier
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carina Demel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Mariana Boroni
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Srignanakshi Iyer
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julien Gagneur
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany
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143
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Welsby I, Goriely S. Regulation of Interleukin-23 Expression in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 941:167-189. [DOI: 10.1007/978-94-024-0921-5_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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144
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Davidovich C, Cech TR. The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2. RNA (NEW YORK, N.Y.) 2015; 21:2007-22. [PMID: 26574518 PMCID: PMC4647455 DOI: 10.1261/rna.053918.115] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Polycomb repressive complex-2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer. Among chromatin modifying factors shown to be recruited and regulated by long noncoding RNAs (lncRNAs), PRC2 is one of the most studied. Mammalian PRC2 binds thousands of RNAs in vivo, and it is becoming a model system for the recruitment of chromatin modifying factors by RNA. Yet, well-defined PRC2-binding motifs within target RNAs have been elusive. From the protein side, PRC2 RNA-binding subunits contain no known RNA-binding domains, complicating functional studies. Here we provide a critical review of existing models for the recruitment of PRC2 to chromatin by RNAs. This discussion may also serve researchers who are studying the recruitment of other chromatin modifiers by lncRNAs.
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Affiliation(s)
- Chen Davidovich
- BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Thomas R Cech
- BioFrontiers Institute and Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309, USA
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145
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Blackinton JG, Keene JD. Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation. Nucleic Acids Res 2015; 44:426-36. [PMID: 26490963 PMCID: PMC4705648 DOI: 10.1093/nar/gkv1066] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/05/2015] [Indexed: 01/30/2023] Open
Abstract
Global mRNA abundance depends on the balance of synthesis and decay of a population of mRNAs. To account for this balance during activation of T cells, we used metabolic labeling to quantify the contributions of RNA transcription and decay over a 4 h time course during activation of leukemia-derived Jurkat T cells. While prior studies suggested more than half of the changes in mRNA abundance were due to RNA stability, we found a smaller but more interesting population of mRNAs changed stability. These mRNAs clustered into functionally related subpopulations that included replicative histones, ribosomal biogenesis and cell motility functions. We then applied a novel analysis based on integrating global protein-RNA binding with concurrent changes in RNA stability at specific time points following activation. This analysis demonstrated robust stabilization of mRNAs by the HuR RNA-binding protein 4 h after activation. Our unexpected findings demonstrate that the temporal regulation of mRNA stability coordinates vital cellular pathways and is in part controlled by the HuR RNA binding protein in Jurkat T cells following activation.
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Affiliation(s)
- Jeff G Blackinton
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jack D Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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146
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Barquist L, Vogel J. Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies. Annu Rev Genet 2015; 49:367-94. [PMID: 26473381 DOI: 10.1146/annurev-genet-112414-054804] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decade, bacterial small RNAs (sRNAs) have gone from a biological curiosity to being recognized as a major class of regulatory molecules. High-throughput methods for sampling the transcriptional output of bacterial cells demonstrate that sRNAs are universal features of bacterial transcriptomes, are plentiful, and appear to vary extensively over evolutionary time. With ever more bacteria coming under study, the question becomes how can we accelerate the discovery and functional characterization of sRNAs in diverse organisms. New technologies built on high-throughput sequencing are emerging that can rapidly provide global insight into the numbers and functions of sRNAs in bacteria of interest, providing information that can shape hypotheses and guide research. In this review, we describe recent developments in transcriptomics (RNA-seq) and functional genomics that we expect to help us develop an integrated, systems-level view of sRNA biology in bacteria.
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Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
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147
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Study of the activated macrophage transcriptome. Exp Mol Pathol 2015; 99:575-80. [PMID: 26439118 DOI: 10.1016/j.yexmp.2015.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 11/22/2022]
Abstract
Transcriptome analysis is a powerful modern tool to study possible alterations of gene expression associated with human diseases. It turns out to be especially promising for evaluation of gene expression changes in immunopathology, as immune cells have flexible gene expression patterns that can be switched in response to infection, inflammatory stimuli and exposure to various cytokines. In particular, macrophage polarization towards pro-inflammatory (M1) and anti-inflammatory (M2) phenotypes can be successfully studied using the modern transcriptome analysis approaches. The two mostly used techniques for transcriptome analysis are microarray and next generation sequencing. In this review we will provide an overview of known gene expression changes associated with immunopathology and discuss the advantage and limitations of different methods of transcriptome analysis.
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148
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Yartseva V, Giraldez AJ. The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming. Curr Top Dev Biol 2015; 113:191-232. [PMID: 26358874 DOI: 10.1016/bs.ctdb.2015.07.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular transitions occur at all stages of organismal life from conception to adult regeneration. Changing cellular state involves three main features: activating gene expression necessary to install the new cellular state, modifying the chromatin status to stabilize the new gene expression program, and removing existing gene products to clear out the previous cellular program. The maternal-to-zygotic transition (MZT) is one of the most profound changes in the life of an organism. It involves gene expression remodeling at all levels, including the active clearance of the maternal oocyte program to adopt the embryonic totipotency. In this chapter, we provide an overview of molecular mechanisms driving maternal mRNA clearance during the MZT, describe the developmental consequences of losing components of this gene regulation, and illustrate how remodeling of gene expression during the MZT is common to other cellular transitions with parallels to cellular reprogramming.
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Affiliation(s)
- Valeria Yartseva
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA.
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149
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Garcin G, Guiraud I, Lacroix M, Genthon C, Rialle S, Joujoux JM, Meunier L, Lavabre-Bertrand T, Stoebner PE, Le Gallic L. AMPK/HuR-Driven IL-20 Post-Transcriptional Regulation in Psoriatic Skin. J Invest Dermatol 2015; 135:2732-2741. [PMID: 26176762 DOI: 10.1038/jid.2015.282] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/18/2015] [Accepted: 06/23/2015] [Indexed: 11/09/2022]
Abstract
IL-20 is involved in the development of skin psoriasis. The molecular mechanisms underlying IL-20 overexpression in psoriatic epidermis remain to be elucidated. We showed that IL-20 was primarily upregulated in psoriatic skin at the post-transcriptional level. The RNA-binding protein HuR relocalized to the cytoplasm of keratinocytes (KCs) of psoriatic patients, suggesting that it stabilizes numerous transcripts, as observed in the human KC cell lines used to assess IL-20 mRNA. We characterized epidermal HuR RNA targets in psoriatic skin using ribonucleoprotein immunoprecipitation analyzed via high-throughput sequencing. Numerous transcripts that are upregulated in psoriasis were targeted by HuR, supporting the participation of HuR in pathogenic processes such as morphological changes, innate and adaptive immune responses, and metabolic inflammatory responses. Finally, we identified the metabolic sensor AMP-activated protein kinase (AMPK) as being responsible for HuR cytoplasmic relocalization because its activity was severely impaired in human psoriatic epidermis, and in vivo drug-mediated AMPK inhibition in mouse epidermis promoted HuR cytoplasmic localization, IL-20 overproduction, acanthosis, and hyperkeratosis. These results provide insights into the molecular links between metabolism and post-transcriptional networks during chronic inflammation.
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Affiliation(s)
- Geneviève Garcin
- Dynamique des Interactions Membranaires Normales et Pathologiques (DIMNP), CNRS UMR 5235, Université de Montpellier, Montpellier, France
| | - Isabelle Guiraud
- Laboratoire d'Histologie-Embryologie-Cytogénétique, Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR 5247, Faculté de Médecine Montpellier-Nîmes, Université de Montpellier, Nîmes, France
| | - Matthieu Lacroix
- Institut de Recherche en Cancérologie de Montpellier (IRCM), Institut régional du Cancer Montpellier (ICM), INSERM U896, Université de Montpellier, Montpellier, France
| | - Clémence Genthon
- Montpellier Genomix (MGX), Institut de Génomique Fonctionnelle (IGF), CNRS INSERM UMS3426, Université de Montpellier, Montpellier, France
| | - Stéphanie Rialle
- Montpellier Genomix (MGX), Institut de Génomique Fonctionnelle (IGF), CNRS INSERM UMS3426, Université de Montpellier, Montpellier, France
| | - Jean-Marie Joujoux
- Service d'Anatomopathologie, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
| | - Laurent Meunier
- Service de Dermatologie, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
| | - Thierry Lavabre-Bertrand
- Laboratoire d'Histologie-Embryologie-Cytogénétique, Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR 5247, Faculté de Médecine Montpellier-Nîmes, Université de Montpellier, Nîmes, France
| | | | - Lionel Le Gallic
- Laboratoire d'Histologie-Embryologie-Cytogénétique, Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR 5247, Faculté de Médecine Montpellier-Nîmes, Université de Montpellier, Nîmes, France.
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150
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Webb JT, Behar M. Topology, dynamics, and heterogeneity in immune signaling. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:285-300. [DOI: 10.1002/wsbm.1306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/14/2015] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Affiliation(s)
- J. Taylor Webb
- Department of Biomedical Engineering; The University of Texas at Austin; Austin TX USA
| | - Marcelo Behar
- Department of Biomedical Engineering; The University of Texas at Austin; Austin TX USA
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