1
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Ietswaart R, Smalec BM, Xu A, Choquet K, McShane E, Jowhar ZM, Guegler CK, Baxter-Koenigs AR, West ER, Fu BXH, Gilbert L, Floor SN, Churchman LS. Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle. Mol Cell 2024; 84:2765-2784.e16. [PMID: 38964322 PMCID: PMC11315470 DOI: 10.1016/j.molcel.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/15/2024] [Accepted: 06/11/2024] [Indexed: 07/06/2024]
Abstract
Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.
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Affiliation(s)
- Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Brendan M Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ziad Mohamoud Jowhar
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chantal K Guegler
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Autum R Baxter-Koenigs
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Luke Gilbert
- Arc Institute, Palo Alto, CA 94305, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Urology, University of California, San Francisco, San Francisco, CA 94518, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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2
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Bedi K, Magnuson B, Narayanan IV, McShane A, Ashaka M, Paulsen MT, Wilson TE, Ljungman M. Isoform and pathway-specific regulation of post-transcriptional RNA processing in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598705. [PMID: 38915566 PMCID: PMC11195214 DOI: 10.1101/2024.06.12.598705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Steady-state levels of RNA transcripts are controlled by their rates of synthesis and degradation. Here we used nascent RNA Bru-seq and BruChase-seq to profile RNA dynamics across 16 human cell lines as part of ENCODE4 Deeply Profiled Cell Lines collection. We show that RNA turnover dynamics differ widely between transcripts of different genes and between different classes of RNA. Gene set enrichment analysis (GSEA) revealed that transcripts encoding proteins belonging to the same pathway often show similar turnover dynamics. Furthermore, transcript isoforms show distinct dynamics suggesting that RNA turnover is important in regulating mRNA isoform choice. Finally, splicing across newly made transcripts appears to be cooperative with either all or none type splicing. These data sets generated as part of ENCODE4 illustrate the intricate and coordinated regulation of RNA dynamics in controlling gene expression to allow for the precise coordination of cellular functions.
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Affiliation(s)
- Karan Bedi
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Magnuson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ariel McShane
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mario Ashaka
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Maizels RJ, Snell DM, Briscoe J. Reconstructing developmental trajectories using latent dynamical systems and time-resolved transcriptomics. Cell Syst 2024; 15:411-424.e9. [PMID: 38754365 DOI: 10.1016/j.cels.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024]
Abstract
The snapshot nature of single-cell transcriptomics presents a challenge for studying the dynamics of cell fate decisions. Metabolic labeling and splicing can provide temporal information at single-cell level, but current methods have limitations. Here, we present a framework that overcomes these limitations: experimentally, we developed sci-FATE2, an optimized method for metabolic labeling with increased data quality, which we used to profile 45,000 embryonic stem (ES) cells differentiating into neural tube identities. Computationally, we developed a two-stage framework for dynamical modeling: VelvetVAE, a variational autoencoder (VAE) for velocity inference that outperforms all other tools tested, and VelvetSDE, a neural stochastic differential equation (nSDE) framework for simulating trajectory distributions. These recapitulate underlying dataset distributions and capture features such as decision boundaries between alternative fates and fate-specific gene expression. These methods recast single-cell analyses from descriptions of observed data to models of the dynamics that generated them, providing a framework for investigating developmental fate decisions.
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Affiliation(s)
- Rory J Maizels
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; University College, London, UK
| | - Daniel M Snell
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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4
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Uriu K, Hernandez-Sanchez JP, Kojima S. Impacts of the feedback loop between sense-antisense RNAs in regulating circadian rhythms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591560. [PMID: 38746188 PMCID: PMC11092440 DOI: 10.1101/2024.04.28.591560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Antisense transcripts are a unique group of non-coding RNAs that are transcribed from the opposite strand of a sense coding gene in an antisense orientation. Even though they do not encode a protein, these transcripts play a regulatory role in a variety of biological processes, including circadian rhythms. We and others found an antisense transcript, Per2AS , that is transcribed from the strand opposite the sense transcript Period2 ( Per2 ) and exhibits a rhythmic and antiphasic expression pattern compared to Per2 in mouse. By assuming that Per2AS and Per2 mutually repress each other, our previous mathematical model predicted that Per2AS regulates the robustness and the amplitude of circadian rhythms. In this study, we revised our previous model and developed a new mathematical model that mechanistically described the mutually repressive relationship between Per2 and Per2AS via transcriptional interference. We found that the simulation results are largely consistent with experimental observations including the counterintuitive ones that could not be fully explained by our previous model. These results indicate that our revised model serves as a foundation to build more detailed models in the future to better understand the impact of Per2AS-Per2 interaction in the mammalian circadian clock. Our mechanistic description of Per2AS-Per2 interaction can also be extended to other mathematical models that involve sense-antisense RNA pairs that mutually repress each other.
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5
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Unruh BA, Weidemann DE, Miao L, Kojima S. Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts. Proc Natl Acad Sci U S A 2024; 121:e2314690121. [PMID: 38315868 PMCID: PMC10873638 DOI: 10.1073/pnas.2314690121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and posttranscriptional mechanisms are considered important to drive rhythmic RNA expression; however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24-h RNA rhythms, while rhythmic degradation is more important for 12-h RNA rhythms. These rhythms were predominantly regulated by Bmal1 and/or the core clock mechanism, and the interplay between rhythmic synthesis and degradation has a significant impact in shaping rhythmic RNA expression patterns. Interestingly, core clock RNAs are regulated by multiple rhythmic processes and have the highest amplitude of synthesis and degradation, presumably critical to sustain robust rhythmicity of cell-autonomous circadian rhythms. Our study yields invaluable insights into the temporal dynamics of both 24- and 12-h RNA rhythms in mouse fibroblasts.
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Affiliation(s)
- Benjamin A. Unruh
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Douglas E. Weidemann
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Lin Miao
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA24061
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6
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Zhou F, Tan P, Liu S, Chang L, Yang J, Sun M, Guo Y, Si Y, Wang D, Yu J, Ma Y. Subcellular RNA distribution and its change during human embryonic stem cell differentiation. Stem Cell Reports 2024; 19:126-140. [PMID: 38134924 PMCID: PMC10828685 DOI: 10.1016/j.stemcr.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/24/2023] Open
Abstract
The spatial localization of RNA within cells is closely related to its function and also involved in cell fate determination. However, the atlas of RNA distribution within cells and dynamic changes during the developmental process are largely unknown. In this study, five subcellular components, including cytoplasmic extract, membrane extract, soluble nuclear extract, chromatin-bound nuclear extract, and cytoskeletal extract, were isolated and the rules of subcellular RNA distribution in human embryonic stem cells (hESCs) and its change during hESC differentiation are summarized for the first time. The overall distribution patterns of coding and non-coding RNAs are revealed. Interestingly, some developmental genes are found to be transcribed but confined to the chromatin in undifferentiated hESC. Unexpectedly, alternative splicing and polyadenylation endow spatial heterogeneity among different isoforms of the same gene. Finally, the dynamic pattern of RNA distribution during hESC differentiation is characterized, which provides new clues for a comprehensive understanding hESC pluripotency and differentiation.
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Affiliation(s)
- Fanqi Zhou
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Puwen Tan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Siqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Le Chang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jiabin Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Mengyao Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yuehong Guo
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yanmin Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China; State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China; Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China.
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7
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Unruh BA, Weidemann DE, Kojima S. Coordination of rhythmic RNA synthesis and degradation orchestrates 24-hour and 12-hour RNA expression patterns in mouse fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550672. [PMID: 37546997 PMCID: PMC10402069 DOI: 10.1101/2023.07.26.550672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and post-transcriptional mechanisms are considered important to drive rhythmic RNA expression, however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24 hr RNA rhythms, while rhythmic degradation is more important for 12 hr RNA rhythms. These rhythms were predominantly regulated by Bmal1 and/or the core clock mechanism, and interplay between rhythmic synthesis and degradation has a significant impact in shaping rhythmic RNA expression patterns. Interestingly, core clock RNAs are regulated by multiple rhythmic processes and have the highest amplitude of synthesis and degradation, presumably critical to sustain robust rhythmicity of cell-autonomous circadian rhythms. Our study yields invaluable insights into the temporal dynamics of both 24 hr and 12 hr RNA rhythms in mouse fibroblasts.
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Affiliation(s)
- Benjamin A Unruh
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Douglas E Weidemann
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA USA
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8
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Sarkar S, Rammohan J. Nearly maximal information gain due to time integration in central dogma reactions. iScience 2023; 26:106767. [PMID: 37235057 PMCID: PMC10206154 DOI: 10.1016/j.isci.2023.106767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/21/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Living cells process information about their environment through the central dogma processes of transcription and translation, which drive the cellular response to stimuli. Here, we study the transfer of information from environmental input to the transcript and protein expression levels. Evaluation of both experimental and analogous simulation data reveals that transcription and translation are not two simple information channels connected in series. Instead, we demonstrate that the central dogma reactions often create a time-integrating information channel, where the translation channel receives and integrates multiple outputs from the transcription channel. This information channel model of the central dogma provides new information-theoretic selection criteria for the central dogma rate constants. Using the data for four well-studied species we show that their central dogma rate constants achieve information gain because of time integration while also keeping the loss because of stochasticity in translation relatively low (<0.5 bits).
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Affiliation(s)
- Swarnavo Sarkar
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jayan Rammohan
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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9
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Agarwal V, Kelley DR. The genetic and biochemical determinants of mRNA degradation rates in mammals. Genome Biol 2022; 23:245. [PMID: 36419176 PMCID: PMC9684954 DOI: 10.1186/s13059-022-02811-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/02/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Degradation rate is a fundamental aspect of mRNA metabolism, and the factors governing it remain poorly characterized. Understanding the genetic and biochemical determinants of mRNA half-life would enable more precise identification of variants that perturb gene expression through post-transcriptional gene regulatory mechanisms. RESULTS We establish a compendium of 39 human and 27 mouse transcriptome-wide mRNA decay rate datasets. A meta-analysis of these data identified a prevalence of technical noise and measurement bias, induced partially by the underlying experimental strategy. Correcting for these biases allowed us to derive more precise, consensus measurements of half-life which exhibit enhanced consistency between species. We trained substantially improved statistical models based upon genetic and biochemical features to better predict half-life and characterize the factors molding it. Our state-of-the-art model, Saluki, is a hybrid convolutional and recurrent deep neural network which relies only upon an mRNA sequence annotated with coding frame and splice sites to predict half-life (r=0.77). The key novel principle learned by Saluki is that the spatial positioning of splice sites, codons, and RNA-binding motifs within an mRNA is strongly associated with mRNA half-life. Saluki predicts the impact of RNA sequences and genetic mutations therein on mRNA stability, in agreement with functional measurements derived from massively parallel reporter assays. CONCLUSIONS Our work produces a more robust ground truth for transcriptome-wide mRNA half-lives in mammalian cells. Using these revised measurements, we trained Saluki, a model that is over 50% more accurate in predicting half-life from sequence than existing models. Saluki succinctly captures many of the known determinants of mRNA half-life and can be rapidly deployed to predict the functional consequences of arbitrary mutations in the transcriptome.
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Affiliation(s)
- Vikram Agarwal
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
- Present Address: mRNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, 02451, USA.
| | - David R Kelley
- Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.
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10
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Poetz F, Lebedeva S, Schott J, Lindner D, Ohler U, Stoecklin G. Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation. Genome Biol 2022; 23:193. [PMID: 36096941 PMCID: PMC9465963 DOI: 10.1186/s13059-022-02760-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/23/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Cytoplasmic polyadenylation element-binding protein 4 (CPEB4) is known to associate with cytoplasmic polyadenylation elements (CPEs) located in the 3' untranslated region (UTR) of specific mRNAs and assemble an activator complex promoting the translation of target mRNAs through cytoplasmic polyadenylation. RESULTS Here, we find that CPEB4 is part of an alternative repressor complex that mediates mRNA degradation by associating with the evolutionarily conserved CCR4-NOT deadenylase complex. We identify human CPEB4 as an RNA-binding protein (RBP) with enhanced association to poly(A) RNA upon inhibition of class I histone deacetylases (HDACs), a condition known to cause widespread degradation of poly(A)-containing mRNA. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis using endogenously tagged CPEB4 in HeLa cells reveals that CPEB4 preferentially binds to the 3'UTR of immediate early gene mRNAs, at G-containing variants of the canonical U- and A-rich CPE located in close proximity to poly(A) sites. By transcriptome-wide mRNA decay measurements, we find that the strength of CPEB4 binding correlates with short mRNA half-lives and that loss of CPEB4 expression leads to the stabilization of immediate early gene mRNAs. Akin to CPEB4, we demonstrate that CPEB1 and CPEB2 also confer mRNA instability by recruitment of the CCR4-NOT complex. CONCLUSIONS While CPEB4 was previously known for its ability to stimulate cytoplasmic polyadenylation, our findings establish an additional function for CPEB4 as the RNA adaptor of a repressor complex that enhances the degradation of short-lived immediate early gene mRNAs.
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Affiliation(s)
- Fabian Poetz
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Svetlana Lebedeva
- Berlin Institute for Molecular Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, 10115, Berlin, Germany
| | - Johanna Schott
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Doris Lindner
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany
| | - Uwe Ohler
- Berlin Institute for Molecular Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, 10115, Berlin, Germany
- Department of Biology, Humboldt Universität Berlin, 10099, Berlin, Germany
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Ludolf-Krehl-Str. 13-17, 68167, Mannheim, Germany.
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120, Heidelberg, Germany.
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11
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Factors influencing degradation kinetics of mRNAs and half-lives of microRNAs, circRNAs, lncRNAs in blood in vitro using quantitative PCR. Sci Rep 2022; 12:7259. [PMID: 35508612 PMCID: PMC9068688 DOI: 10.1038/s41598-022-11339-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
RNAs are rapidly degraded in samples and during collection, processing and testing. In this study, we used the same method to explore the half-lives of different RNAs and the influencing factors, and compared the degradation kinetics and characteristics of different RNAs in whole blood and experimental samples. Fresh anticoagulant blood samples were incubated at room temperature for different durations, RNAs were extracted, and genes, including internal references, were amplified by real-time quantitative PCR. A linear half-life model was established according to cycle threshold (Ct) values. The effects of experimental operations on RNA degradation before and after RNA extraction were explored. Quantitative analysis of mRNA degradation in samples and during experimental processes were explored using an orthogonal experimental design. The storage duration of blood samples at room temperature had the greatest influence on RNA degradation. The half-lives of messenger RNAs (mRNAs) was 16.4 h. The half-lives of circular RNAs (circRNAs), long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were 24.56 ± 5.2 h, 17.46 ± 3.0 h and 16.42 ± 4.2 h, respectively. RNA degradation occurred mainly in blood samples. The half-life of mRNAs was the shortest among the four kinds of RNAs. Quantitative experiments related to mRNAs should be completed within 2 h. The half-lives of circRNAs and lncRNAs were longer than those of the former two.
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12
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Faucillion ML, Johansson AM, Larsson J. Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression. Nucleic Acids Res 2022; 50:4372-4388. [PMID: 35390159 PMCID: PMC9071389 DOI: 10.1093/nar/gkac208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/09/2022] [Accepted: 03/17/2022] [Indexed: 01/02/2023] Open
Abstract
The steady state levels of RNAs, often referred to as expression levels, result from a well-balanced combination of RNA transcription and decay. Alterations in RNA levels will therefore result from tight regulation of transcription rates, decay rates or both. Here, we explore the role of RNA stability in achieving balanced gene expression and present genome-wide RNA stabilities in Drosophila melanogaster male and female cells as well as male cells depleted of proteins essential for dosage compensation. We identify two distinct RNA-stability mediated responses involved in regulation of gene expression. The first of these responds to acute and global changes in transcription and thus counteracts potentially harmful gene mis-expression by shifting the RNA stability in the direction opposite to the transcriptional change. The second response enhances inter-individual differential gene expression by adjusting the RNA stability in the same direction as a transcriptional change. Both mechanisms are global, act on housekeeping as well as non-housekeeping genes and were observed in both flies and mammals. Additionally, we show that, in contrast to mammals, modulation of RNA stability does not detectably contribute to dosage compensation of the sex-chromosomes in D. melanogaster.
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Affiliation(s)
| | | | - Jan Larsson
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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13
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Behrens G, Heissmeyer V. Cooperation of RNA-Binding Proteins – a Focus on Roquin Function in T Cells. Front Immunol 2022; 13:839762. [PMID: 35251035 PMCID: PMC8894612 DOI: 10.3389/fimmu.2022.839762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/31/2022] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional gene regulation by RNA-binding proteins (RBPs) is important in the prevention of inflammatory and autoimmune diseases. With respect to T cell activation and differentiation, the RBPs Roquin-1/2 and Regnase-1 play pivotal roles by inducing degradation and/or translational silencing of target mRNAs. These targets encode important proinflammatory mediators and thus Roquin and Regnase-1 functions dampen cellular programs that can lead to inflammation and autoimmune disease. Recent findings demonstrate direct physical interaction of both RBPs. Here, we propose that cooperativity of trans-acting factors may be more generally used to reinforce the regulatory impact on selected targets and promote specific cell fate decisions. We develop this concept for Roquin and Regnase-1 function in resting and activated T cells and discuss the involvement in autoimmunity as well as how the therapeutic potential can be used in anti-tumor therapies.
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Affiliation(s)
- Gesine Behrens
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
- *Correspondence: Vigo Heissmeyer,
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14
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Kuang J, McGinley C, Lee MJC, Saner NJ, Garnham A, Bishop DJ. Interpretation of exercise-induced changes in human skeletal muscle mRNA expression depends on the timing of the post-exercise biopsies. PeerJ 2022; 10:e12856. [PMID: 35186464 PMCID: PMC8820226 DOI: 10.7717/peerj.12856] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/09/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Exercise elicits a range of adaptive responses in skeletal muscle, which include changes in mRNA expression. To better understand the health benefits of exercise training, it is important to investigate the underlying molecular mechanisms of skeletal muscle adaptation to exercise. However, most studies have assessed the molecular events at only a few time-points within a short time frame post-exercise, and the variations of gene expression kinetics have not been addressed systematically. METHODS We assessed the mRNA expression of 23 gene isoforms implicated in the adaptive response to exercise at six time-points (0, 3, 9, 24, 48, and 72 h post exercise) over a 3-day period following a single session of high-intensity interval exercise. RESULTS The temporal patterns of target gene expression were highly variable and the expression of mRNA transcripts detected was largely dependent on the timing of muscle sampling. The largest fold change in mRNA expression of each tested target gene was observed between 3 and 72 h post-exercise. DISCUSSION AND CONCLUSIONS Our findings highlight an important gap in knowledge regarding the molecular response to exercise, where the use of limited time-points within a short period post-exercise has led to an incomplete understanding of the molecular response to exercise. Muscle sampling timing for individual studies needs to be carefully chosen based on existing literature and preliminary analysis of the molecular targets of interest. We propose that a comprehensive time-course analysis on the exercise-induced transcriptional response in humans will significantly benefit the field of exercise molecular biology.
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Affiliation(s)
- Jujiao Kuang
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia,Australia Institute for Musculoskeletal Sciences, Melbourne, Victoria, Australia
| | - Cian McGinley
- Sportscotland Institute of Sport, Stirling, United Kingdom
| | - Matthew J-C Lee
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Nicholas J. Saner
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia,Human Integrative Physiology, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Andrew Garnham
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - David J. Bishop
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
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15
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Shang J, He L, Wang J, Tong A, Xiang Y. In Situ Visualizing Nascent RNA by Exploring DNA-Templated Oxidative Amination of 4-Thiouridine. Bioconjug Chem 2022; 33:164-171. [PMID: 34910465 DOI: 10.1021/acs.bioconjchem.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tracking and mapping the nascent RNA molecules in cells is essential for deciphering embryonic development and neuronal differentiation. Here, we utilized 4-thiouridine (s4U) as a metabolic tag to label nascent RNA and developed a fluorescence imaging method based on the DNA-templated oxidative amination (DTOA) reaction of s4U. The DTOA reaction occurred between amine-modified DNA and s4U-containing RNA with high sequence specificity and chemical selectivity. Target nascent mRNAs in HeLa cells, including those encoding green fluorescent proteins (GFPs) and endogenous BAG-1, were thus lit up selectively by DTOA-based fluorescence in situ hybridization (DTOA FISH). We believe the DTOA conjugation chemistry shown in this study could be generally applied to investigate the spatial distribution of nascent transcription dynamics in cellular processes.
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Affiliation(s)
- Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Luo He
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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16
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Potemkin N, Cawood SMF, Treece J, Guévremont D, Rand CJ, McLean C, Stanton JAL, Williams JM. A method for simultaneous detection of small and long RNA biotypes by ribodepleted RNA-Seq. Sci Rep 2022; 12:621. [PMID: 35022475 PMCID: PMC8755727 DOI: 10.1038/s41598-021-04209-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identification and quantification of many different species of RNA from the same sample at the same time. In this study we describe a novel protocol for simultaneous detection of coding and non-coding transcripts using modifications to the Ion Total RNA-Seq kit v2 protocol, with integration of QIASeq FastSelect rRNA removal kit. We report highly consistent sequencing libraries can be produced from both frozen high integrity mouse hippocampal tissue and the more challenging post-mortem human tissue. Removal of rRNA using FastSelect was extremely efficient, resulting in less than 1.5% rRNA content in the final library. We identified > 30,000 unique transcripts from all samples, including protein-coding genes and many species of non-coding RNA, in biologically-relevant proportions. Furthermore, the normalized sequencing read count for select genes significantly negatively correlated with Ct values from qRT-PCR analysis from the same samples. These results indicate that this protocol accurately and consistently identifies and quantifies a wide variety of transcripts simultaneously. The highly efficient rRNA depletion, coupled with minimized sample handling and without complicated and high-loss size selection protocols, makes this protocol useful to researchers wishing to investigate whole transcriptomes.
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Affiliation(s)
- Nikita Potemkin
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
- Brain Health Research Centre, Brain Research New Zealand-Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Sophie M F Cawood
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
- Brain Health Research Centre, Brain Research New Zealand-Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Jackson Treece
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Diane Guévremont
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
- Brain Health Research Centre, Brain Research New Zealand-Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
| | - Christy J Rand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Catriona McLean
- Victorian Brain Bank, The Florey Institute of Neuroscience and Mental Health, Melbourne, VIC, Australia
- Anatomical Pathology, The Alfred Hospital, Melbourne, VIC, Australia
| | - Jo-Ann L Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Joanna M Williams
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, New Zealand.
- Brain Health Research Centre, Brain Research New Zealand-Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand.
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17
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Abstract
The control of mRNA stability is fundamental to gene regulation, and a deeper understanding of this post-transcriptional regulatory step can provide key insights into gene function. Measuring mRNA half-lives directly, however, is challenging. The most common strategies for evaluating mRNA stability and decay involve blocking general transcription and then measuring the decline in mRNA levels over time. The downside of these approaches, however, is that they severely impact cell function and viability, indirectly perturbing gene expression. Here, we describe Roadblock-qPCR, a simple method for measuring mRNA decay kinetics in living cells that is both economical and quick. Cells are first incubated with the nucleoside analog 4-thiouridine (4sU), which is readily incorporated into nascent mRNAs during transcription. RNA is then extracted and treated with N-ethylmaleimide (NEM), a sulfhydryl alkylating agent that selectively modifies 4sU, before proceeding to cDNA synthesis. Because the NEM-modified 4sU creates a chemical "roadblock" that interferes with reverse transcription, this treatment ultimately results in the depletion of the nascent 4sU-containing transcripts from the cDNA pool. As such, the decay rate of the non-4sU-labeled pre-existing mRNAs can be monitored by quantitative PCR (qPCR). In combination with spike-in standards, this approach can be used to efficiently and accurately measure the half-lives of endogenous mRNAs with a wide range of stabilities, while avoiding the artifacts of transcription shutoff strategies. © 2022 Wiley Periodicals LLC. Basic Protocol: Roadblock-qPCR Support Protocol: Synthesis of spike-in mRNA.
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Affiliation(s)
- Maegan J. Watson
- Department of Cellular and Molecular Physiology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06510
| | - Carson C. Thoreen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06510,To whom correspondence should be addressed.
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18
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Microtubule-based transport is essential to distribute RNA and nascent protein in skeletal muscle. Nat Commun 2021; 12:6079. [PMID: 34707124 PMCID: PMC8551216 DOI: 10.1038/s41467-021-26383-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
While the importance of RNA localization in highly differentiated cells is well appreciated, basic principles of RNA localization in skeletal muscle remain poorly characterized. Here, we develop a method to detect and quantify single molecule RNA localization patterns in skeletal myofibers, and uncover a critical role for directed transport of RNPs in muscle. We find that RNAs localize and are translated along sarcomere Z-disks, dispersing tens of microns from progenitor nuclei, regardless of encoded protein function. We find that directed transport along the lattice-like microtubule network of myofibers becomes essential to achieve this localization pattern as muscle development progresses; disruption of this network leads to extreme accumulation of RNPs and nascent protein around myonuclei. Our observations suggest that global active RNP transport may be required to distribute RNAs in highly differentiated cells and reveal fundamental mechanisms of gene regulation, with consequences for myopathies caused by perturbations to RNPs or microtubules.
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19
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Hu T, Wei L, Li S, Cheng T, Zhang X, Wang X. Single-cell Transcriptomes Reveal Characteristics of MicroRNA in Gene Expression Noise Reduction. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:394-407. [PMID: 34606979 PMCID: PMC8864250 DOI: 10.1016/j.gpb.2021.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 04/29/2021] [Accepted: 08/01/2021] [Indexed: 11/30/2022]
Abstract
Isogenic cells growing in identical environments show cell-to-cell variations because of the stochasticity in gene expression. High levels of variation or noise can disrupt robust gene expression and result in tremendous consequences for cell behaviors. In this work, we showed evidence from single-cell RNA sequencing data analysis that microRNAs (miRNAs) can reduce gene expression noise at the mRNA level in mouse cells. We identified that the miRNA expression level, number of targets, target pool abundance, and miRNA–target interaction strength are the key features contributing to noise repression. miRNAs tend to work together in cooperative subnetworks to repress target noise synergistically in a cell type-specific manner. By building a physical model of post-transcriptional regulation and observing in synthetic gene circuits, we demonstrated that accelerated degradation with elevated transcriptional activation of the miRNA target provides resistance to extrinsic fluctuations. Together, through the integrated analysis of single-cell RNA and miRNA expression profiles, we demonstrated that miRNAs are important post-transcriptional regulators for reducing gene expression noise and conferring robustness to biological processes.
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Affiliation(s)
- Tao Hu
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shuailin Li
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Tianrun Cheng
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Bioinformatics Division, Beijing National Research Center for Information Science and Technology, Department of Automation, Tsinghua University, Beijing 100084, China.
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20
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Shi K, Liu T, Fu H, Li W, Zheng X. Genome-wide analysis of lncRNA stability in human. PLoS Comput Biol 2021; 17:e1008918. [PMID: 33861746 PMCID: PMC8081339 DOI: 10.1371/journal.pcbi.1008918] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/28/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Transcript stability is associated with many biological processes, and the factors affecting mRNA stability have been extensively studied. However, little is known about the features related to human long noncoding RNA (lncRNA) stability. By inhibiting transcription and collecting samples in 10 time points, genome-wide RNA-seq studies was performed in human lung adenocarcinoma cells (A549) and RNA half-life datasets were constructed. The following observations were obtained. First, the half-life distributions of both lncRNAs and messanger RNAs (mRNAs) with one exon (lnc-human1 and m-human1) were significantly different from those of both lncRNAs and mRNAs with more than one exon (lnc-human2 and m-human2). Furthermore, some factors such as full-length transcript secondary structures played a contrary role in lnc-human1 and m-human2. Second, through the half-life comparisons of nucleus- and cytoplasm-specific and common lncRNAs and mRNAs, lncRNAs (mRNAs) in the nucleus were found to be less stable than those in the cytoplasm, which was derived from transcripts themselves rather than cellular location. Third, kmers-based protein−RNA or RNA−RNA interactions promoted lncRNA stability from lnc-human1 and decreased mRNA stability from m-human2 with high probability. Finally, through applying deep learning−based regression, a non-linear relationship was found to exist between the half-lives of lncRNAs (mRNAs) and related factors. The present study established lncRNA and mRNA half-life regulation networks in the A549 cell line and shed new light on the degradation behaviors of both lncRNAs and mRNAs. Transcript stability is important for many biological processes. However, little is known about the features related to human lncRNA stability. Through quantitative analysis between the half-lives of lncRNAs (mRNAs) and various factors, we found a nonlinear relationship between the half-lives of lncRNAs (mRNAs) and the related factors and their combinations. Our research provided a comprehensive understanding of lncRNA stability. Further efforts are needed to develop an accurate quantitative prediction model for the half-lives of lncRNA (mRNA).
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Affiliation(s)
- Kaiwen Shi
- Institute of Military Cognition and Brain Sciences, Academy of Military Medicine, Beijing, China
| | - Tao Liu
- Institute of Military Cognition and Brain Sciences, Academy of Military Medicine, Beijing, China
| | - Hanjiang Fu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Wuju Li
- Institute of Military Cognition and Brain Sciences, Academy of Military Medicine, Beijing, China
- * E-mail: (WL); (XZ)
| | - Xiaofei Zheng
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
- * E-mail: (WL); (XZ)
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21
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Jefsen OH, Elfving B, Wegener G, Müller HK. Transcriptional regulation in the rat prefrontal cortex and hippocampus after a single administration of psilocybin. J Psychopharmacol 2021; 35:483-493. [PMID: 33143539 DOI: 10.1177/0269881120959614] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Psilocybin is a serotonergic psychedelic found in "magic mushrooms" with a putative therapeutic potential for treatment-resistant depression, anxiety, obsessive-compulsive disorder, and addiction. In rodents, psilocybin acutely induces plasticity-related immediate early genes in cortical tissue; however, studies into the effects on subcortical regions, of different doses, and the subsequent translation of corresponding proteins are lacking. METHODS We examined the acute effects of a single administration of psilocybin (0.5-20 mg/kg) on the expression of selected genes in the prefrontal cortex and hippocampus. In total, 46 target genes and eight reference genes were assessed using real-time quantitative polymerase chain reaction. Corresponding protein levels of the three most commonly regulated genes were assessed using Western blotting. RESULTS In the prefrontal cortex, psilocybin increased the expression of Cebpb, c-Fos, Dups1, Fosb, Junb, Iκβ-α, Nr4a1, P11, Psd95, and Sgk1, and decreased the expression of Clk1. In the hippocampus, psilocybin strongly increased the expression of Arrdc2, Dusp1, Iκβ-α, and Sgk1 in a dose-dependent manner, and decreased the expression of Arc, Clk1, Egr2, and Ptgs2. Protein levels of Sgk1, Dusp1, and Iκβ-α showed only partial agreement with transcriptional patterns, stressing the importance of assessing downstream translation when investigating rapid gene responses. CONCLUSION The present study demonstrates that psilocybin rapidly induces gene expression related to neuroplasticity, biased towards the prefrontal cortex, compared to the hippocampus. Our findings provide further evidence for the rapid plasticity-promoting effects of psilocybin.
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Affiliation(s)
- Oskar Hougaard Jefsen
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Betina Elfving
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Gregers Wegener
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,AUGUST Centre, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Heidi Kaastrup Müller
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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22
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Maeda R, Kami D, Shikuma A, Suzuki Y, Taya T, Matoba S, Gojo S. RNA decay in processing bodies is indispensable for adipogenesis. Cell Death Dis 2021; 12:285. [PMID: 33731683 PMCID: PMC7969960 DOI: 10.1038/s41419-021-03537-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 12/19/2022]
Abstract
The RNA decay pathway plays key regulatory roles in cell identities and differentiation processes. Although adipogenesis is transcriptionally and epigenetically regulated and has been thoroughly investigated, how RNA metabolism that contributes to the stability of phenotype-shaping transcriptomes participates in differentiation remains elusive. In this study, we investigated Ddx6, an essential component of processing bodies (PBs) that executes RNA decay and translational repression in the cytoplasm and participates in the cellular transition of reprogramming. Upon adipogenic induction, Ddx6 dynamically accumulated to form PBs with a binding partner, 4E-T, at the early phase prior to emergence of intracellular lipid droplets. In contrast, preadipocytes with Ddx6 knockout (KO) or 4E-T knockdown (KD) failed to generate PBs, resulting in significant suppression of adipogenesis. Transcription factors related to preadipocytes and negative regulators of adipogenesis that were not expressed under adipogenic stimulation were maintained in Ddx6-KO and 4E-T-KD preadipocytes under adipogenic induction. Elimination of Dlk1, a major negative regulator of adipogenesis, in 3T3L1 Ddx6-KO cells did not restore adipogenic differentiation capacity to any extent. Similar to murine cells, human primary mesenchymal stem cells, which can differentiate into adipocytes upon stimulation with adipogenic cocktails, required DDX6 to maturate into adipocytes. Therefore, RNA decay of the entire parental transcriptome, rather than removal of a strong negative regulator, could be indispensable for adipogenesis.
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Affiliation(s)
- Ryotaro Maeda
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akira Shikuma
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yosuke Suzuki
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshihiko Taya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.
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23
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Uriu K, Tei H. Complementary phase responses via functional differentiation of dual negative feedback loops. PLoS Comput Biol 2021; 17:e1008774. [PMID: 33684114 PMCID: PMC7971863 DOI: 10.1371/journal.pcbi.1008774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/18/2021] [Accepted: 02/05/2021] [Indexed: 11/18/2022] Open
Abstract
Multiple feedback loops are often found in gene regulations for various cellular functions. In mammalian circadian clocks, oscillations of Period1 (Per1) and Period2 (Per2) expression are caused by interacting negative feedback loops (NFLs) whose protein products with similar molecular functions repress each other. However, Per1 expression peaks earlier than Per2 in the pacemaker tissue, raising the question of whether the peak time difference reflects their different dynamical functions. Here, we address this question by analyzing phase responses of the circadian clock caused by light-induced transcription of both Per1 and Per2 mRNAs. Through mathematical analyses of dual NFLs, we show that phase advance is mainly driven by light inputs to the repressor with an earlier expression peak as Per1, whereas phase delay is driven by the other repressor with a later peak as Per2. Due to the complementary contributions to phase responses, the ratio of light-induced transcription rates between Per1 and Per2 determines the magnitude and direction of phase shifts at each time of day. Specifically, stronger Per1 light induction than Per2 results in a phase response curve (PRC) with a larger phase advance zone than delay zone as observed in rats and hamsters, whereas stronger Per2 induction causes a larger delay zone as observed in mice. Furthermore, the ratio of light-induced transcription rates required for entrainment is determined by the relation between the circadian and light-dark periods. Namely, if the autonomous period of a circadian clock is longer than the light-dark period, a larger light-induced transcription rate of Per1 than Per2 is required for entrainment, and vice versa. In short, the time difference between Per1 and Per2 expression peaks can differentiate their dynamical functions. The resultant complementary contributions to phase responses can determine entrainability of the circadian clock to the light-dark cycle.
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Affiliation(s)
- Koichiro Uriu
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
- * E-mail:
| | - Hajime Tei
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
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24
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Tanner MK, Tang Z, Thornton CA. Targeted splice sequencing reveals RNA toxicity and therapeutic response in myotonic dystrophy. Nucleic Acids Res 2021; 49:2240-2254. [PMID: 33503262 PMCID: PMC7913682 DOI: 10.1093/nar/gkab022] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/03/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
Biomarker-driven trials hold promise for therapeutic development in chronic diseases, such as muscular dystrophy. Myotonic dystrophy type 1 (DM1) involves RNA toxicity, where transcripts containing expanded CUG-repeats (CUGexp) accumulate in nuclear foci and sequester splicing factors in the Muscleblind-like (Mbnl) family. Oligonucleotide therapies to mitigate RNA toxicity have emerged but reliable measures of target engagement are needed. Here we examined muscle transcriptomes in mouse models of DM1 and found that CUGexp expression or Mbnl gene deletion cause similar dysregulation of alternative splicing. We selected 35 dysregulated exons for further study by targeted RNA sequencing. Across a spectrum of mouse models, the individual splice events and a composite index derived from all events showed a graded response to decrements of Mbnl or increments of CUGexp. Antisense oligonucleotides caused prompt reduction of CUGexp RNA and parallel correction of the splicing index, followed by subsequent elimination of myotonia. These results suggest that targeted splice sequencing may provide a sensitive and reliable way to assess therapeutic impact in DM1.
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Affiliation(s)
- Matthew K Tanner
- Medical Scientist Training Program, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Zhenzhi Tang
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
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25
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Regulation of ddb2 expression in blind cavefish and zebrafish reveals plasticity in the control of sunlight-induced DNA damage repair. PLoS Genet 2021; 17:e1009356. [PMID: 33544716 PMCID: PMC7891740 DOI: 10.1371/journal.pgen.1009356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/18/2021] [Accepted: 01/12/2021] [Indexed: 11/19/2022] Open
Abstract
We have gained considerable insight into the mechanisms which recognize and repair DNA damage, but how they adapt to extreme environmental challenges remains poorly understood. Cavefish have proven to be fascinating models for exploring the evolution of DNA repair in the complete absence of UV-induced DNA damage and light. We have previously revealed that the Somalian cavefish Phreatichthys andruzzii, lacks photoreactivation repair via the loss of light, UV and ROS-induced photolyase gene transcription mediated by D-box enhancer elements. Here, we explore whether other systems repairing UV-induced DNA damage have been similarly affected in this cavefish model. By performing a comparative study using P. andruzzii and the surface-dwelling zebrafish, we provide evidence for a conservation of sunlight-regulated Nucleotide Excision Repair (NER). Specifically, the expression of the ddb2 gene which encodes a key NER recognition factor is robustly induced following exposure to light, UV and oxidative stress in both species. As in the case of the photolyase genes, D-boxes in the ddb2 promoter are sufficient to induce transcription in zebrafish. Interestingly, despite the loss of D-box-regulated photolyase gene expression in P. andruzzii, the D-box is required for ddb2 induction by visible light and oxidative stress in cavefish. However, in the cavefish ddb2 gene this D-box-mediated induction requires cooperation with an adjacent, highly conserved E2F element. Furthermore, while in zebrafish UV-induced ddb2 expression results from transcriptional activation accompanied by stabilization of the ddb2 mRNA, in P. andruzzii UV induces ddb2 expression exclusively via an increase in mRNA stability. Thus, we reveal plasticity in the transcriptional and post transcriptional mechanisms regulating the repair of sunlight-induced DNA damage under long-term environmental challenges.
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Abstract
Circadian rhythms are constituted by a complex dynamical system with intertwined feedback loops, molecular switches, and self-sustained oscillations. Mathematical modeling supports understanding available heterogeneous kinetic data, highlights basic mechanisms, and can guide experimental research. Here, we introduce the basic steps from a biological question to simple models providing insight into gene-regulatory mechanisms. We illustrate the general approach by three examples: modeling decay processes, clock-controlled genes, and self-sustained oscillations.
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Affiliation(s)
- J Patrick Pett
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Pål O Westermark
- Leibniz Institute for Farm Animal Biology, Institute of Genetics and Biometry, Dummerstorf, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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27
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Wen S, Wei Y, Zen C, Xiong W, Niu Y, Zhao Y. Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine. Mol Cancer 2020; 19:171. [PMID: 33308223 PMCID: PMC7733260 DOI: 10.1186/s12943-020-01293-4] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
Background N6-methyladenosine (m6A) is the most prevalent messenger RNA modification in mammalian cells. However, the disease relevant function of m6A on specific oncogenic long non-coding RNAs (ncRNAs) is not well understood. Methods We analyzed the m6A status using patients samples and bone metastatic PDXs. Through m6A high-throughput sequencing, we identified the m6A sites on NEAT1–1 in prostate bone metastatic PDXs. Mass spec assay showed interaction among NEAT1–1, CYCLINL1 and CDK19. RNA EMSA, RNA pull-down, mutagenesis, CLIP, western blot, ChIP and ChIRP assays were used to investigate the molecular mechanisms underlying the functions of m6A on NEAT1–1. Loss-of function and rescued experiments were executed to detect the biological roles of m6A on NEAT1–1 in the PDX cell phenotypes in vivo. Results In this study, we identified 4 credible m6A sites on long ncRNA NEAT1–1. High m6A level of NEAT1–1 was related to bone metastasis of prostate cancer and m6A level of NEAT1–1 was a powerful predictor of eventual death. Transcribed NEAT1–1 served as a bridge to facility the binding between CYCLINL1 and CDK19 and promoted the Pol II ser2 phosphorylation. Importantly, depletion of NEAT1–1or decreased m6A of NEAT1–1 impaired Pol II Ser-2p level in the promoter of RUNX2. Overexpression of NEAT1–1 induced cancer cell metastasis to lung and bone; xenograft growth and shortened the survival of mice, but NEAT1–1 with m6A site mutation failed to do these. Conclusion Collectively, the findings indicate that m6A on ncRNA NEAT1–1 takes critical role in regulating Pol II ser2 phosphorylation and may be novel specific target for bone metastasis cancer therapy and diagnosis. New complex CYCLINL1/CDK19/NEAT1–1 might provide new insight into the potential mechanism of the pathogenesis and development of bone metastatic prostate cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-020-01293-4.
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Affiliation(s)
- Simeng Wen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300211, China
| | - Yulei Wei
- Department of Gynecology and Obstetrics, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Chong Zen
- Department of Urology, Central South University, Changsha, 410011, China
| | - Wei Xiong
- Department of Urology, Central South University, Changsha, 410011, China
| | - Yuanjie Niu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300211, China.
| | - Yu Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
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28
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Watson M, Park Y, Thoreen C. Roadblock-qPCR: A simple and inexpensive strategy for targeted measurements of mRNA stability. RNA (NEW YORK, N.Y.) 2020; 27:rna.076885.120. [PMID: 33288682 PMCID: PMC7901842 DOI: 10.1261/rna.076885.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
The stability of mRNAs is fundamental to determining expression level and dynamics. Nonetheless, current approaches for measuring transcript half-lives (e.g. transcription shutoff) are generally toxic or technically complex. Here we describe an alternative strategy for targeted measurements of endogenous mRNA stability that is simple, inexpensive, and non-toxic. Cells are first metabolically labelled with the nucleoside analog 4-thiouridine (4sU). Extracted mRNA can then be treated with the thiol-reactive compound N-ethylmaleimide. This compound modifies 4sU nucleotides and sterically interferes with reverse transcription of 4sU-containing transcripts, disrupting their conversion into cDNA. The decay rate of non-4sU-containing pre-existing mRNA can then be monitored by quantitative PCR (qPCR). Importantly, this approach avoids the biochemical isolation of 4sU-labelled transcripts and/or RNA-seq analysis required for other metabolic-labelling strategies. In summary, our method combines the simplicity of "transcription shutoff" strategies with the accuracy of metabolic-labelling strategies for measurements of mRNA stability across a wide range of half-lives.
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29
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Kajitani N, Schwartz S. Role of Viral Ribonucleoproteins in Human Papillomavirus Type 16 Gene Expression. Viruses 2020; 12:E1110. [PMID: 33007936 PMCID: PMC7600041 DOI: 10.3390/v12101110] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 02/06/2023] Open
Abstract
Human papillomaviruses (HPVs) depend on the cellular RNA-processing machineries including alternative RNA splicing and polyadenylation to coordinate HPV gene expression. HPV RNA processing is controlled by cis-regulatory RNA elements and trans-regulatory factors since the HPV splice sites are suboptimal. The definition of HPV exons and introns may differ between individual HPV mRNA species and is complicated by the fact that many HPV protein-coding sequences overlap. The formation of HPV ribonucleoproteins consisting of HPV pre-mRNAs and multiple cellular RNA-binding proteins may result in the different outcomes of HPV gene expression, which contributes to the HPV life cycle progression and HPV-associated cancer development. In this review, we summarize the regulation of HPV16 gene expression at the level of RNA processing with focus on the interactions between HPV16 pre-mRNAs and cellular RNA-binding factors.
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Affiliation(s)
- Naoko Kajitani
- Department of Laboratory Medicine, Lund University, 22184 Lund, Sweden;
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30
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Furlan M, Galeota E, Gaudio ND, Dassi E, Caselle M, de Pretis S, Pelizzola M. Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling. Genome Res 2020; 30:1492-1507. [PMID: 32978246 PMCID: PMC7605262 DOI: 10.1101/gr.260984.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022]
Abstract
The quantification of the kinetic rates of RNA synthesis, processing, and degradation are largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT−, a computational method based on the mathematical modeling of premature and mature RNA expression that is able to quantify kinetic rates from steady-state or time course total RNA-seq data without requiring any information on nascent transcripts. Our approach outperforms available solutions, closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcript half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions in which nascent transcription cannot be readily profiled. Finally, we applied INSPEcT− to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady-state or time course data, with or without the profiling of nascent RNA.
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Affiliation(s)
- Mattia Furlan
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy.,Physics Department and INFN, University of Turin, 10125 Turin, Italy
| | - Eugenia Galeota
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Nunzio Del Gaudio
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Erik Dassi
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Michele Caselle
- Physics Department and INFN, University of Turin, 10125 Turin, Italy
| | - Stefano de Pretis
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy
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31
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Rayon T, Stamataki D, Perez-Carrasco R, Garcia-Perez L, Barrington C, Melchionda M, Exelby K, Lazaro J, Tybulewicz VLJ, Fisher EMC, Briscoe J. Species-specific pace of development is associated with differences in protein stability. Science 2020; 369:eaba7667. [PMID: 32943498 PMCID: PMC7116327 DOI: 10.1126/science.aba7667] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Although many molecular mechanisms controlling developmental processes are evolutionarily conserved, the speed at which the embryo develops can vary substantially between species. For example, the same genetic program, comprising sequential changes in transcriptional states, governs the differentiation of motor neurons in mouse and human, but the tempo at which it operates differs between species. Using in vitro directed differentiation of embryonic stem cells to motor neurons, we show that the program runs more than twice as fast in mouse as in human. This is not due to differences in signaling, nor the genomic sequence of genes or their regulatory elements. Instead, there is an approximately two-fold increase in protein stability and cell cycle duration in human cells compared with mouse cells. This can account for the slower pace of human development and suggests that differences in protein turnover play a role in interspecies differences in developmental tempo.
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Affiliation(s)
- Teresa Rayon
- The Francis Crick Institute, London NW1 1AT, UK.
| | | | - Ruben Perez-Carrasco
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Mathematics, University College London, London WC1E 6BT, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | | | | | | | | | - Victor L J Tybulewicz
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College, London W12 0NN, UK
| | - Elizabeth M C Fisher
- UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
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32
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Tian Y, Zeng Z, Li X, Wang Y, Chen R, Mattijssen S, Gaidamakov S, Wu Y, Maraia RJ, Peng W, Zhu J. Transcriptome-wide stability analysis uncovers LARP4-mediated NFκB1 mRNA stabilization during T cell activation. Nucleic Acids Res 2020; 48:8724-8739. [PMID: 32735645 PMCID: PMC7470963 DOI: 10.1093/nar/gkaa643] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 06/30/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Motivated by our previous finding that intron retention (IR) could lead to transcript instability, in this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells. Computational modeling was then applied to quantify the stability of spliced and intron-retained transcripts on a genome-wide scale. Beyond substantiating that intron-retained transcripts were considerably less stable than spliced transcripts, we found a global stabilization of spliced mRNAs upon T cell activation, although the stability of intron-retained transcripts remained relatively constant. In addition, we identified that La-related protein 4 (LARP4), an RNA-binding protein (RBP) known to enhance mRNA stability, was involved in T cell activation-dependent mRNA stabilization. Knocking out Larp4 in mice destabilized Nfκb1 mRNAs and reduced secretion of interleukin-2 (IL2) and interferon-gamma (IFNγ), two factors critical for T cell proliferation and function. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to control spatiotemporal gene expression during T cell activation.
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Affiliation(s)
- Yi Tian
- Department of Physics, George Washington University, Washington, DC 20052, USA
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Zhouhao Zeng
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Xiang Li
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Yiyin Wang
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Runsen Chen
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Sandy Mattijssen
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sergei Gaidamakov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Richard J Maraia
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Weiqun Peng
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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33
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de Pretis S, Furlan M, Pelizzola M. INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species. Front Genet 2020; 11:759. [PMID: 32765590 PMCID: PMC7379887 DOI: 10.3389/fgene.2020.00759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/26/2020] [Indexed: 12/23/2022] Open
Abstract
The abundance of RNA species and their response to perturbations are set by the kinetics rates of RNA synthesis, processing, and degradation. However, the visualization, interpretation, and manipulation of these data require familiarity with mathematical modeling and command line tools. INSPEcT-GUI is an R-Shiny interface that allows researchers without specific training to effortlessly explore how the fine kinetic regulation of the RNA life cycle can shape gene expression programs. In particular, it allows to: (i) interactively visualize gene-level RNA dynamics; (ii) refine the model fit of experimental data; (iii) test alternative regulatory models; (iv) explore, independently from the availability of data, how the combined action of the RNA kinetic rates impacts on premature and mature RNA. INSPEcT-GUI is freely available within the R/Bioconductor package INSPEcT at http://bioconductor.org/packages/INSPEcT/. An HTML vignette including documentation on the tool startup and usage, executable examples, and a video demonstration, are available at: http://bioconductor.org/packages/release/bioc/vignettes/INSPEcT/inst/doc/INSPEcT_GUI.html.
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Affiliation(s)
- Stefano de Pretis
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy
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34
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Wang X, He S, Li J, Wang J, Wang C, Wang M, He D, Lv X, Zhong Q, Wang H, Wang Z. pulseTD: RNA life cycle dynamics analysis based on pulse model of 4sU-seq time course sequencing data. PeerJ 2020; 8:e9371. [PMID: 32714656 PMCID: PMC7353919 DOI: 10.7717/peerj.9371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 05/27/2020] [Indexed: 11/20/2022] Open
Abstract
The life cycle of intracellular RNA mainly involves transcriptional production, splicing maturation and degradation processes. Their dynamic changes are termed as RNA life cycle dynamics (RLCD). It is still challenging for the accurate and robust identification of RLCD under unknow the functional form of RLCD. By using the pulse model, we developed an R package named pulseTD to identify RLCD by integrating 4sU-seq and RNA-seq data, and it provides flexible functions to capture continuous changes in RCLD rates. More importantly, it also can predict the trend of RNA transcription and expression changes in future time points. The pulseTD shows better accuracy and robustness than some other methods, and it is available on the GitHub repository (https://github.com/bioWzz/pulseTD_0.2.0).
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Affiliation(s)
- Xin Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang, China
| | - Siyu He
- College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang, China
| | - Jian Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang, China
| | - Jun Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang, China
| | - Chengyi Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang, China
| | - Mingwei Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang, China
| | - Danni He
- College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang, China
| | - Xingfeng Lv
- College of Computer Science and Technology, Heilongjiang University, Harbin, China
| | | | - Hongjiu Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
- School of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
- College of Science, Heilongjiang University of Science and Technology, Harbin, China
| | - Zhenzhen Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
- School of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
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35
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Browning JWL, Rambo TME, McKay BC. Comparative genomic analysis of the 3' UTR of human MDM2 identifies multiple transposable elements, an RLP24 pseudogene and a cluster of novel repeat sequences that arose during primate evolution. Gene 2020; 741:144557. [PMID: 32171824 DOI: 10.1016/j.gene.2020.144557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/08/2020] [Indexed: 01/09/2023]
Abstract
The MDM2 oncogene is a negative regulator of the p53 tumour suppressor. This relationship appears to have originated over a billion years ago. The human MDM2 gene encodes a variety of mRNAs with exceptionally long 3'UTRs (up to 5.7 kb); however, it was unclear whether MDM2 3'UTRs from other species are similarly long or conserved at the sequence level. Here, we report that all but one of the primate species most closely related to humans (greater and lesser apes) have similarly long 3'UTRs with high sequence similarity across their entire length. More distantly related species (Old world monkeys and new world monkeys) tend to have shorter MDM2 3'UTRs homologous to the corresponding position of the human MDM2 3'UTR while non-primate species exhibit little similarity at all. Remarkably, DNA sequences downstream of the shorter primate 3'UTRs are syntenic with distal regions in the human and other ape MDM2 3'UTRs. These homologous non-transcribed intergenic and transcribed 3'UTR-encoding regions are comprised of a variety of transposable elements, an RLP24 pseudogene and a cluster of novel repeat sequences suggestive of another unknown transposable element. Our analysis suggests that the primary difference between long and short MDM2 3'UTRs is a switch in polyA site usage to include conserved transposable elements that remain intergenic in more distantly related primates. It will be important to determine the relative contribution of these elements to post-transcriptional and translational regulation of MDM2 and hence p53-mediated tumour suppression.
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Affiliation(s)
| | | | - Bruce C McKay
- Department of Biology and Institute of Biochemistry, Ottawa, ON, Canada.
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36
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Takahashi A, Suzuki T, Soeda S, Takaoka S, Kobori S, Yamaguchi T, Mohamed HMA, Yanagiya A, Abe T, Shigeta M, Furuta Y, Kuba K, Yamamoto T. The CCR4-NOT complex maintains liver homeostasis through mRNA deadenylation. Life Sci Alliance 2020; 3:3/5/e201900494. [PMID: 32238456 PMCID: PMC7119370 DOI: 10.26508/lsa.201900494] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 03/11/2020] [Accepted: 03/14/2020] [Indexed: 12/12/2022] Open
Abstract
The biological significance of deadenylation in global gene expression is not fully understood. Here, we show that the CCR4-NOT deadenylase complex maintains expression of mRNAs, such as those encoding transcription factors, cell cycle regulators, DNA damage response-related proteins, and metabolic enzymes, at appropriate levels in the liver. Liver-specific disruption of Cnot1, encoding a scaffold subunit of the CCR4-NOT complex, leads to increased levels of mRNAs for transcription factors, cell cycle regulators, and DNA damage response-related proteins because of reduced deadenylation and stabilization of these mRNAs. CNOT1 suppression also results in an increase of immature, unspliced mRNAs (pre-mRNAs) for apoptosis-related and inflammation-related genes and promotes RNA polymerase II loading on their promoter regions. In contrast, mRNAs encoding metabolic enzymes become less abundant, concomitant with decreased levels of these pre-mRNAs. Lethal hepatitis develops concomitantly with abnormal mRNA expression. Mechanistically, the CCR4-NOT complex targets and destabilizes mRNAs mainly through its association with Argonaute 2 (AGO2) and butyrate response factor 1 (BRF1) in the liver. Therefore, the CCR4-NOT complex contributes to liver homeostasis by modulating the liver transcriptome through mRNA deadenylation.
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Affiliation(s)
- Akinori Takahashi
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Toru Suzuki
- Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
| | - Shou Soeda
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shohei Takaoka
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shungo Kobori
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tomokazu Yamaguchi
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | | | - Akiko Yanagiya
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Mayo Shigeta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yasuhide Furuta
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Graduate School of Medicine, Akita University, Akita, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan .,Laboratory for Immunogenetics, Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
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37
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Chen Y, Wu F, Chen Z, He Z, Wei Q, Zeng W, Chen K, Xiao F, Yuan Y, Weng X, Zhou Y, Zhou X. Acrylonitrile-Mediated Nascent RNA Sequencing for Transcriptome-Wide Profiling of Cellular RNA Dynamics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1900997. [PMID: 32328408 PMCID: PMC7175251 DOI: 10.1002/advs.201900997] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 01/25/2020] [Accepted: 02/13/2020] [Indexed: 06/10/2023]
Abstract
RNA sequencing has greatly facilitated gene expression studies but is weak in studying temporal RNA dynamics; this issue can be addressed by analyzing nascent RNAs. A famous method for nascent RNA analysis is metabolic labeling with noncanonic nucleoside followed by affinity purification, however, purification processes can always introduce biases into data analysis. Here, a chemical method for nascent RNA sequencing that avoids affinity purification based on acrylonitrile-mediated uridine-to-cytidine (U-to-C) conversion (AMUC-seq) via 4-thiouridine (s4U) cyanoethylation is presented. This method converts s4U base-pairing with guanine through the nucleophilic addition of s4U to acrylonitrile. The high reaction efficiency permits AMUC-seq directly and efficiently to recover nascent RNA information from total RNAs. AMUC-seq is validated by being used to detect mRNA half-lives and investigating the direct gene targets of a G-quadruplex stabilizer, which can be regarded as potential anticancer drug, in human cells. Thousands of direct gene targets of this drug are verified (these genes are significantly enriched in cancer such as SRC and HRAS). AMUC-seq also confirms G-quadruplex stabilization that impacts RNA polyadenylation. These results show AMUC-seq is qualified for the study of temporal RNA dynamics, and it can be a promising strategy to study the therapeutic mechanism of transcription-modulating drugs.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Fan Wu
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Zonggui Chen
- The Institute for Advanced StudiesWuhan UniversityWuhan430072P. R. China
| | - Zhiyong He
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Qi Wei
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Weiwu Zeng
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Kun Chen
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Feng Xiao
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Yushu Yuan
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Yu Zhou
- The Institute for Advanced StudiesWuhan UniversityWuhan430072P. R. China
- State Key Laboratory of VirologyCollege of Life SciencesWuhan UniversityWuhan430072P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
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Forrest ME, Pinkard O, Martin S, Sweet TJ, Hanson G, Coller J. Codon and amino acid content are associated with mRNA stability in mammalian cells. PLoS One 2020; 15:e0228730. [PMID: 32053646 PMCID: PMC7018022 DOI: 10.1371/journal.pone.0228730] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/21/2020] [Indexed: 12/31/2022] Open
Abstract
Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in the cell and is a major control point for modulating gene expression. In yeast and other model organisms, codon identity is a powerful determinant of transcript stability, contributing broadly to impact half-lives. General principles governing mRNA stability are poorly understood in mammalian systems. Importantly, however, the degradation machinery is highly conserved, thus it seems logical that mammalian transcript half-lives would also be strongly influenced by coding determinants. Herein we characterize the contribution of coding sequence towards mRNA decay in human and Chinese Hamster Ovary cells. In agreement with previous studies, we observed that synonymous codon usage impacts mRNA stability in mammalian cells. Surprisingly, however, we also observe that the amino acid content of a gene is an additional determinant correlating with transcript stability. The impact of codon and amino acid identity on mRNA decay appears to be associated with underlying tRNA and intracellular amino acid concentrations. Accordingly, genes of similar physiological function appear to coordinate their mRNA stabilities in part through codon and amino acid content. Together, these results raise the possibility that intracellular tRNA and amino acid levels interplay to mediate coupling between translational elongation and mRNA degradation rate in mammals.
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Affiliation(s)
- Megan E. Forrest
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Otis Pinkard
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Sophie Martin
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas J. Sweet
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Gavin Hanson
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jeff Coller
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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39
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Cambridge SB. Hypothesis: protein and RNA attributes are continuously optimized over time. BMC Genomics 2019; 20:1012. [PMID: 31870287 PMCID: PMC6929361 DOI: 10.1186/s12864-019-6371-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 12/05/2019] [Indexed: 02/01/2023] Open
Abstract
Background Little is known why proteins and RNAs exhibit half-lives varying over several magnitudes. Despite many efforts, a conclusive link between half-lives and gene function could not be established suggesting that other determinants may influence these molecular attributes. Results Here, I find that with increasing gene age there is a gradual and significant increase of protein and RNA half-lives, protein structure, and other molecular attributes that tend to affect protein abundance. These observations are accommodated in a hypothesis which posits that new genes at ‘birth’ are not optimized and thus their products exhibit low half-lives and less structure but continuous mutagenesis eventually improves these attributes. Thus, the protein and RNA products of the oldest genes obtained their high degrees of stability and structure only after billions of years while the products of younger genes had less time to be optimized and are therefore less stable and structured. Because more stable proteins with lower turnover require less transcription to maintain the same level of abundance, reduced transcription-associated mutagenesis (TAM) would fixate the changes by increasing gene conservation. Conclusions Consequently, the currently observed diversity of molecular attributes is a snapshot of gene products being at different stages along their temporal path of optimization.
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Affiliation(s)
- Sidney B Cambridge
- Department of Functional Neuroanatomy, Heidelberg University, Heidelberg, Germany.
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40
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Jermakowicz WJ, Carballosa-Gautam MM, Vitores AA, Hentall ID. Brainstem-Evoked Transcription of Defensive Genes After Spinal Cord Injury. Front Cell Neurosci 2019; 13:510. [PMID: 31803022 PMCID: PMC6877476 DOI: 10.3389/fncel.2019.00510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
The spinal cord after injury shows altered transcription in numerous genes. We tested in a pilot study whether the nucleus raphé magnus, a descending serotonergic brainstem region whose stimulation improves recovery after incomplete spinal cord injury (SCI), can influence these transcriptional changes. Rats received 2 h of low-frequency electrical stimulation in the raphé magnus 3 days after an impact contusion at segment T8. Comparison groups lacked injuries or activated stimulators or both. Immediately following stimulation, spinal cords were extracted, their RNA transcriptome sequenced, and differential gene expression quantified. Confirming many previous studies, injury primarily increased inflammatory and immune transcripts and decreased those related to lipid and cholesterol synthesis and neuronal signaling. Stimulation plus injury, contrasted with injury alone, caused significant changes in 43 transcripts (39 increases, 4 decreases), all protein-coding. Injury itself decreased only four of these 43 transcripts, all reversed by stimulation, and increased none of them. The non-specific 5-HT7 receptor antagonist pimozide reversed 25 of the 43 changes. Stimulation in intact rats principally caused decreases in transcripts related to oxidative phosphorylation, none of which were altered by stimulation in injury. Gene ontology (biological process) annotations comparing stimulation with either no stimulation or pimozide treatment in injured rats highlighted defense responses to lipopolysaccharides and microorganisms, and also erythrocyte development and oxygen transport (possibly yielding cellular oxidant detoxification). Connectivity maps of human orthologous genes generated in the CLUE database of perturbagen-response transcriptional signatures showed that drug classes whose effects in injured rats most closely resembled stimulation without pimozide include peroxisome proliferator-activated receptor agonists and angiotensin receptor blockers, which are reportedly beneficial in SCI. Thus the initial transcriptional response of the injured spinal cord to raphé magnus stimulation is upregulation of genes that in various ways are mostly protective, some probably located in recently arrived myeloid cells.
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Affiliation(s)
- Walter J Jermakowicz
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, Miami, FL, United States
| | - Melissa M Carballosa-Gautam
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, Miami, FL, United States
| | - Alberto A Vitores
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, Miami, FL, United States
| | - Ian D Hentall
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, Miami, FL, United States
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41
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Chen Y, Shen Y, Lin P, Tong D, Zhao Y, Allesina S, Shen X, Wu CI. Gene regulatory network stabilized by pervasive weak repressions: microRNA functions revealed by the May-Wigner theory. Natl Sci Rev 2019; 6:1176-1188. [PMID: 34691996 PMCID: PMC8291590 DOI: 10.1093/nsr/nwz076] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 01/01/2023] Open
Abstract
Food web and gene regulatory networks (GRNs) are large biological networks, both of which can be analyzed using the May-Wigner theory. According to the theory, networks as large as mammalian GRNs would require dedicated gene products for stabilization. We propose that microRNAs (miRNAs) are those products. More than 30% of genes are repressed by miRNAs, but most repressions are too weak to have a phenotypic consequence. The theory shows that (i) weak repressions cumulatively enhance the stability of GRNs, and (ii) broad and weak repressions confer greater stability than a few strong ones. Hence, the diffuse actions of miRNAs in mammalian cells appear to function mainly in stabilizing GRNs. The postulated link between mRNA repression and GRN stability can be seen in a different light in yeast, which do not have miRNAs. Yeast cells rely on non-specific RNA nucleases to strongly degrade mRNAs for GRN stability. The strategy is suited to GRNs of small and rapidly dividing yeast cells, but not the larger mammalian cells. In conclusion, the May-Wigner theory, supplanting the analysis of small motifs, provides a mathematical solution to GRN stability, thus linking miRNAs explicitly to 'developmental canalization'.
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Affiliation(s)
- Yuxin Chen
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yang Shen
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
- Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach an der Riß, Germany
| | - Pei Lin
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ding Tong
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT 06520, UK
| | - Yixin Zhao
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Stefano Allesina
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, UK
| | - Xu Shen
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chung-I Wu
- School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, UK
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42
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Lindeboom RGH, Vermeulen M, Lehner B, Supek F. The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy. Nat Genet 2019; 51:1645-1651. [PMID: 31659324 PMCID: PMC6858879 DOI: 10.1038/s41588-019-0517-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022]
Abstract
Premature termination codons (PTCs) can result in the production of truncated proteins or the degradation of messenger RNAs by nonsense-mediated mRNA decay (NMD). Which of these outcomes occurs can alter the effect of a mutation, with the engagement of NMD being dependent on a series of rules. Here, by applying these rules genome-wide to obtain a resource called NMDetective, we explore the impact of NMD on genetic disease and approaches to therapy. First, human genetic diseases differ in whether NMD typically aggravates or alleviates the effects of PTCs. Second, failure to trigger NMD is a cause of ineffective gene inactivation by CRISPR-Cas9 gene editing. Finally, NMD is a determinant of the efficacy of cancer immunotherapy, with only frameshifted transcripts that escape NMD predicting a response. These results demonstrate the importance of incorporating the rules of NMD into clinical decision-making. Moreover, they suggest that inhibiting NMD may be effective in enhancing cancer immunotherapy.
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Affiliation(s)
- Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
| | - Fran Supek
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain. .,Institut de Recerca Biomedica Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
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43
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Baum K, Schuchhardt J, Wolf J, Busse D. Of Gene Expression and Cell Division Time: A Mathematical Framework for Advanced Differential Gene Expression and Data Analysis. Cell Syst 2019; 9:569-579.e7. [PMID: 31521604 DOI: 10.1016/j.cels.2019.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/15/2019] [Accepted: 07/23/2019] [Indexed: 12/31/2022]
Abstract
Estimating fold changes of average mRNA and protein molecule counts per cell is the most common way to perform differential expression analysis. However, these gene expression data may be affected by cell division, an often-neglected phenomenon. Here, we develop a quantitative framework that links population-based mRNA and protein measurements to rates of gene expression in single cells undergoing cell division. The equations we derive are easy-to-use and widely robust against biological variability. They integrate multiple "omics" data into a coherent, quantitative description of single-cell gene expression and improve analysis when comparing systems or states with different cell division times. We explore these ideas in the context of resting versus activated B cells. Analyzing differences in protein synthesis rates enables to account for differences in cell division times. We demonstrate that this improves the resolution and hit rate of differential gene expression analysis when compared to analyzing population protein abundances alone.
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Affiliation(s)
- Katharina Baum
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Luxembourg Institute of Health, 1A-B rue Thomas Edison, L-1445 Strassen, Luxembourg.
| | | | - Jana Wolf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany.
| | - Dorothea Busse
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Integrative Research Institute for the Life Sciences, Humboldt University Berlin, Philippstr. 13, 10115 Berlin, Germany.
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44
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Sirey TM, Roberts K, Haerty W, Bedoya-Reina O, Rogatti-Granados S, Tan JY, Li N, Heather LC, Carter RN, Cooper S, Finch AJ, Wills J, Morton NM, Marques AC, Ponting CP. The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity. eLife 2019; 8:e45051. [PMID: 31045494 PMCID: PMC6542586 DOI: 10.7554/elife.45051] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
To generate energy efficiently, the cell is uniquely challenged to co-ordinate the abundance of electron transport chain protein subunits expressed from both nuclear and mitochondrial genomes. How an effective stoichiometry of this many constituent subunits is co-ordinated post-transcriptionally remains poorly understood. Here we show that Cerox1, an unusually abundant cytoplasmic long noncoding RNA (lncRNA), modulates the levels of mitochondrial complex I subunit transcripts in a manner that requires binding to microRNA-488-3p. Increased abundance of Cerox1 cooperatively elevates complex I subunit protein abundance and enzymatic activity, decreases reactive oxygen species production, and protects against the complex I inhibitor rotenone. Cerox1 function is conserved across placental mammals: human and mouse orthologues effectively modulate complex I enzymatic activity in mouse and human cells, respectively. Cerox1 is the first lncRNA demonstrated, to our knowledge, to regulate mitochondrial oxidative phosphorylation and, with miR-488-3p, represent novel targets for the modulation of complex I activity.
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Affiliation(s)
- Tamara M Sirey
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Kenny Roberts
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Wilfried Haerty
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Oscar Bedoya-Reina
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Sebastian Rogatti-Granados
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Jennifer Y Tan
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Nick Li
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
| | - Lisa C Heather
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Roderick N Carter
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research InstituteUniversity of EdinburghEdinburghUnited Kingdom
| | - Sarah Cooper
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Andrew J Finch
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
| | - Jimi Wills
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
| | - Nicholas M Morton
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research InstituteUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular MedicineUniversity of Edinburgh, Western General HospitalEdinburghUnited Kingdom
- MRC Functional Genomics UnitUniversity of OxfordOxfordUnited Kingdom
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45
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Detection and quantification of RNA decay intermediates using XRN1-resistant reporter transcripts. Nat Protoc 2019; 14:1603-1633. [DOI: 10.1038/s41596-019-0152-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
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46
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Shaker OG, Mahmoud RH, Abdelaleem OO, Ibrahem EG, Mohamed AA, Zaki OM, Abdelghaffar NK, Ahmed TI, Hemeda NF, Ahmed NA, Mansour DF. LncRNAs, MALAT1 and lnc-DC as potential biomarkers for multiple sclerosis diagnosis. Biosci Rep 2019; 39:BSR20181335. [PMID: 30514825 PMCID: PMC6331681 DOI: 10.1042/bsr20181335] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in gene regulation and show greater tissue specificity and complexity of biological functions. There is on-going research in their contribution in autoimmune diseases like multiple sclerosis (MS). Our study aimed at the evaluation of serum levels of lncRNAs, MALAT1 and lnc-DC in MS patients and the investigation of the association between these lncRNAs and the disease activity. Serum from 45 MS patients and 45 healthy controls was separated. MALAT1 and lnc-DC expression levels were assayed by qRT-PCR. MALAT1 and lnc-DC were significantly increased in MS patients (P=0.004 and P=0.006, respectively) in comparison with controls. There was a significant increase in expression of MALAT1 in secondary progressive MS (SPMS) subgroup compared with controls (P<0.0001); however, significant elevation of lnc-DC was demonstrated in relapsing remitting MS (RRMS) subtype (P=0.003) compared with normal controls. A positive association between the expression levels of MALAT1 and lnc-DC (r = 0.513, P < 0.0001) in MS patients was detected. Moreover, positive correlation was observed between MALAT1and lnc-DC in RRMS (r = 0.569, P = 0.001). Serum levels of MALAT1 and lnc-DC may serve as potential novel molecular biomarkers for MS diagnosis and may provide a new direction for its treatment.
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MESH Headings
- Adult
- Biomarkers/blood
- Case-Control Studies
- Female
- Humans
- Male
- Multiple Sclerosis, Chronic Progressive/blood
- Multiple Sclerosis, Chronic Progressive/diagnosis
- Multiple Sclerosis, Chronic Progressive/genetics
- Multiple Sclerosis, Chronic Progressive/pathology
- Multiple Sclerosis, Relapsing-Remitting/blood
- Multiple Sclerosis, Relapsing-Remitting/diagnosis
- Multiple Sclerosis, Relapsing-Remitting/genetics
- Multiple Sclerosis, Relapsing-Remitting/pathology
- RNA, Long Noncoding/blood
- RNA, Long Noncoding/genetics
- Severity of Illness Index
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Affiliation(s)
- Olfat G Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rania H Mahmoud
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Omayma O Abdelaleem
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Enas G Ibrahem
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Abdelrahmaan A Mohamed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Othman M Zaki
- Department of Clinical pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Noha K Abdelghaffar
- Department of Clinical pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Tarek I Ahmed
- Department of Internal medicine, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Nada F Hemeda
- Department of Genetics, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Naglaa A Ahmed
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig, Sharkea, Egypt
| | - Dina F Mansour
- Department of Neurology, Faculty of Medicine, Minia University, Minia, Egypt
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47
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Hausser J, Mayo A, Keren L, Alon U. Central dogma rates and the trade-off between precision and economy in gene expression. Nat Commun 2019; 10:68. [PMID: 30622246 PMCID: PMC6325141 DOI: 10.1038/s41467-018-07391-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/18/2018] [Indexed: 12/31/2022] Open
Abstract
Steady-state protein abundance is set by four rates: transcription, translation, mRNA decay and protein decay. A given protein abundance can be obtained from infinitely many combinations of these rates. This raises the question of whether the natural rates for each gene result from historical accidents, or are there rules that give certain combinations a selective advantage? We address this question using high-throughput measurements in rapidly growing cells from diverse organisms to find that about half of the rate combinations do not exist: genes that combine high transcription with low translation are strongly depleted. This depletion is due to a trade-off between precision and economy: high transcription decreases stochastic fluctuations but increases transcription costs. Our theory quantitatively explains which rate combinations are missing, and predicts the curvature of the fitness function for each gene. It may guide the design of gene circuits with desired expression levels and noise.
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Affiliation(s)
- Jean Hausser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.
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48
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Duffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1513. [PMID: 30370679 DOI: 10.1002/wrna.1513] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022]
Abstract
Cellular RNA levels are the result of a juggling act between RNA transcription, processing, and degradation. By tuning one or more of these parameters, cells can rapidly alter the available pool of transcripts in response to stimuli. While RNA sequencing (RNA-seq) is a vital method to quantify RNA levels genome-wide, it is unable to capture the dynamics of different RNA populations at steady-state or distinguish between different mechanisms that induce changes to the steady-state (i.e., altered rate of transcription vs. degradation). The dynamics of different RNA populations can be studied by targeted incorporation of noncanonical nucleosides. 4-Thiouridine (s4 U) is a commonly used and versatile RNA metabolic label that allows the study of many properties of RNA metabolism from synthesis to degradation. Numerous experimental strategies have been developed that leverage the power of s4 U to label newly transcribed RNA in whole cells, followed by enrichment with activated disulfides or chemistry to induce C mutations at sites of s4 U during sequencing. This review presents existing methods to study RNA population dynamics genome-wide using s4 U metabolic labeling, as well as a discussion of considerations and challenges when designing s4 U metabolic labeling experiments. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Jeremy A Schofield
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
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49
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Yamada T, Akimitsu N. Contributions of regulated transcription and mRNA decay to the dynamics of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1508. [PMID: 30276972 DOI: 10.1002/wrna.1508] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022]
Abstract
Organisms have acquired sophisticated regulatory networks that control gene expression in response to cellular perturbations. Understanding of the mechanisms underlying the coordinated changes in gene expression in response to external and internal stimuli is a fundamental issue in biology. Recent advances in high-throughput technologies have enabled the measurement of diverse biological information, including gene expression levels, kinetics of gene expression, and interactions among gene expression regulatory molecules. By coupling these technologies with quantitative modeling, we can now uncover the biological roles and mechanisms of gene regulation at the system level. This review consists of two parts. First, we focus on the methods using uridine analogs that measure synthesis and decay rates of RNAs, which demonstrate how cells dynamically change the regulation of gene expression in response to both internal and external cues. Second, we discuss the underlying mechanisms of these changes in kinetics, including the functions of transcription factors and RNA-binding proteins. Overall, this review will help to clarify a system-level view of gene expression programs in cells. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Regulation of RNA Stability RNA Methods > RNA Analyses in vitro and In Silico.
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Affiliation(s)
- Toshimichi Yamada
- Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
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Tyrovola JB. The "mechanostat" principle in cell differentiation. The osteochondroprogenitor paradigm. J Cell Biochem 2018; 120:37-44. [PMID: 30144147 DOI: 10.1002/jcb.27509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/25/2018] [Indexed: 12/13/2022]
Abstract
The "mechanostat" principle may be depicted as an oscillating signal of a signaling molecule, in which the amplitude, frequency, cumulative level, delay, and duration of the curve encode the information for concrete cellular responses and biological activities. When the oscillating signal is kept sustained (present delay), cell exit may be performed, whereas when the oscillating signal remains robust, cell proliferation may take place. B-catenin-Wnt signaling pathway has a key role in the differentiation of osteochondroprogenitor cells. Sustained downregulation of the β-catenin-Wnt pathway forces osteochondroprogenitors to a chondrogenic fate instead of an osteoblastic one. Other signaling, for example, bone morphogenetic protein and Notch signaling pathways interact with the Wnt pathway. The crosstalk between biochemical and mechanical stimuli produces the final information that leads to the final cell fate decisions, through the "mechanostat" principle.
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